^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE148077
!Series_title = Cell atlas of the human fovea and peripheral retina
!Series_geo_accession = GSE148077
!Series_status = Public on Jun 22 2020
!Series_submission_date = Apr 03 2020
!Series_last_update_date = Jun 22 2020
!Series_pubmed_id = 32555229
!Series_summary = Most irreversible blindness results from retinal disease. To advance our understanding of the etiology of blinding diseases, we used single-cell RNA-sequencing (scRNA-seq) to analyze the transcriptomes of ~85,000 cells from the fovea and peripheral reti-na of seven adult human donors. Utilizing computational methods, we identified 58 cell types within 6 classes: photoreceptor, horizontal, bipolar, amacrine, retinal gangli-on and non-neuronal cells. Nearly all types are shared between the two retinal re-gions, but there are notable differences in gene expression and proportions between foveal and peripheral cohorts of shared types. We then used the human retinal atlas to map expression of 636 genes implicated as causes of or risk factors for blinding dis-eases. Many are expressed in striking cell class-, type-, or region-specific patterns. Fi-nally, we compared gene expression signatures of cell types between human and the cynomolgus macaque monkey, Macaca fascicularis. We show that over 90% of human types correspond transcriptomically to those previously identified in macaque, and that expression of disease-related genes is largely conserved between the two species. These results validate the use of the macaque for modeling blinding disease, and pro-vide a foundation for investigating molecular mechanisms underlying visual pro-cessing.
!Series_overall_design = To generate a comprehensive cell atlas of human retina, we obtained eight retinas from seven genetically unrelated human donors with no clinical history of ocular disease. We dissected fovea (~1.5 mm diameter centered on the foveal pit, which was visible under a dissecting microscope) and peripheral samples (> 5 mm from the fovea) from whole retina, pooling peripheral pieces from all four quadrants. Foveal samples were dissociated into single cells, which were profiled without further processing using high-throughput droplet sequencing. For peripheral samples, in which rod photoreceptors and RGC comprise ~80% and <2 % of total cells respectively, we depleted rods using magnetic beads conjugated to anti-CD73 or enriched RGCs using anti-CD90-conjugated beads prior to collection , using protocols established in our study on macaque retina. Libraries were prepared from foveal and peripheral samples, and sequenced. Altogether, we obtained 84,982 high-quality transcriptomes, 55,736 from fovea and 29,246 from peripheral retina. The median number of unique transcripts captured per cell was 2,577 and the median number of genes detected was 1,308.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Wenjun,,Yan
!Series_contributor = Yi-Rong,,Peng
!Series_contributor = Tavé,,van Zyl
!Series_contributor = Aviv,,Regev
!Series_contributor = Karthik,,Shekhar
!Series_contributor = Dejan,,Juric
!Series_contributor = Joshua,R,Sanes
!Series_sample_id = GSM4453751
!Series_sample_id = GSM4453752
!Series_sample_id = GSM4453753
!Series_sample_id = GSM4453754
!Series_sample_id = GSM4453755
!Series_sample_id = GSM4453756
!Series_sample_id = GSM4453757
!Series_sample_id = GSM4453758
!Series_sample_id = GSM4453759
!Series_sample_id = GSM4453760
!Series_sample_id = GSM4453761
!Series_sample_id = GSM4453762
!Series_sample_id = GSM4453763
!Series_sample_id = GSM4453764
!Series_sample_id = GSM4453765
!Series_sample_id = GSM4453766
!Series_sample_id = GSM4453767
!Series_sample_id = GSM4453768
!Series_sample_id = GSM4453769
!Series_contact_name = Wenjun,,Yan
!Series_contact_email = wey334@g.harvard.edu
!Series_contact_laboratory = Joshua Sanes
!Series_contact_department = Department of Molecular  and Cellular Biology
!Series_contact_institute = Harvard University
!Series_contact_address = 52 Oxford Street
!Series_contact_city = Cambridge
!Series_contact_state = MA
!Series_contact_zip/postal_code = 02138
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148077/suppl/GSE148077_count_mat_donor_H1.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148077/suppl/GSE148077_count_mat_donor_H11.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148077/suppl/GSE148077_count_mat_donor_H2.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148077/suppl/GSE148077_count_mat_donor_H3.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148077/suppl/GSE148077_count_mat_donor_H4.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148077/suppl/GSE148077_count_mat_donor_H5.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE148nnn/GSE148077/suppl/GSE148077_count_mat_donor_H9.csv.gz
!Series_platform_id = GPL16791
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA623011
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP255195
^PLATFORM = GPL16791
!Platform_title = Illumina HiSeq 2500 (Homo sapiens)
!Platform_geo_accession = GPL16791
!Platform_status = Public on Mar 14 2013
!Platform_submission_date = Mar 14 2013
!Platform_last_update_date = Mar 27 2019
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Homo sapiens
!Platform_taxid = 9606
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM4453751
!Sample_title = H1CD73dpS1
!Sample_geo_accession = GSM4453751
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Peripheral retina cells depleted by anti-CD73  followed by anti-mouse IgG1 microbeads
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Peripheral retina of left eye from donor 1
!Sample_description = count_mat_donor_H1.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535097
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055047
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453752
!Sample_title = H1CD90S1
!Sample_geo_accession = GSM4453752
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Peripheral retina cells enriched with CD90 microbeads
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Peripheral retina of left eye from donor 1
!Sample_description = count_mat_donor_H1.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535068
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055048
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453753
!Sample_title = H2Fovea1S1
!Sample_geo_accession = GSM4453753
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of right eye from donor 2
!Sample_description = count_mat_donor_H2.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535067
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055049
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453754
!Sample_title = H2Fovea2S1
!Sample_geo_accession = GSM4453754
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of left eye from donor 2
!Sample_description = count_mat_donor_H2.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535066
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055050
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453755
!Sample_title = H3CD73dpS1
!Sample_geo_accession = GSM4453755
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Peripheral retina cells depleted by anti-CD73  followed by anti-mouse IgG1 microbeads
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Peripheral retina of right eye from donor 3
!Sample_description = count_mat_donor_H3.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535065
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055051
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453756
!Sample_title = H3CD73dpS2
!Sample_geo_accession = GSM4453756
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Peripheral retina cells depleted by anti-CD73  followed by anti-mouse IgG1 microbeads
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Peripheral retina of right eye from donor 3
!Sample_description = count_mat_donor_H3.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535064
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055052
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453757
!Sample_title = H3CD90S1
!Sample_geo_accession = GSM4453757
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Peripheral retina cells enriched with CD90 microbeads
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Peripheral retina of right eye from donor 3
!Sample_description = count_mat_donor_H3.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535063
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055053
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453758
!Sample_title = H3CD90S2
!Sample_geo_accession = GSM4453758
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Peripheral retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Peripheral retina cells enriched with CD90 microbeads
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Peripheral retina of right eye from donor 3
!Sample_description = count_mat_donor_H3.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535062
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055054
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453759
!Sample_title = H3FoveaS1
!Sample_geo_accession = GSM4453759
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of right eye from donor 3
!Sample_description = count_mat_donor_H3.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535061
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055058
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453760
!Sample_title = H3FoveaS2
!Sample_geo_accession = GSM4453760
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of right eye from donor 3
!Sample_description = count_mat_donor_H3.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535060
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055059
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453761
!Sample_title = H3FoveaS3
!Sample_geo_accession = GSM4453761
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of right eye from donor 3
!Sample_description = count_mat_donor_H3.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535059
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055060
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453762
!Sample_title = H4FoveaS1
!Sample_geo_accession = GSM4453762
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of left eye from donor 4
!Sample_description = count_mat_donor_H4.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535058
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055061
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453763
!Sample_title = H5FoveaS1
!Sample_geo_accession = GSM4453763
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of left eye from donor 5
!Sample_description = count_mat_donor_H5.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535057
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055062
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453764
!Sample_title = H5FoveaS2
!Sample_geo_accession = GSM4453764
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of left eye from donor 5
!Sample_description = count_mat_donor_H5.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535056
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055063
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453765
!Sample_title = H5FoveaS3
!Sample_geo_accession = GSM4453765
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of left eye from donor 5
!Sample_description = count_mat_donor_H5.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535118
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055064
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453766
!Sample_title = H5FoveaS4
!Sample_geo_accession = GSM4453766
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of left eye from donor 5
!Sample_description = count_mat_donor_H5.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535117
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055065
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453767
!Sample_title = H5FoveaS5
!Sample_geo_accession = GSM4453767
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of left eye from donor 5
!Sample_description = count_mat_donor_H5.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535116
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055055
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453768
!Sample_title = H9FoveaS1
!Sample_geo_accession = GSM4453768
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of left eye from donor 9
!Sample_description = count_mat_donor_H9.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535114
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055056
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0
^SAMPLE = GSM4453769
!Sample_title = H11FoveaS1
!Sample_geo_accession = GSM4453769
!Sample_status = Public on Jun 22 2020
!Sample_submission_date = Apr 03 2020
!Sample_last_update_date = Jun 22 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Fovea retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = cell type: Fovea retina cells
!Sample_treatment_protocol_ch1 = All human eyes used for sequencing and histological studies were collected 3-14 hours post mortem through the Rapid Autopsy Program, Massachusetts General Hospital, with all but one collected ≤6.5 hours post mortem. The globe was immediately transported back to the lab in a humid chamber. Hemisection was performed to remove the anterior chamber, and the posterior pole was immersed in Ames equilibrated with 95% O2/5% CO2 before further dissection and dissociation. All donors were confirmed to have no history or clinical evidence of ocular disease or intraocular surgery.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Single cell libraries were generated by minor modifications of methods developed for macaque retina. Briefly, a ~1.5 mm diameter circular region centered on the foveal pit was dissected from the retina, and peripheral retinal pieces were pooled from all retinal quadrants. Dissected tissues were digested with papain (Worthington, LS003126) for 30min at 37oC. Following digestion, samples were dissociated and triturated into single cell suspensions with 0.04% bovine serum albumin (BSA) in Ames. Dissociated cells from digested peripheral retinas were incubated with CD90 microbeads (Miltenyi Biotec, 130-096-253; 1 ml per 107 cells) to enrich RGCs or with anti-CD73 (BD Biosciences, clone AD2; 5 ml per 107 cells) followed by anti-mouse IgG1 microbeads (Miltenyi Biotec, 130-047-102; 10 ml per 107 cells) to deplete rods. Incubations were at room temperature for 10 min. CD90 positive cells or CD73 negative cells were selected via large cell columns through a MiniMACS Separator (Miltenyi Biotec). Foveal samples were used without further processing.
!Sample_extract_protocol_ch1 = Single cell libraries were made with Chromium 3’ v2 or V3 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on Illumina HiSeq 2500.
!Sample_extract_protocol_ch1 = Chromium 3’ v2/v3 platform (10X Genomics, Pleasanton, CA) 
!Sample_description = Fovea retina of right eye from donor 11
!Sample_description = count_mat_donor_H11.csv
!Sample_data_processing = Sample demultiplexing with the mkfastq function from Cell Ranger software( version 2.1.0 and version 3.0.2, 10X Genomics)
!Sample_data_processing = Sample alignment with the count function from Cell Ranger software (version 2.1.0 and version 3.0.2,10X Genomics)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Csv files including gene count matrix from each donor
!Sample_platform_id = GPL16791
!Sample_contact_name = Wenjun,,Yan
!Sample_contact_email = wey334@g.harvard.edu
!Sample_contact_laboratory = Joshua Sanes
!Sample_contact_department = Department of Molecular  and Cellular Biology
!Sample_contact_institute = Harvard University
!Sample_contact_address = 52 Oxford Street
!Sample_contact_city = Cambridge
!Sample_contact_state = MA
!Sample_contact_zip/postal_code = 02138
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN14535112
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX8055057
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE148077
!Sample_data_row_count = 0