^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 = GSE138002
!Series_title = scRNA-seq of the developing human retina
!Series_geo_accession = GSE138002
!Series_status = Public on May 07 2020
!Series_submission_date = Sep 25 2019
!Series_last_update_date = May 11 2020
!Series_pubmed_id = 32386599
!Series_summary = Time-series of single-cell RNA-sequencing performed on stem cell derived retinal organoids or post-mortem tissue from the developing and adult retina
!Series_overall_design = 10x Genomics V2 single-cell RNA-sequencing
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Seth,,Blackshaw
!Series_contributor = Brian,S,Clark
!Series_contributor = James,T,Handa
!Series_contributor = Rod,,Bremner
!Series_contributor = Donald,J,Zack
!Series_sample_id = GSM4096494
!Series_sample_id = GSM4096495
!Series_sample_id = GSM4096496
!Series_sample_id = GSM4096497
!Series_sample_id = GSM4096498
!Series_sample_id = GSM4096499
!Series_sample_id = GSM4096500
!Series_sample_id = GSM4096501
!Series_sample_id = GSM4096502
!Series_sample_id = GSM4096503
!Series_sample_id = GSM4096504
!Series_sample_id = GSM4096505
!Series_contact_name = Brian,,Clark
!Series_contact_laboratory = Clark
!Series_contact_department = Ophthalmology and Visual Sciences
!Series_contact_institute = Washington University
!Series_contact_address = 660 S Euclid Ave; Campus Box #8096
!Series_contact_city = St. Louis
!Series_contact_state = Missouri
!Series_contact_zip/postal_code = 63110
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138002/suppl/GSE138002_All_barcodes.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138002/suppl/GSE138002_All_cells.mtx.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138002/suppl/GSE138002_Final_barcodes.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138002/suppl/GSE138002_Final_matrix.mtx.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE138nnn/GSE138002/suppl/GSE138002_genes.csv.gz
!Series_platform_id = GPL18573
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA574132
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP223254
^PLATFORM = GPL18573
!Platform_title = Illumina NextSeq 500 (Homo sapiens)
!Platform_geo_accession = GPL18573
!Platform_status = Public on Apr 15 2014
!Platform_submission_date = Apr 15 2014
!Platform_last_update_date = Mar 26 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 = GSM4096494
!Sample_title = 24 days in culture human retinal organoid
!Sample_geo_accession = GSM4096494
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retinal organoid
!Sample_characteristics_ch1 = cell source: retinal cells from IMR-90 induced pluripotent stem cells
!Sample_growth_protocol_ch1 = (Wahlin et al., 2015; PMID 28396597)
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Day 24 in culture single cells from human retinal organoids processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842178
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902952
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096495
!Sample_title = 30 days in culture human retinal organoid
!Sample_geo_accession = GSM4096495
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retinal organoid
!Sample_characteristics_ch1 = cell source: retinal cells from IMR-90 induced pluripotent stem cells
!Sample_growth_protocol_ch1 = (Wahlin et al., 2015; PMID 28396597)
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Day 30 in culture single cells from human retinal organoids processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842177
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902953
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096496
!Sample_title = 42 days in culture human retinal organoid
!Sample_geo_accession = GSM4096496
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retinal organoid
!Sample_characteristics_ch1 = cell source: retinal cells from IMR-90 induced pluripotent stem cells
!Sample_growth_protocol_ch1 = (Wahlin et al., 2015; PMID 28396597)
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Day 42 in culture single cells from human retinal organoids processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842176
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902954
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096497
!Sample_title = 59 days in culture human retinal organoid
!Sample_geo_accession = GSM4096497
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retinal organoid
!Sample_characteristics_ch1 = cell source: retinal cells from IMR-90 induced pluripotent stem cells
!Sample_growth_protocol_ch1 = (Wahlin et al., 2015; PMID 28396597)
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Day 59 in culture single cells from human retinal organoids processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842175
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902955
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096498
!Sample_title = Hgw9 retina scRNA-seq
!Sample_geo_accession = GSM4096498
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retina
!Sample_characteristics_ch1 = cell source: primary tissue
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Single retinal cells from gestational week 9 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842173
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902956
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096499
!Sample_title = Hgw11 retina scRNA-seq
!Sample_geo_accession = GSM4096499
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retina
!Sample_characteristics_ch1 = cell source: primary tissue
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Single retinal cells from gestational week 11 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842172
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902957
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096500
!Sample_title = Hgw13 retina scRNA-seq
!Sample_geo_accession = GSM4096500
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retina
!Sample_characteristics_ch1 = cell source: primary tissue
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Single retinal cells from gestational week 13 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842170
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902958
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096501
!Sample_title = Hgw15 retina scRNA-seq
!Sample_geo_accession = GSM4096501
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retina
!Sample_characteristics_ch1 = cell source: primary tissue
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Single retinal cells from gestational week 15 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842169
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902959
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096502
!Sample_title = Hgw17 retina scRNA-seq
!Sample_geo_accession = GSM4096502
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retina
!Sample_characteristics_ch1 = cell source: primary tissue
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Single retinal cells from gestational week 17 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842168
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902960
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096503
!Sample_title = Hgw19 replicate 1 retina scRNA-seq
!Sample_geo_accession = GSM4096503
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retina
!Sample_characteristics_ch1 = cell source: primary tissue
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Single retinal cells from gestational week 19 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842167
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902961
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096504
!Sample_title = Hgw19 replicate 2 retina scRNA-seq
!Sample_geo_accession = GSM4096504
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retina
!Sample_characteristics_ch1 = cell source: primary tissue
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Single retinal cells from gestational week 19 human retinas processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842166
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902962
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0
^SAMPLE = GSM4096505
!Sample_title = 86 year old Adult retina scRNA-seq
!Sample_geo_accession = GSM4096505
!Sample_status = Public on May 07 2020
!Sample_submission_date = Sep 25 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Retinal Cells
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: dissociated retina
!Sample_characteristics_ch1 = cell source: primary tissue
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = 10x Genomics 3' v2 Single Cell RNA-sequencing
!Sample_description = Single retinal cells from an 86 year old healthy adult retina processed via 10x Genomics Chromium v2 3' Single Cell RNA-sequencing
!Sample_description = Read 1: 98bp, Read 2: 26bp; i7:8bp
!Sample_data_processing = fastq files were aligned to Hg38 using Cellranger 2.0.1 or newer versions using the refdata-cellranger-GRCh38-3.0.0 reference index provided by 10x. Count matrices were manually aggregated and used as input into Monocle2.99. single cell RNAseq framework
!Sample_data_processing = only retinal and potential RPE cells were included in the finalized matrix (Final_matrix.mtx), however, all cells on which sequencing profiles were obtained are included in the All_cells.mtx file.
!Sample_data_processing = Genome_build: Hg38 (refdata-cellranger-GRCh38-3.0.0)
!Sample_data_processing = Supplementary_files_format_and_content: Final_matrix.mtx: Expression data of the finalized retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: genes.csv: Gene features for all expression matrices. Rownames of genes.tsv correspond to the rownames of Final_matrix.mtx and All_cells.mtx files
!Sample_data_processing = Supplementary_files_format_and_content: Final_barcodes.csv: Cell features of the final retina matrix (118,555 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_cells.mtx: Expression data of all sequenced cells (138,672 cells)
!Sample_data_processing = Supplementary_files_format_and_content: All_barcodes.csv: Cell features of all sequenced cells (138.672 cells)
!Sample_platform_id = GPL18573
!Sample_contact_name = Brian,,Clark
!Sample_contact_laboratory = Clark
!Sample_contact_department = Ophthalmology and Visual Sciences
!Sample_contact_institute = Washington University
!Sample_contact_address = 660 S Euclid Ave; Campus Box #8096
!Sample_contact_city = St. Louis
!Sample_contact_state = Missouri
!Sample_contact_zip/postal_code = 63110
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NextSeq 500
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12842165
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6902963
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE138002
!Sample_data_row_count = 0