^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 = GSE122970
!Series_title = Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development
!Series_geo_accession = GSE122970
!Series_status = Public on May 07 2020
!Series_submission_date = Nov 26 2018
!Series_last_update_date = May 13 2020
!Series_pubmed_id = 32386599
!Series_summary = The development of single-cell RNA-Sequencing (scRNA-Seq) has allowed high resolution analysis of cell type diversity and transcriptional networks controlling cell fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-Seq over retinal organoid and in vivo retinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene expression across retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we examined gene expression differences between developing macula and periphery and between two distinct populations of horizontal cells. We also identify both shared and species-specific patterns of gene expression during human and mouse retinal development. Finally, we identify an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development, and may help guide the design of cell-based therapies for treating retinal dystrophies.
!Series_overall_design = More than 45000 single cells from the developing human retina, ranging from gestational weeks (GW)12-27, and postnatal retina on day 8 were analyzed via single cell RNA-sequencing.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Yufeng,,Lu
!Series_contributor = Wenyang,,Yi
!Series_contributor = Qian,,Wu
!Series_contributor = Tian,,Xue
!Series_contributor = Xiaoqun,,Wang
!Series_sample_id = GSM3964256
!Series_sample_id = GSM3964257
!Series_contact_name = Yufeng,,Lu
!Series_contact_email = luyufeng@ibp.ac.cn
!Series_contact_institute = Institute of Biophysics, Chinese Academy of Sciences
!Series_contact_address = 15 Datun Road, Chaoyang District
!Series_contact_city = Beijing
!Series_contact_zip/postal_code = 100101
!Series_contact_country = China
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122970/suppl/GSE122970_retina_aggr_day8_barcodes.tsv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122970/suppl/GSE122970_retina_aggr_day8_genes.tsv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE122nnn/GSE122970/suppl/GSE122970_retina_aggr_day8_matrix.mtx.gz
!Series_platform_id = GPL20301
!Series_platform_taxid = 9606
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA507018
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP170761
^PLATFORM = GPL20301
!Platform_title = Illumina HiSeq 4000 (Homo sapiens)
!Platform_geo_accession = GPL20301
!Platform_status = Public on Jun 09 2015
!Platform_submission_date = Jun 09 2015
!Platform_last_update_date = Mar 21 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 = GSM3964256
!Sample_title = postnatal_day8_macula
!Sample_geo_accession = GSM3964256
!Sample_status = Public on May 07 2020
!Sample_submission_date = Jul 23 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = human neonatal retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = developmental stage: postnatal_day8
!Sample_characteristics_ch1 = tissue: retina
!Sample_characteristics_ch1 = region: macula
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Fetal retina tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS
!Sample_extract_protocol_ch1 = Chromium™ Single Cell 3’ Reagent Kits v2
!Sample_data_processing = Illumina Casava1.8 software used for basecalling
!Sample_data_processing = Reads were aligned to GRCh38 human genome by Cellranger(v2.0.1)
!Sample_data_processing = Filtered count matrix was merged by Seurat R Package(v2.1.0)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format
!Sample_platform_id = GPL20301
!Sample_contact_name = Yufeng,,Lu
!Sample_contact_email = luyufeng@ibp.ac.cn
!Sample_contact_institute = Institute of Biophysics, Chinese Academy of Sciences
!Sample_contact_address = 15 Datun Road, Chaoyang District
!Sample_contact_city = Beijing
!Sample_contact_zip/postal_code = 100101
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12344580
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6492438
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE122970
!Sample_data_row_count = 0
^SAMPLE = GSM3964257
!Sample_title = postnatal_day8_periphery
!Sample_geo_accession = GSM3964257
!Sample_status = Public on May 07 2020
!Sample_submission_date = Jul 23 2019
!Sample_last_update_date = May 07 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = human neonatal retina
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = developmental stage: postnatal_day8
!Sample_characteristics_ch1 = tissue: retina
!Sample_characteristics_ch1 = region: periphery
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Fetal retina tissue samples were collected in ice-cold artificial cerebrospinal fluid (ACSF), single cell was selected by FACS
!Sample_extract_protocol_ch1 = Chromium™ Single Cell 3’ Reagent Kits v2
!Sample_data_processing = Illumina Casava1.8 software used for basecalling
!Sample_data_processing = Reads were aligned to GRCh38 human genome by Cellranger(v2.0.1)
!Sample_data_processing = Filtered count matrix was merged by Seurat R Package(v2.1.0)
!Sample_data_processing = Genome_build: GRCh38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered count matrix was formatted by mtx, and barcode and gene information was with tsv format
!Sample_platform_id = GPL20301
!Sample_contact_name = Yufeng,,Lu
!Sample_contact_email = luyufeng@ibp.ac.cn
!Sample_contact_institute = Institute of Biophysics, Chinese Academy of Sciences
!Sample_contact_address = 15 Datun Road, Chaoyang District
!Sample_contact_city = Beijing
!Sample_contact_zip/postal_code = 100101
!Sample_contact_country = China
!Sample_instrument_model = Illumina HiSeq 4000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN12344579
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX6492439
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE122970
!Sample_data_row_count = 0