|
Status |
Public on Nov 16, 2021 |
Title |
Hu7 [snATAC-seq] |
Sample type |
SRA |
|
|
Source name |
Adult human retina
|
Organism |
Homo sapiens |
Characteristics |
donor apparent sex: Female donor age: 50 years donor apparent race: black postmortem interval: 10:46 molecule subtype: single nucleus ATAC library type: Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1
|
Treatment protocol |
Enhancer knockout iPSCs generated as described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254
|
Growth protocol |
Human induced pluripotent stem cells (hiPSCs) and Retinal Organoids were generated according to Olemacher et al., (2015) doi:10.1002/9780470151808.sc01h08s32 ; Gantner et al., (2020) doi:10.1056/NEJMoa1815111
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Nuclear isolation from flash frozen tissue described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254 10X Genomics scATAC-Seq and scRNA-Seq protocols. Detail described in Thomas et al. bioRxiv 2021.07.31.454254; doi: https://doi.org/10.1101/2021.07.31.454254 single-nucleus (sn)ATAC-Seq and snRNA-Seq
|
|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Cell Ranger (for snRNA-seq experiments) or Cell Ranger ATAC (for snATAC-seq experiments) was used to demultiplex input files and generate feature-barcode matrices, which were then further analyzed via Seurat (RNA) or ArchR (ATAC). Specific details including software versions and parameters are described in Thomas, et al bioRxiv 2021.07.31.454254. Genome_build: hg38 Supplementary_files_format_and_content: .tsv; fragment/feature/barcode matrices for each sample
|
|
|
Submission date |
Sep 08, 2021 |
Last update date |
Nov 16, 2021 |
Contact name |
David Beier |
E-mail(s) |
david.beier@seattlechildrens.org
|
Organization name |
Seattle Children's Research Institute
|
Department |
CDBRM
|
Lab |
Beier Lab
|
Street address |
1900 9th Avenue
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98101 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE183684 |
Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk. |
|
Relations |
BioSample |
SAMN21357498 |
SRA |
SRX12104009 |