|
| Status |
Public on Nov 16, 2021 |
| Title |
16wk/d113 [snATAC-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Developing human retina
|
| Organism |
Homo sapiens |
| Characteristics |
donor apparent sex: Female
donor age: 113 days
donor apparent race: unknown
postmortem interval: 7:25
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 |
SAMN21357495 |
| SRA |
SRX12104006 |
