|
| Status |
Public on Apr 30, 2022 |
| Title |
ATAC-seq, primary RPE, biol rep1 |
| Sample type |
SRA |
| |
|
| Source name |
RPE
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: RPE
genotype: healthy
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh cells were washed with ice cold PBS containing protease inhibitor and nuclei were extracted prior to library construction.
The standard ATAC-seq protocol was used, with the transposase reaction carried out for 30 minutes at 37C. 8-10 cycles of amplification were performed and dual size selection was performed with Ampure XP beads.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ATAC-seq_primary_RPE.bed
|
| Data processing |
All reads were trimmed to 50 bp prior to processing. For libraries having undergone paired-end sequencing, only the first read was used.
All libaries were processed using the ENCODE ATAC-seq pipeline.
Optimal IDR and optimal overlap peaks called by MACS2 were used.
Assembly: hg38
Supplementary files format and content: Narrow peaks called in bed format for merged replicates
Supplementary files format and content: Signal tracks in bigwig format for individual libraries
|
| |
|
| Submission date |
Apr 27, 2022 |
| Last update date |
Apr 30, 2022 |
| Contact name |
Kirsty Jamieson |
| E-mail(s) |
kirstyjamieson@gmail.com
|
| Organization name |
University of California
|
| Street address |
400 Parnassus Ave
|
| City |
San Francisco |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE201677 |
Dissecting genetic components associated with eye disease using integrative genomic analysis [ATAC-seq] |
| GSE201681 |
Dissecting genetic components associated with eye disease using integrative genomic analysis |
|
| Relations |
| BioSample |
SAMN27914601 |
| SRA |
SRX15014521 |
