|
| Status |
Public on Apr 11, 2016 |
| Title |
PBMC_mergedReplicates_sample8 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: M
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
PBMCs were isolated from buffy coats using a Ficoll gradient. 50,000 cells were used for each transposition reaction.
ATAC-seq libraries were prepared as described in Buenrostro et al 2013
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Read counts per peak from ATAC-seq
|
| Data processing |
ATAC-seq libraries were prepared as described in Buenrostro et al 2013
Sequencing reads were mapped to the reference genome (hg19) and reads passing QC (MAQ>30) were used for peak calling.
Peak calling was performed by pooling by all samples (N=20) together and calling peaks using MACS2
Peaks were defined as the 250 upstream and downstream of the midpoint of each peak called by MACS2
Read counts over each peak was called per sample using HT-Seq
Genome_build: hg19
Supplementary_files_format_and_content: Bed files with read counts per peak for specific sample
|
| |
|
| Submission date |
Jun 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Montgomery |
| E-mail(s) |
smontgom@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
300 Pasteur Lane
|
| City |
Stanford |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE69749 |
Sex-specific chromatin accessibility profiling in human PBMCs |
|
| Relations |
| BioSample |
SAMN03768939 |
| SRA |
SRX1055363 |
