|
| Status |
Public on Mar 08, 2022 |
| Title |
A_S7063 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
donor type: Young
donor id: ND333012
age: 26
Sex: Male
cmv serostatus: Positive
cell type: CD8
cell subset: CD8_EMRA
library preparation group: 3
sample acquisition location: UPenn
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Transposed DNA was prepared with Tn5 (Illumina #FC-121-1031) as described in Buenrostro et al. 2013 using 0.1% Tween 20 instead of IGEPAL CA-630.Libraries were barcoded with Nextera Index Kit (Illumina # FC-121-1012)
The libraries were sequenced on an Illumina NextSeq machine using a 150 cycle high output flow cell
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PBMC_Young_CD8_EMRA
|
| Data processing |
The fastqs were aligned to hg19 using bowtie2.
Unmapped, unpaired, and mitochondrial reads were removed using samtools.
ENCODE Blacklist regions were removed.
PCR duplicates were removed using Picard.
Peak calling was performed with MACS2 with a FDR q-value < 0.001. Peaks present in at least 2 samples were iincluded
Normalization and differential accessibility analysis was done with DESeq2.
Batch correction was performed using combat for library preparation group and sample location.
Genome_build: hg19
Supplementary_files_format_and_content: chromatin accessbility counts file
|
| |
|
| Submission date |
Jul 06, 2021 |
| Last update date |
Mar 08, 2022 |
| Contact name |
E JOHN WHERRY |
| Organization name |
University of Pennsylvania
|
| Department |
Systems Pharmacology and Translational Therapeutics,Institute for Immunology
|
| Street address |
421 Curie Blvd,354 BRB II/III
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE179593 |
Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers [ATAC HD] |
| GSE179613 |
Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers |
|
| Relations |
| BioSample |
SAMN20085317 |
| SRA |
SRX11365258 |