 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 03, 2019 |
| Title |
WT P14 T-cells_Day 8 |
| Sample type |
SRA |
| |
|
| Source name |
WT_Day8
|
| Organism |
Mus musculus |
| Characteristics |
cell type: P14 T-cells
genotype: WT
infection: LCMV-c13 infection
time: day 8
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed and lysed to generate a crude nuclei preparation
Tn5 transposase tagmentation simultaneously fragments the genome and tags the resulting DNA with Illumina sequencing adapters. DNA fragments were PCR amplified and subsequently purified using Qiagen MinElute PCR Purification Kit (Qiagen, Maryland, USA). Final library quality and quantity was analyzed and measured by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) and Life Technologies Qubit3.0 Fluorometer (Life Technologies, Carlsbad, CA), respectively.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (trimglore) and mapped to the mm10 genome by bwa
nucleosome free reads were extracted and nucleosome free peaks were called by MACS2
Genome_build: mm10
Supplementary_files_format_and_content: nucleosome free peaks in bed format
|
| |
|
| Submission date |
May 22, 2019 |
| Last update date |
Jul 03, 2019 |
| Contact name |
yiping fan |
| E-mail(s) |
yiping.fan@stjude.org
|
| Phone |
9015955716
|
| Organization name |
st jude children's hospital
|
| Street address |
262 Danny Thomas Place
|
| City |
memphis |
| State/province |
tn |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE131638 |
Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection [ATAC-seq] |
| GSE131643 |
Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection |
|
| Relations |
| BioSample |
SAMN11823461 |
| SRA |
SRX5883255 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3791558_WT_Day8_merge_peaks.narrowPeak.gz |
1007.0 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
