|
| Status |
Public on Jul 28, 2024 |
| Title |
Wild type progenitor exhausted CD8+ T cells, replicate 1, ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD8+ T cells
cell state: progenitor exhausted
tissue: Spleen
strain: B6-Pdcd1tm23kbenhWnh/J Tg(TcrLCMV)327Sdz
age: 8-15 weeks old
sequencing batch: batch 1 and batch 2
genotype: Wild type
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was purified using a QIAgen MinElute Reaction Cleanup kit
Post-PCR bead cleanup was done using Agencourt AMPure XP bead cleanup (Beckman Coulter/Agencourt), and library quality was verified using Tapestation analysis.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ProgExh_WT_1
NormCountsATAC.txt
|
| Data processing |
Raw fastq files were downloaded from Illumina BaseSpace and merged across lanes
Quality trimming and primer removal in raw fastq files were done with Trimmomatric (v.0.36) using the following parameters: LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:30 CROP:35.
Trimmed reads were aligned to mm10 with Bowtie2 (v.2.2.9) using a maximum insert size of 1,000.
Aligned bams were sorted, duplicates marked (Picard v.2.8.0) , and reads mapping to the blacklist region removed.
Peak-calling using MACS (v.2.1.1) was performed on merged bam files (Samtools v. 1.3.1) from biological replicates using a q-value threshold of 0.001. Consensus peaks from all biological conditions were merged to create a single peak universe. Cut sites were extracted from each biological replicate and the number of cuts in each peak region was quantified to generate a raw counts matrix.
Normalization and differential expression were performed using DESeq2 (v 1.28.1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each sample at each peak
Supplementary files format and content: TDF files for each sample
Supplementary files format and content: tab-delimited text file including DESeq2 normalized counts
|
| |
|
| Submission date |
Sep 01, 2022 |
| Last update date |
Jul 28, 2024 |
| Contact name |
Amy Huang |
| Organization name |
Harvard Medical School
|
| Department |
Immunology
|
| Lab |
Sharpe
|
| Street address |
25 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE212506 |
Deletion of a state-specific PD-1 enhancer modulates exhausted T cell fate and function [ATAC-seq] |
| GSE212507 |
Deletion of a state-specific PD-1 enhancer modulates exhausted T cell fate and function |
|
| Relations |
| BioSample |
SAMN30629411 |
| SRA |
SRX17392570 |
