|
| Status |
Public on Oct 23, 2019 |
| Title |
No Help 2 H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
No Help H3K4me3
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6JRj
tissue: spleen
cell type: memory CD8 T cells
treatment: No CD4 T cell help
chip antibody: aH3K4me3 mAb (#9272, Cell Singaling Technology)
|
| Treatment protocol |
Help or No Help intraepidermal vaccination.
|
| Growth protocol |
Cells isolated from spleens after vaccination.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Between 6-9 x 10^4 E7-specific memory CD8+ T cells per sample were subjected to ULI-NChIP procedure
ChIP libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Single-end fastq files were aligned to mm10 (GrCm38.77) using bwa (v. 0.7.17)
Resulting alignments were filtered for mapping quality > MQ20 using samtools version 1.5
Peak calling for H3K27me3 ChIP-seq was performed using MACS2 (v. 2.1.1) with detection for broad peaks using input for normalization
For H3K4me3 we performed narrow peak calling using MACS (v. 2.1.1) with input normalization
For differential binding, we used the R package Diffbind (v. 2.2.1) to determine differentially bound peaks found in all replicates for “No help” vs “Help” with the EdgeR method
We annotated the bound regions using BEDTools (v. 2.17.0) closestBed reporting the first feature against a file of genes and locations determined from GRCm38.77 gtf file selecting for ‘gene_name’
Genome_build: GRCm38.77
Supplementary_files_format_and_content: Processed data contain BED files (narrowPeak, broadPeak) with all the called peaks for each experimental sample.
|
| |
|
| Submission date |
Aug 06, 2018 |
| Last update date |
Oct 23, 2019 |
| Contact name |
Tomasz Ahrends |
| Organization name |
The Rockefellere University
|
| Lab |
Mucosal Immunology
|
| Street address |
1230 York Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE118159 |
Epigenetic basis of CD4 T cel help for memory CD8 T cell formation |
| GSE118160 |
CD4+ T-cell help creates effector memory CTLs with innate and help-independent recall capacities |
|
| Relations |
| BioSample |
SAMN09768322 |
| SRA |
SRX4510526 |
