|
| Status |
Public on Mar 02, 2021 |
| Title |
KO-1: EGR2 KO replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Sorted LCMV-specific CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
cell type: LCMV H-2Kb GP33-41-specific CD8+ T cell
genotype: CD4-cre+ Egr2 flox/flox
disease state: chronic LCMV infection
|
| Treatment protocol |
CD4 depleted WT or cKO mice were infected with 2x10^6 pfu LCMV-Cl13 i.v.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
At day 20 p.i., CD8+CD44int-hi H-2DbGP33-41-tetramer stained cells were isolated by fluorescence activated cell sorting and subjected to ATACseq analysis
ATACseq library preparation was conducted based on a published protocol (Buenrostro et al, Nat Methods, 2013).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed in paired-end mode using Trim_Galore version 0.4.5_dev
Trimmed reads were aligned to GRCm38.p6 using BWA MEM v0.7.17
The resulting bam files were deduplicated with MarkDuplicates (Picard) v2.19.0
Bam converted to bedGraph using genomeCoverageBed from bedtools
bedGraph coverted to Bigwig using bedGraphToBigWig from KentUtils
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Bigwig (bw)
|
| |
|
| Submission date |
Jun 24, 2020 |
| Last update date |
Mar 03, 2021 |
| Contact name |
Ian Parish |
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE134710 |
Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance |
| GSE153136 |
Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [ATACseq] |
|
| Relations |
| BioSample |
SAMN15356964 |
| SRA |
SRX8608422 |
