|
| Status |
Public on Mar 13, 2017 |
| Title |
TE_Input_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
KLRG1hiIL7Rlo terminal effector CD8 T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: six to seven weeks
tissue: Spleen
|
| Treatment protocol |
OT1 transfer and Lm-OVA infection for 8 days or >60 days
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Splenocytes were isolated and specific CD8 T cell subsets were sorted by FACS
ATAC-seq library was constructed by Nextera DNA Sample Prep Kit (Illumina). For ChIP-seq library, DNA was end-repaired using End-it End-repair kit (Epicentre) and then added an “A” base to the 3’ end of DNA fragments using Klenow (NEB). Then DNA was ligated with adaptors using quick DNA ligase (NEB) at 25°C for 15 min followed by size selection of 200-400 bp using AMPure SPRI beads (Beckman Coulter). The adaptor ligated DNA was amplified using NEBNext High-Fidelity 2X PCR master mix (NEB).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
TE_Input.bw
|
| Data processing |
Reads were aligned to mm10 by BWA
Reads with low quality (MAPQ < 30) were filtered out. If multiple reads were mapped to the exact same location, only one read was kept.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Oct 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Howard Y Chang |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5168 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE95237 |
Genome-wide maps of chromatin state and chromatin accessibility in CD8 T cell subsets |
| GSE95238 |
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation |
|
| Relations |
| Reanalyzed by |
GSE111902 |
| BioSample |
SAMN05933579 |
| SRA |
SRX2606546 |
| SRA |
SRX2263375 |
