|
| Status |
Public on Apr 05, 2024 |
| Title |
LN_C6M9 Day 8, replicate 2, WGBS |
| Sample type |
SRA |
| |
|
| Source name |
lymph node
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lymph node
cell type: CD8 T cells
cell subset: CD8CD90.1CD44
gp33 status: Low Affinity GP33
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from the sorted cells and then bisulfite treated using an EZ DNA Methylation-Direct kit (Zymo Research).
Bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicentre) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina NovaSeq 6000 systems
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
XL018
|
| Data processing |
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the HG19 genome using the BSMAP v.2.90 software
CpG methylation levels were determined by methratio.py script from BSMAP
Assembly: mm10
Supplementary files format and content: txt files with columns of chr, loc, cov, meth
|
| |
|
| Submission date |
Mar 29, 2024 |
| Last update date |
Apr 05, 2024 |
| Contact name |
Tian Mi |
| E-mail(s) |
tmi@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Immunology
|
| Street address |
262 Danny Thomas Pl MS351
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE262843 |
Antitumor progenitor exhausted CD8 T cells are sustained with TCR engagement [WGBS] |
| GSE262845 |
Antitumor progenitor exhausted CD8 T cells are sustained with TCR engagement |
|
| Relations |
| BioSample |
SAMN40658961 |
| SRA |
SRX24106119 |
