|
| Status |
Public on Nov 08, 2021 |
| Title |
Week1 - rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CD19-CAR T cells
|
| Organism |
Homo sapiens |
| Characteristics |
disease: B-cell acute lymphoblastic leukemia
cell type: CD8+ T cells
time point: Week 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from the sorted cells by using a DNA-extraction kit (Qiagen) and then bisulfite treated using an EZ DNA methylation 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 NovaSeq 6000 system.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GMP: Good Manufacturing Practice (cells have chimeric antigen vector added following drug production practices).
|
| Data processing |
Basecalling was performed using Illumina Casava 1.7.
Sequencing reads were aligned to the HG19 genome using the BSMAP v.2.74 software.
CpG methylation levels were determined by methratio.py script from BSMAP.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files with columns of chr, loc, cov, meth.
|
| |
|
| Submission date |
Nov 05, 2021 |
| Last update date |
Nov 08, 2021 |
| Contact name |
Tian Mi |
| E-mail(s) |
[email protected]
|
| 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 |
GPL24676 |
| Series (1) |
| GSE188325 |
CD19-CAR T cells undergo exhaustion epigenetic programming in patients with acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN22938874 |
