|
Status |
Public on Nov 22, 2021 |
Title |
BC088 DNMT3a Knockout 1 |
Sample type |
SRA |
|
|
Source name |
T cells
|
Organism |
Homo sapiens |
Characteristics |
time point: Week 1 genotype/variation: KO CAR
|
Growth protocol |
WT and CAR T cells were serially stimulated by culturing with tumor cells containing the cognate antigen. Tumor cells were replaced weekly.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted followed by bisulfite treatment for library prepration. Nuclei were exteacted for ATAC-Seq. Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer. The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Novaseq 6000 following the manufacturer's protocols.
|
|
|
Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Basecalling was performed using Illumina RealTimeAnalysis software FASTQ sequences adapter trimmed (trimglore) and mapped to the hg19 by BSMAP2.7.4 CpGs were extracted by the methratio.py in the BSMAP package Genome_build: hg19 (human WGBS) Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG
|
|
|
Submission date |
Sep 21, 2021 |
Last update date |
Nov 22, 2021 |
Contact name |
yiping fan |
E-mail(s) |
yiping.fan@stjude.org
|
Phone |
9015955716
|
Organization name |
st jude children's hospital
|
Street address |
262 Danny Thomas Place
|
City |
memphis |
State/province |
tn |
ZIP/Postal code |
38105 |
Country |
USA |
|
|
Platform ID |
GPL24676 |
Series (1) |
GSE184568 |
Deleting DNMT3A in CAR T cells prevents exhaustion and 1 enhances antitumor activity |
|
Relations |
BioSample |
SAMN21547042 |
SRA |
SRX12292990 |