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Sample GSM5592694 Query DataSets for GSM5592694
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

Supplementary file Size Download File type/resource
GSM5592694_2-1295993_methylation_value.bed.gz 208.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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