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Sample GSM6500672 Query DataSets for GSM6500672
Status Public on Sep 07, 2022
Title A20 with sgRNA activating CD4 gene replicate 1
Sample type SRA
 
Source name A20 B cell lymphoma cell line
Organism Mus musculus
Characteristics tissue: A20 B cell lymphoma cell line
strain: BALB/C
activation: CD4
Treatment protocol Cells transduced with lentiviral vector overexpressing the TETact system together with either the non-targeting control sgRNA or CD4-promoter targeting sgRNA.
Growth protocol RPMI 1640 with 2 mM GlutaMAX, 50 μM β-mercaptoethanol and 10% heat-inactivated foetal calf serum (FCS).
Extracted molecule genomic DNA
Extraction protocol DNeasy Blood & Tissue kit (Qiagen)
NEBNext Enzymatic Methyl-seq kit (NEB)
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model NextSeq 2000
 
Data processing Adapters and reads of poor quality scores were trimmed using TrimGalore v0.6.7
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using bismark v0.20.0
Duplicated reads were removed using bismark's deduplicate_bismark function.
Methylation calls were made using bismark's bismark_methylation_extractor function
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text giving chromosome number, start and end position of the CpG site, methylation proportion, the number of methylated Cs, and the number of unmethylated Cs
 
Submission date Aug 22, 2022
Last update date Sep 07, 2022
Contact name Yunshun Chen
E-mail(s) yuchen@wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department ACRF Cancer Biology and Stem Cells
Lab Chen
Street address 1G Royal Parade
City Parkville
State/province VIC
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL30172
Series (2)
GSE211754 Whole genome enzymatic methyl-seq of A20 mouse cells using a novel TETact activation of CD4
GSE212345 RNA-seq and methyl-seq of A20 mouse cells using a novel TETact activation of CD4
Relations
BioSample SAMN30437996
SRA SRX17171792

Supplementary file Size Download File type/resource
GSM6500672_CD41BS.bismark.cov.gz 201.0 Mb (ftp)(http) COV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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