|
Status |
Public on Sep 07, 2022 |
Title |
Wild-type A20 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: None
|
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 |
SAMN30437998 |
SRA |
SRX17171790 |