|
| Status |
Public on Sep 07, 2022 |
| Title |
A20 with non-targeting control sgRNA 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: Control
|
| 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 |
SAMN30437994 |
| SRA |
SRX17171794 |
