|
| Status |
Public on Sep 07, 2022 |
| Title |
A20 with sgRNA activating CD4 gene replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
A20 B cell lymphoma cell line
|
| Organism |
Mus musculus |
| Characteristics |
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 |
polyA RNA |
| Extraction protocol |
NucleoSpin RNA Plus (Macherey-Nagel) with gDNA removal column
Illumina TruSeq RNA (100ng plus) v1.0 protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using Rsubread::align.
Genewise counts were obtained using featureCounts with Rsubread's inbuilt mm10 annotation.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text giving Entrez Gene IDs, gene length (number of bases in union of all exons) and the number of read-pairs assigned to that read.
|
| |
|
| Submission date |
May 17, 2022 |
| Last update date |
Sep 07, 2022 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL30172 |
| Series (2) |
| GSE203162 |
RNA-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 |
SAMN28487627 |
| SRA |
SRX15302450 |
