|
| Status |
Public on Jul 08, 2022 |
| Title |
MEF cells [2_MEFs_2] |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Mouse embryonic fibroblasts
cell type: Mouse embryonic fibroblast cells
genotype: dCas9-SAM
treatment: none
|
| Treatment protocol |
No treatment applied.
|
| Growth protocol |
MEF cells were cultured in DMEM supplemented with 10% FBS and 1 mM L-glutamine at 37C with 10% CO2. Lymphoma cells were cultured in FMA media at 37C with 10% CO2. Leukemia cells were cultured in IMDM media supplemented with 10% FBS with IL7 at 37C with 10% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Direct-zol RNA Microprep kit (Zymo Research). 1 ug of total RNA was used for the construction of sequencing libraries. Leukemia sample RNA was harvested using Qiagen RNA kit (Qiagen) and 1 ug of total RNA was used for sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
| |
|
| Description |
2_MEFs_2_S2_L001
|
| Data processing |
Graphpad Prism software version 8.2.0 and The R Project for Statistical Computing version 4.1.3
Sequence reads were mapped to GrCM38/mm10 using Rsubread version 2.2.6
Read count extraction and CPM normalization were performed using edgeR Bioconductor package version 3.34.15
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM normalised values for each sample
|
| |
|
| Submission date |
Jun 06, 2022 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Goknur Giner |
| Organization name |
The Walter and Eliza Hall Institute of Medical Research
|
| Department |
Blood Cells and Blood Cancer
|
| Street address |
1G Royal Parade
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL32159 |
| Series (1) |
| GSE205509 |
A novel CRISPR activation mouse enables modelling of aggressive lymphoma and interrogation of venetoclax resistance |
|
| Relations |
| BioSample |
SAMN28869875 |
| SRA |
SRX15595930 |
