|
| Status |
Public on Jan 25, 2024 |
| Title |
#162 preB leukaemia, DMSO |
| Sample type |
SRA |
| |
|
| Source name |
preB cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: preB cells
cell type: preB leukaemia
genotype: P190T/+;CreERT2T/+;Ergfl/fl
treatment: DMSO
|
| Growth protocol |
Leukemia cells were cultured in IMDM media supplemented with 10% FBS with IL7 at 37C with 10% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
preB and leukemia sample RNA was harvested using Qiagen RNA kit (Qiagen) and 500ng-1 ug of total RNA was used for sequencing libraries. ChiP-seq sample lysate were isolated from formaldehyde cross-linked cells and sonicated to release chromatin.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) following manufacturer's protocols. ChIP-seq libraries were prepared with KAPA Hyper Prep Kit (Kapa Biosystems)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 1000 |
| |
|
| Data processing |
Illumina Casava 1.8.2 software was used for basecalling.
Sequence reads were mapped to GrCM38/mm10
RNA-seq Read count extraction and normalization were performed using edgeR Bioconductor package version 3.34.15. Peak-calling was performed using MACS2 for ChiP-seq.
Assembly: mm10
Supplementary files format and content: RNA-seq and ChIP-seq: bigwig files created using deepTools version 3.5.0
|
| |
|
| Submission date |
Sep 20, 2022 |
| Last update date |
Jan 25, 2024 |
| Contact name |
Ashley P Ng |
| E-mail(s) |
ang@wehi.edu.au
|
| Organization name |
The Walter and Eliza Hall Institute of Medical Research
|
| Street address |
1G Royal Parade, Parkville
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3050 |
| Country |
Australia |
| |
|
| Platform ID |
GPL32159 |
| Series (1) |
| GSE213791 |
ERG and c-MYC Co-regulate a Critical Gene Network in BCR-ABL1 B-cell Acute Lymphoblastic Leukemia |
|
| Relations |
| BioSample |
SAMN30935543 |
| SRA |
SRX17641623 |
