|
Status |
Public on Jan 25, 2024 |
Title |
preB #1 |
Sample type |
SRA |
|
|
Source name |
preB cells
|
Organism |
Mus musculus |
Characteristics |
tissue: preB cells cell type: preB genotype: C57BL/6 treatment: NA
|
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 |
Illumina HiSeq 2500 |
|
|
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 |
GPL17021 |
Series (1) |
GSE213791 |
ERG and c-MYC Co-regulate a Critical Gene Network in BCR-ABL1 B-cell Acute Lymphoblastic Leukemia |
|
Relations |
BioSample |
SAMN30935558 |
SRA |
SRX17641608 |