|
| Status |
Public on Dec 07, 2020 |
| Title |
BaF3+BCR-Abl treated with DMSO replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line
|
| Organism |
Mus musculus |
| Characteristics |
strain: C3H
cell line: BaF3 pro B cells
genotype/variation: expressing BCR-Abl
agent: control
|
| Treatment protocol |
BaF3 cells expressing BCR-Abl were treated with 20µM DJ-34 (investigational drug) or DMSO control for 6 hrs.
|
| Growth protocol |
BaF3 cells expressing BCR-Abl were cultured on RPMI-1640 medium supplemented with 10% heat inactivated FBS and 1% Pen/strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by RNeasy mini kit Qiagen followed by DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Clean reads (as provided by BGI) were mapped to the GRCm38.85 genome assembly using Tophat2 (v. 2.1.1), then using default options BAM files were indexed using SAMtools.
Differential expression data was produced using cuffquant and cuffdiff with default options, from the cufflinks suite (v 2.2.1 / SVN rev 4237).
Reference genome for the primary assembly and gene annotations used are revision 85 of GRCm38, from ensembl.org.
Genome_build: GRCm38.85 genome assembly
Supplementary_files_format_and_content: xlsx format with raw gene count, average gene count and FPKM values for each sample.
.tdf files were used for visualization in IGV.
|
| |
|
| Submission date |
Jun 30, 2017 |
| Last update date |
Dec 07, 2020 |
| Contact name |
Jorrit Enserink |
| E-mail(s) |
jorrit.enserink@rr-research.no
|
| Organization name |
The Norwegian Radium Hospital
|
| Department |
Molecular Cell Biology
|
| Street address |
Ullernchausseen 70
|
| City |
Oslo |
| ZIP/Postal code |
N-0379 Oslo |
| Country |
Norway |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE100678 |
A cell competition-based drug screen identifies a novel compound that targets c-Myc addiction of leukemia cells |
|
| Relations |
| BioSample |
SAMN07303435 |
| SRA |
SRX2973185 |
