|
| Status |
Public on Jun 12, 2016 |
| Title |
DMSO Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
MV4;11_DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
tissue source: peripheral blood
cell line: MV4;11
cell type: Mixed lineage leukemia (MLL) fusion protein (FP) leukemia cell line
treated with: 0.1% DMSO
|
| Treatment protocol |
Cell lines were grown in 0.1% DMSO, 500nM of I-BET151 and/or 5uM of SGC0946
|
| Growth protocol |
Cell lines were grown in RPMI-1640 supplemented with 20% fetal calf serum, penicillin (100 units/mL) and streptomycin (100 ug/mL)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was prepared using the Qiagnen RNeasy kit
TruSeq RNA Sample Preparation protocol (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Replicate 1
|
| Data processing |
Illumina Casava1.8.2 software was used for basecalling.
Reads were aligned to the human genome (G1k V37) using tophat2 and bowtie2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genes with a false discovery rate below 0.05 and a fold‐change greater than 2 were considered significantly differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of normalised expression values for all Samples
|
| |
|
| Submission date |
Aug 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Dawson |
| E-mail(s) |
mark.dawson@petermac.org
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE71777 |
RNASeq of MV4;11 cell treated with DMSO, I-BET, SGC0946 and combination of I-BET and SGC0946 |
| GSE71780 |
Functional interdependency of BRD4 and DOT1L in MLL leukaemia |
|
| Relations |
| SRA |
SRX1134753 |
| BioSample |
SAMN03979592 |
