|
| Status |
Public on Jul 13, 2017 |
| Title |
MV4;11_JQ1_RNA-seq Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
MV4;11_JQ1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MV4;11
tissue source: peripheral blood
cell type: macrophage
treated with: JQ1
|
| Treatment protocol |
Cell lines were grown in 0.1% DMSO, 500nM JQ1 or 500nM JQ1–PA
|
| 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 2
|
| 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 |
Oct 14, 2016 |
| 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) |
| GSE88750 |
Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [RNA-seq] |
| GSE88751 |
Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies |
|
| Relations |
| BioSample |
SAMN05908473 |
| SRA |
SRX2245539 |
