|
| Status |
Public on Apr 09, 2014 |
| Title |
40.24hr.U266.NMP.B |
| Sample type |
SRA |
| |
|
| Source name |
Multiple myeloma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue source: peripheral blood
cell line: U266
treatment: NMP
timepoint: 24hr
|
| Treatment protocol |
For panobinostat and NMP single agent treatments cells were treated for 4h or 24h prior to harvest; For 5-Azacytidine treatment, cells were pretreated with 5-Azycytidine for 24h then harvested after a further 4h and 24h; For combination treatments, cells were pre-treated with 5-Azacytidine for 24h then treated with panobinostat and harvested after 4h and 24h.
|
| Growth protocol |
JJN3 cells cultured in Dulbecco's Modified Eagle's Medium : Iscove's MDM (1 : 1) + 20% fetal bovine serum (FBS) + Pen/Strep; U266 cells cultured in RPMI medium + 10% FBS + Pen/Strep.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNA extraction as per kit instructions.
RNA libraries were prepared for sequencing using the Illumina TruSeq v2 kit and standard Illumina protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
Reads were quality checked by FastQC and trimmed if necessary for low base quality or adaptor, and then mapped to the human reference genome (GRCh37) using Tophat2 v.2.0.8b with maximum number of multiple hits set to 1 and using the option to map first to the reference transcriptome (Ensembl v.69).
Counts per gene were obtained using HTSeq v.0.5.3p9 with mode intersection-nonempty and normalised using limma-voom v3.14.4 was used to normalise.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include voom normalised log2 values for each Sample
|
| |
|
| Submission date |
Apr 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Geoffrey Mark Matthews |
| E-mail(s) |
geoff.matthews@petermac.org
|
| Phone |
+61396563724
|
| Organization name |
Peter MacCallum Cancer Centre
|
| Department |
Cancer Therapeutics
|
| Lab |
Gene Regulation
|
| Street address |
St Andrews Place
|
| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3002 |
| Country |
Australia |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE56623 |
RNAseq to investigate transcriptional changes in human MM cell lines due to panobinostat, 5-Azacytidine, panobinostat+5-Azacytidine or n-methyl-2-pyrroldine (NMP) treatments. |
|
| Relations |
| BioSample |
SAMN02721657 |
| SRA |
SRX513351 |
