|
| Status |
Public on Sep 25, 2015 |
| Title |
SET2_DMSO_4hrs_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
SET2 cells, DMSO, 4hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SET2
treatment: DMSO 4hrs
cell type: essential thrombocythemia
|
| Treatment protocol |
Cells were plated (24-well) in triplicate at 1,000,000 cells/mL and incubated in the presence of DMSO or 25nM CA for 4hrs. Cells were then washed three times with cold PBS, and snap frozen.
|
| Growth protocol |
SET2 cells were grown in RPMI-1640 supplemented with 20% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Qiagen RNeasy Mini Plus Kit
Libraries from 1 ug total RNA were prepared for sequencing using the mRNA direct Micro kit (Life Technologies) and standard Ion Proton protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
2,000,000 cells were treated with DMSO for 4hrs
|
| Data processing |
Ion Torrent Suite Software software used for basecalling.
Convert BAM to FASTQ
Trim to BASEQ==10 using fastq_quality_trimmer MINREAD_LEN==50
Pass 1 mapping with rnaStar v2.3.0e
Pass 2 mapping of unmapped reads with BWA v0.7.5a
Merge mapped reads and ount using htseq-count -s yes -m intersection-strict (HTSeq v0.5.3p3)
Count normalization, sample clustering, and differential expression analysis using Bioconductor package DESeq. Genes with minimum absolute fold change log2(2), FDR 0.05 were deemed to be differentially expressed.
Genome_build: hg19
|
| |
|
| Submission date |
Jan 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew D. Shair |
| Organization name |
Harvard University
|
| Department |
Chemistry and Chemical Biology
|
| Lab |
Shair
|
| Street address |
12 Oxford Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platform ID |
GPL17301 |
| Series (2) |
| GSE65105 |
Effect of 4hr cortistatin A treatment on gene expression in SET2 cells. |
| GSE65161 |
Mediator kinase inhibition further activates super-enhancer-associated genes in AML |
|
| Relations |
| BioSample |
SAMN03290564 |
| SRA |
SRX849364 |
