|
| Status |
Public on Sep 25, 2015 |
| Title |
HCT116_DMSO_3hrs_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116 cells, DMSO, 3hrs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
treatment: DMSO
cell type: essential thrombocythemia
|
| Treatment protocol |
Cells were plated (15cm dish) in triplicate and grown to approximately 80% confluency, then incubated in the presence of DMSO or 100nM CA for 3hrs. Cells were then washed twice with cold PBS, and immediately harvested in Trizol.
|
| Growth protocol |
HCT116 cells were grown in DMEM supplemented with 10% FBS, 100 U/mL penicillin and 100 μg/mL streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent, then was further purified using the RNeasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
approx. 16 million cells were treated with DMSO for 3hrs
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
fastX version 0.0.13.2 software used for quality assement of raw fastq files. Commands used for tophat mapping all fastq files = -p 16 --b2-very-sensitive --no-novel-juncs --microexon-search --no-convert-bam --no-mixed --library-type fr-firststrand -G hg19.gtf
Aligned .sam files were then converted to bam files using samtools version 0.1.16 and reads aligned over annotated genes were quantified using htSeq version 0.6.1. Commands used for htSeq = count -f bam -s reverse -m intersection-nonempty -t exon -I gene_id .
DESeq counts are in the tab-delimited text file HCT116_3hrs_CA_DESeqFormattedIndividualValues.txt containing Transcript_ID in the first column and values for each sample in subsequent columns.
For use with GSEA, DESeq counts were normalized using the voom function of the R/Bioconductor package limma (as described in Genome Biol. 2014 Feb 3;15(2):R29). Normalized values are in the tab-delimited text file HCT116_3hrs_CA_vomo-normalized_DESeqValues.txt containing Transcript_ID in the first column and values for each sample in subsequent columns.
Genome_build: hg19
|
| |
|
| Submission date |
Jan 15, 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 |
GPL11154 |
| Series (2) |
| GSE65030 |
Effect in HCT116 cells of 3hr cortistatin A treatment on gene expression. |
| GSE65161 |
Mediator kinase inhibition further activates super-enhancer-associated genes in AML |
|
| Relations |
| BioSample |
SAMN03290555 |
| SRA |
SRX849356 |
