|
| Status |
Public on Sep 17, 2013 |
| Title |
Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [RNA-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The RNA samples from HT-29 (ATCC) colon cancer cell line were reverse transcribed to build cDNA libraries and categorized into 3 groups with different concentrations of 5-aza-deoxy-cytidine (5-Aza); in each group three replicative 150 mm cultures were treated with: 1) dimethyl sulfoxide (vehicle alone, 0 μM 5-Aza); 2) 5μM 5-Aza and 3) 10 μM 5-Aza; for five days. This experiment was also performed parallel on a commercial Affymetrix microarray [GSE41364] and the aim of the study was to compare the two platforms on gene expression measurements and differentially expressed gene (DEG) detection. The results showed a strong correlation between the two platforms, yet it also confirmed the existence of fixed and proportional biases on the gene expression measurements between microarray and RNA-Seq. The DEG analysis indicated the relative superiority of DESeq method in terms of its performance; high consistency was confirmed between DESeq, baySeq methods from RNA-Seq and SAM/eBayes from microarray data.
|
| |
|
| Overall design |
Experiment on human colon cancer HT29 cell line treated with 3 concentrations of 5-aza-deoxy-cytidine
|
| |
|
| Contributor(s) |
Li E, Williams J, Antoniou E, McCombie WR, Denoya P, Xu X |
| Citation(s) |
23902433 |
| Submission date |
Oct 15, 2012 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Xiao Xu |
| E-mail(s) |
slowsmile820@gmail.com
|
| Organization name |
Stony Brook University BME
|
| Street address |
Stony Brook University
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
|
| Samples (9)
|
| GSM1019738 |
HT29 at 5 μM of 5-Aza, biological rep1 |
| GSM1019739 |
HT29 at 5 μM of 5-Aza, biological rep2 |
| GSM1019740 |
HT29 at 5 μM of 5-Aza, biological rep3 |
| GSM1019741 |
HT29 at 10 μM of 5-Aza, biological rep1 |
| GSM1019742 |
HT29 at 10 μM of 5-Aza, biological rep2 |
| GSM1019743 |
HT29 at 10 μM of 5-Aza, biological rep3 |
|
| This SubSeries is part of SuperSeries: |
| GSE41588 |
Expression data for HT29 cells treated with 5-aza-deoxy-cytidine |
|
| Relations |
| BioProject |
PRJNA177604 |
| SRA |
SRP016118 |
Less...
More...