| Series GSE41586 | Query DataSets for GSE41586 |
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| 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) | [email protected] |
| 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) |
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Samples (9) Less...  More... | | GSM1019735 | HT29 at 0 μM of 5-Aza, biological rep1 | | GSM1019736 | HT29 at 0 μM of 5-Aza, biological rep2 | | GSM1019737 | HT29 at 0 μM of 5-Aza, biological rep3 |
| 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 |
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| This SubSeries is part of SuperSeries: |
| GSE41588 | Expression data for HT29 cells treated with 5-aza-deoxy-cytidine |
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| Relations |
| BioProject | PRJNA177604 |
| SRA | SRP016118 |
