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| Status |
Public on Jun 02, 2016 |
| Title |
PolyA RNAseq from HCT116 cells in normoxia and hypoxia |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To determine the effects of depleting TIP60, CDK8, or HIF1A on the transcriptional response to hypoxia, we performed RNAseq analysis of four HCT116 colorectal carcinoma cell lines (shNT, HIF1A-/-, shTIP60 and shCDK8) in normoxic and hypoxic (24hrs, 1% O2) conditions.
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| Overall design |
PolyA RNA for two independent biological replicates was purified from HCT116 cells stably expressing an shRNA against a non-targeting control (shNT), TIP60 (shTIP60) or CDK8 (shCDK8), or genetically deleted HIF1A (HIF1A-/-) subjected to 24hrs 1% O2 (hypoxia) or maintained under ambient oxygen (21%; normoxia) was sequenced on the Ion Torrent platform. Reads were aligned to the human genome and gene-level counts were used for differential expression analysis.
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| Contributor(s) |
Galbraith MD, Dengler VL, Pandey A |
| Citation(s) |
27320910, 33654095 |
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| Submission date |
Apr 27, 2015 |
| Last update date |
Apr 06, 2021 |
| Contact name |
Matthew D Galbraith |
| Organization name |
University of Colorado Anschutz Medical Campus
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| Department |
Pharmacology & Linda Crnic Institute for Down Syndrome
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| Street address |
RC1-N, Mail Stop 8303, Rm. P18-6114 12800 E. 19th Ave.
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platforms (1) |
| GPL17303 |
Ion Torrent Proton (Homo sapiens) |
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| Samples (16)
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| GSM1667176 |
shTIP60, normoxia, replicate 2 |
| GSM1667177 |
shCDK8, normoxia, replicate 1 |
| GSM1667178 |
shCDK8, normoxia, replicate 2 |
| GSM1667179 |
HIF1A-/-, normoxia, replicate 1 |
| GSM1667180 |
HIF1A-/-, normoxia, replicate 2 |
| GSM1667181 |
shNT, hypoxia, replicate 1 |
| GSM1667182 |
shNT, hypoxia, replicate 2 |
| GSM1667183 |
shTIP60, hypoxia, replicate 1 |
| GSM1667184 |
shTIP60, hypoxia, replicate 2 |
| GSM1667185 |
shCDK8, hypoxia, replicate 1 |
| GSM1667186 |
shCDK8, hypoxia, replicate 2 |
| GSM1667187 |
HIF1A-/-, hypoxia, replicate 1 |
| GSM1667188 |
HIF1A-/-, hypoxia, replicate 2 |
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| Relations |
| BioProject |
PRJNA282396 |
| SRA |
SRP057708 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE68297_HCT116_hypoxia_ALL_counts_forDESeq.txt.gz |
569.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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