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Status |
Public on Sep 17, 2013 |
Title |
HT29 at 10 μM of 5-Aza, biological rep3 |
Sample type |
RNA |
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Source name |
HT29 treated with 10 μM of 5-Aza
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Organism |
Homo sapiens |
Characteristics |
tissue: Human colon cancer cell line cell line: HT29 treatment: 10 μM of 5-Aza
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Treatment protocol |
Triplicate cultures of HT-29 cells were treated in the following three experimental groups: 1.) Vehicle (DMSO) alone or 0 µM 5-Aza-deoxycytidine (5-Aza); 2.) 5 µM 5-Aza; 3.) 10 µM 5-Aza
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Growth protocol |
HT-29 colon cancer cells were cultured as monolayers in 150 mm dishes in DMEM with 10% fetal bovine serum, 1% kanamycin, streptomycin-penicillin at 37 CO2 5% .
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Extracted molecule |
total RNA |
Extraction protocol |
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.
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Label |
biotin
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Label protocol |
standard Affymetrix protocol
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Hybridization protocol |
The biotinylated cRNA was hybridized on the Affymetrix hgu133 plus2.0 arrays. Gene chips were washed and stained using the Affymetrix GeneChip® Fluidics Station 450
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Scan protocol |
Gene chips were scanned using the Affymetrix GeneChip® Scanner 3000 7G
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Description |
RNA samples from human colon cancer HT29 cell line
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Data processing |
Gene expression intensities were initially extracted from the CEL files and proceeded with 75% percentile scalling and RMA normalization. Subsequently a filter step was applied to remove probes with one or more absence flags in a given group. The software we used for data normalization are GeneSpring GX (Agilent Inc) and R bioconductor package affy (v 1.14.2).
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Submission date |
Oct 05, 2012 |
Last update date |
Sep 17, 2013 |
Contact name |
Xiao Xu |
E-mail(s) |
slowsmile820@gmail.com
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Organization name |
Stony Brook University BME
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Street address |
Stony Brook University
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City |
Stony Brook |
State/province |
NY |
ZIP/Postal code |
11794 |
Country |
USA |
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Platform ID |
GPL570 |
Series (2) |
GSE41364 |
Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [Affymetrix] |
GSE41588 |
Expression data for HT29 cells treated with 5-aza-deoxy-cytidine |
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