|
| Status |
Public on Jan 01, 2016 |
| Title |
TCDD, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
HepaRG cells treated with 25nM TCDD for 30 hours
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HepaRG cells
|
| Treatment protocol |
DMSO was removed from the medium for twenty-four hours before treating the cells for 30 hours with 25nM TCDD, 10μM alphaendosulfan, the mixture of the two pollutants or the vehicle (0.15% DMSO).
|
| Growth protocol |
HepaRG were differentiated as described previously except that 1.5% DMSO was used for cell differentiation (Aninat et al. 2006).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from HepaRG cells (one well from a six-well plate) was prepared using the RNeasy mini kit from Qiagen (France) as described previously (Bui et al. 2009) except that a DNase I step was included in the protocol. For the microarray studies, the quality of the RNA (RIN value) was assessed with a Bionalyzer (Agilent Technologies).
|
| Label |
biotin
|
| Label protocol |
ssDNA (sense single stranded DNA) was synthetized using the Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay kit, according to the manufacturer’s protocol. ssDNA samples were then fragmented according to the Affymetrix protocol. The purified ssDNA was quantified and its quality was assessed with a Bioanalyzer. Subsequent labeling of the samples was performed by synthesis of Biotin-labeled ssDNA using the GeneChip WT Terminal Labeling kit (Affymetrix).
|
| |
|
| Hybridization protocol |
ssDNA targets were hybridized onto high-density microarrays (Affymetrix Human Genome 1.0 ST GeneChip array) according to the Affymetrix Eukaryotic Target manual.The microarrays were then washed and stained using the Affymetrix fluidics station 450/250 and Genechip Operating Software.
|
| Scan protocol |
The microarrays were scanned with an Affymetrix GeneArray scanner.
|
| Description |
Gene expression data from HepaRG cells treated with25nM TCDD for 30 hours.
|
| Data processing |
The datasets obtained were processed and normalized using the plier program in R.
|
| |
|
| Submission date |
May 13, 2013 |
| Last update date |
Jan 01, 2016 |
| Contact name |
Lawrence Aggerbeck |
| E-mail(s) |
lawrence.aggerbeck@parisdescartes.fr
|
| Organization name |
INSERM UMR S-747
|
| Street address |
45 rue des Saints Peres
|
| City |
Paris |
| ZIP/Postal code |
75006 |
| Country |
France |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE46874 |
Effects of Combined Persistant Organic Pollutants on Global Gene Expression in Human HepaRG Cells |
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