|
| Status |
Public on Sep 12, 2012 |
| Title |
control rep5 |
| Sample type |
RNA |
| |
|
| Source name |
whole liver extract
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
gender: male
treatment: control
animal id: 5
age: 29-32 days
strain: B6C3F1/Crl (C57BL/6 male x C3H/He female)
|
| Treatment protocol |
Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days
|
| Growth protocol |
29–32 days old male B6C3F1/Crl (C57BL/6 ♂ x C3H/He ♀) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups of five animals each. Phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behaviour and sacrificed on the last day of dosing (day 28)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen liver and kidney samples were homogenized in TRIzol reagent (Invitrogen) and subsequently purified on a silica-gel-based-membrane (RNeasy, Qiagen) according to the manufacturer's instructions. RNA quality was assessed by measuring the RIN (RNA Integrity Number) using an Agilent 2100 Bioanalyzer. RNA was stored at −80°C until GeneChip® experiment analysis.
|
| Label |
biotin
|
| Label protocol |
Processing of GeneChip® experiments was conducted as recommended by the manufacturer of the GeneChip® system (Affymetrix). For tissue samples, double stranded cDNA was synthesized with a starting amount of 0.1 µg total RNA. For RNA reverse transcription, the GeneChip® 3′ IVT Express Labelling Assay (lot ID 0904012, Affymetrix) was used in the presence of a T7-(dT)24 DNA oligonucleotide primer (Affymetrix). The cDNA was then transcribed in vitro in the presence of biotinylated ribonucleotides to form biotin-labelled amplified RNA (aRNA). The labelled aRNA was then purified and quantified by UV spectrophotometry at 260 nm and fragmented
|
| |
|
| Hybridization protocol |
The arrays were washed and stained with the GeneChip® Hybridization Wash and Stain kit (Affymetrix). The washing and staining steps were performed with GeneChip® Fluidics Workstation 450 (Affymetrix).
|
| Scan protocol |
Arrays were scanned using a solid-state laser scanner (GeneArray® Scanner 3000 combined with the GeneChip® autoloader, Affymetrix).
|
| Description |
gene expression data of control liver
|
| Data processing |
The Affymetrix GeneChip® Operating Software (GCOS) was used to generate the primary and secondary raw data files.
|
| |
|
| Submission date |
Sep 11, 2012 |
| Last update date |
Oct 05, 2012 |
| Contact name |
John Paterson Thomson |
| E-mail(s) |
john.thomson@igmm.ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
MRC Human Genetics Unit
|
| Lab |
Meehan
|
| Street address |
Crewe Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE40540 |
IP of 5-hydroxymethylcytosine (5-hmC) and 5-methylcytosine (5-mC) enriched DNA fragments from control and PB treated mouse livers |
| GSE40773 |
Dynamic changes in liver 5-hydroxymethylcytosine profiles upon non-genotoxic carcinogen exposure |
|
