|
| Status |
Public on Mar 25, 2013 |
| Title |
NUID-0000-0100-9069 |
| Sample type |
RNA |
| |
|
| Source name |
01 day, Control
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6C3F1/Crl (C57BL/6 male x C3H/He female)
tissue: whole liver extract
treatment: Control
duration: 1 day
|
| 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 mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divide
|
| 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 |
01 day, Control
|
| Data processing |
The Affymetrix GeneChip® Operating Software (GCOS) was used to generate the primary and secondary raw data files.
|
| |
|
| Submission date |
Mar 25, 2013 |
| Last update date |
Mar 25, 2013 |
| 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 |
| GSE45465 |
Dynamic changes in liver 5-hydroxymethylcytosine profiles upon non-genotoxic carcinogen exposure [Replicated control vs. pb treated study] |
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