|
| Status |
Public on Jan 23, 2019 |
| Title |
Liver_PparaKO_fasted_replicate2 |
| Sample type |
RNA |
| |
|
| Source name |
Liver of a Ppara knockout mouse, fasted for 16hrs
|
| Organism |
Mus musculus |
| Characteristics |
Sex: male
genotype: PPARalpha-/-
treatment: fasting, 16hrs
|
| Treatment protocol |
The four different mouse lines (wildtype, PPARα-/-, CREB3L3-/-, and PPARα/CREB3L3-/-) were either fasted for 16 hours or fed a ketogenic diet for 4 days (# F3666, Bio-Serv). The mice used for experiments were all male and approximately 8 weeks old. The euthanasia was carried out at around 10 a.m., with the ketogenic diet group being non-fasted (ad libitum fed). Livers were snap-frozen in liquid nitrogen.
|
| Growth protocol |
CREB3L3-/- mice were backcrossed onto a C57BL/6 background at least 10 times. PPARα-/- mice that had been backcrossed on a pure C57Bl/6J background for more than 10 generations were acquired from Jackson Laboratories (no. 008154, B6;129S4-Pparatm1Gonz/J). The two lines were interbred to generate combined PPARα/CREB3L3-/- mice. Mice were housed in a specific pathogen free facility at the Weill Cornell Medical College on a 12h light/dark cycles and fed ad libitum standard chow diet (PicoLab Rodent diet 20, #5058, Lab diet).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using TRIzol reagent (Life Technologies, Bleiswijk, The Netherlands) and subsequently purified using the RNeasy Micro kit (Qiagen, Venlo, The Netherlands). RNA integrity was verified with RNA 6000 Nano chips on an Agilent 2100 bioanalyzer (Agilent Technologies, Amsterdam, The Netherlands). RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
|
| Label |
biotin
|
| Label protocol |
Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
|
| |
|
| Hybridization protocol |
Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).
|
| |
|
| Submission date |
Oct 10, 2018 |
| Last update date |
Jan 23, 2019 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
guido.hooiveld@wur.nl
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11533 |
| Series (1) |
| GSE121096 |
Transcriptional profiling of PPARα-/- and CREB3L3-/- livers reveals disparate regulation of hepatoproliferative and metabolic functions of PPARα |
|
