|
| Status |
Public on May 01, 2013 |
| Title |
Liver_Fasted_vs_Fed_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
mouse liver, fasted 24hr
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/Bl6
tissue: liver
condition: Fasted 24h
|
| Treatment protocol |
Fasted mice had food removed from their cages for 24h prior to liver harvest. Re-fed mice had food removed from their cages for 24h, and then were given access to food for 2h prior to liver harvest.
|
| Growth protocol |
All mice used in this study were 8-12 week-old male C57BL/6J mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from livers collected from fasted and re-fed mice using the RNeasy Kit (Qiagen), then assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy5
|
| Label protocol |
200ng of total RNA from each fasted and re-fed mouse livers (n = 4 per group) were amplified and labeled with Cy3 or Cy5 using Low Input Quick Amp Labeling Kit, two-color (Agilent, #5190-2306) with a dye swap experimental design.
|
| |
|
| Channel 2 |
| Source name |
mouse liver, refed 2hr
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/Bl6
tissue: liver
condition: Fasted 24h, Re-fed 2h
|
| Treatment protocol |
Fasted mice had food removed from their cages for 24h prior to liver harvest. Re-fed mice had food removed from their cages for 24h, and then were given access to food for 2h prior to liver harvest.
|
| Growth protocol |
All mice used in this study were 8-12 week-old male C57BL/6J mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from livers collected from fasted and re-fed mice using the RNeasy Kit (Qiagen), then assayed for quantity and quality with the Agilent 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
200ng of total RNA from each fasted and re-fed mouse livers (n = 4 per group) were amplified and labeled with Cy3 or Cy5 using Low Input Quick Amp Labeling Kit, two-color (Agilent, #5190-2306) with a dye swap experimental design.
|
| |
|
| |
| Hybridization protocol |
Labeled samples were purified using the RNeasy Kit (Qiagen) and hybridized overnight to the Agilent 4X44 Whole Mouse Genome Array.
|
| Scan protocol |
After hybridization the arrays were washed and scanned with the Agilent DNA Microarray Scanner G2565B. Median intensities of each array element were captured with Agilent Feature Extraction v10.5.1.1.
|
| Description |
Comparison of total RNA from paired fasted and re-fed mouse livers
|
| Data processing |
Median feature intensities were normalized by the print tip loess method in LIMMA (Smyth GK, et al. Bioinformatics 2005). Differentially expressed gene calls were performed by SAM (Tusher VG, et al. PNAS 2001) at 10% FDR and absolute fold-change cutoff of 1.5.
|
| |
|
| Submission date |
Apr 03, 2013 |
| Last update date |
May 01, 2013 |
| Contact name |
Logan J Everett |
| Organization name |
U.S. Environmental Protection Agency
|
| Department |
Office of Research and Development
|
| Lab |
Center for Computational Toxicology and Exposure
|
| Street address |
109 T.W. Alexander Dr
|
| City |
RTP |
| State/province |
North Carolina |
| ZIP/Postal code |
27711 |
| Country |
USA |
| |
|
| Platform ID |
GPL10333 |
| Series (2) |
| GSE45731 |
Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver [array] |
| GSE45733 |
Integrative genomic analysis of CREB defines a critical role for transcription factor networks in mediating the fed/fasted switch in liver |
|
