|
| Status |
Public on Oct 18, 2012 |
| Title |
Liver B6 M rep1 |
| Sample type |
RNA |
| |
|
| Source name |
liver tissue, C57BL/6J strain, male
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
gender: Male
tissue: liver
|
| Treatment protocol |
The large lobe of the liver was collected and kept in RNA later at room temperature for 24 hours and then kept at -80deg until RNA extraction
|
| Growth protocol |
The mice were kept on a chow diet until 8 weeks of age. They were separated individually for 3 days and fasted for 4 hours prior to the tissue collection. After sacrifice by cervical dislocation, the mice were perfused with PBS and the large lobe of the liver was collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed using Ambion's PureLink RNA Mini Kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared according to the Affymetrix protocol from 300ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay, Affymetrix 2005-2009) & (GeneChip WT Terminal Labeling and Hybridization User Manual 2009-2011)
|
| |
|
| Hybridization protocol |
Following fragmentation and labeling, ~25ng/µl (according to manual) cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. (GeneChip Whole Transcript (WT) Sense Target Labeling Assay, Affymetrix 2005-2009) & (GeneChip Expression Wash, Stain and Scan User Manual, Affymetrix 2008)
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
|
| Data processing |
Average signal intensities for each probe set within arrays were calculated by the rma function provided within the affy package for R using a custom (Entrez Gene v13) CDF file (available via http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp). The RMA method incorporates convolution background correction, sketch-quantile normalization, and summarization based on a multi-array model fit robustly using the median polish algorithm. For this experiment, six pairwise comparisons were used to statistically resolve gene/probe set expression differences between strains and genders using the R/maanova analysis package. Specifically, differentially expressed genes/probe sets were detected by using Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package. Statistical significance levels of the pairwise comparisons were calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method. Differentially expressed genes/probe sets were declared at an FDR q-value threshold of 0.05.
|
| |
|
| Submission date |
Apr 19, 2012 |
| Last update date |
Oct 18, 2012 |
| Contact name |
Magalie S Leduc |
| E-mail(s) |
[email protected]
|
| Phone |
210-258-9609
|
| Organization name |
Texas Biomedical Research Institute
|
| Street address |
7620 NW Loop 410
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78227 |
| Country |
USA |
| |
|
| Platform ID |
GPL11078 |
| Series (1) |
| GSE37429 |
Gene expression comparison of liver tissue from C57BL/6J and KK/HIJ mice |
|
