|
| Status |
Public on Aug 26, 2014 |
| Title |
Wt, DSS-saline treated, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Wt, DSS-saline treated
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colon
strain: C57BL/6
genotype/variation: Wild-type
|
| Treatment protocol |
Except for the controls, a final concentration of 2.5% DSS was added to the drinking water of all treatment groups for 7 consecutive days. TSP-1 peptides (3TSR, TSR2, TSR2+RFK) were injected subcutaneously in respective TSR-treated mice.
|
| Growth protocol |
Mice were bred at room temperature at a vivarium facility of Wilkes University. Drinking bottles of the same capacity (4 oz) and antidrip system were used for the DSS treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using the RNAqueous®-4PCR kit (Applied Biosystems) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Fragmentation and labeling of 20 ng total RNA per sample were performed using the Ovation EXON and Encore Biotin Module (NuGEN Technologies).
|
| |
|
| Hybridization protocol |
Hybridization cocktails for Mini Array (169 format) were heated to 99oC for 2 minutes then incubated for 45oC for 5 min followed by centrifugation at 13,000 RPM for 5 min. Entire volume, 110 µl, was loaded onto arrays and hybridized for 17 hrs at 45oC. Washing and staining were performed on a Affymetrix FS 450 station.
|
| Scan protocol |
GeneChips were scanned on a GeneChip 3000 7G scanner using GeneChip® Command Console Software (AGCC).
|
| Description |
gene expression data from colon of WT mouse treated with DSS and saline
|
| Data processing |
Further statistical analysis of the CEL files was done using GeneSpring GX 11 software. Signals were quantile normalized using PLIER16 algorithm and base line transformed to the median of all samples. The log2 normalized signal values were then filtered to remove entities that show signal in the bottom 20th percentile across all samples. This list was further filtered to only include entities where at least 1 out of 8 conditions have CV < 10%. The list was then subjected to ANOVA with Benjamini-Hochberg False Discovery Rate correction (p < .05) applied. A 1.5-fold filter was applied to identify genes that are differentially expressed between any two specific conditions.
|
| |
|
| Submission date |
Oct 07, 2011 |
| Last update date |
Aug 26, 2014 |
| Contact name |
Sridar V Chittur |
| E-mail(s) |
schittur@albany.edu
|
| Phone |
518-591-7215
|
| Organization name |
SUNY-University at Albany
|
| Department |
Center for Functional Genomics
|
| Lab |
Microarray Core
|
| Street address |
One Discovery Drive, CRC 342G
|
| City |
Rensselaer |
| State/province |
NY |
| ZIP/Postal code |
12144 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE32697 |
Thrombospondin-1 type 1 repeats in a model of inflammatory bowel disease: genetic profile and therapeutic effects |
|
