|
| Status |
Public on Jan 31, 2018 |
| Title |
ColonBasalWT8 |
| Sample type |
RNA |
| |
|
| Source name |
Colon tissues
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
treatment group: Basal after the WT intestinal microbial transfer
strain: C57BL/6N
|
| Treatment protocol |
One control group of untreated mice were given free water, whereas a second group of mice received 3% DSS ad libitum for 5 days, then free water until sacrifice, and finally a third group composed of axenic mice received, 3 weeks after fecal microbiota transplantation, 3% DSS ad libitum for 5 days, then free water until sacrifice.
|
| Growth protocol |
Colon tissues were collected at day 12 of treatment, flash frozen in liquid nitrogen and stored at -80°C until total RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracts were prepared using the Ambion mirVana miRNA Isolation Kit (#AM1560) according to Ambion recommendations.
|
| Label |
terminal deoxynucleotidyl transferase (TdT)
|
| Label protocol |
Biotinylated single strand cDNA targets were prepared, starting from 200 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.
|
| |
|
| Hybridization protocol |
1.9 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.
|
| Description |
ColonBasalWT
|
| Data processing |
CEL files were further processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.
|
| |
|
| Submission date |
Jan 13, 2015 |
| Last update date |
Jan 31, 2018 |
| Contact name |
christophe desterke |
| E-mail(s) |
[email protected]
|
| Phone |
+33 (0)145595316
|
| Organization name |
university Paris Sud11
|
| Department |
UFR medecine institute Andre Lwoff
|
| Lab |
hopital Paul Brousse Batiment Lavoisier
|
| Street address |
14-16 avenue Paul Vaillant Couturier
|
| City |
VILLEJUIF |
| ZIP/Postal code |
94807 |
| Country |
France |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE64932 |
Transcriptome study of colon epithelial cells in Reg3a-transgenic mice |
|
