|
| Status |
Public on Nov 26, 2011 |
| Title |
13_vehicle_biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
mIMCD-3 cells_vehicle (0.1% ethanol and 0.1% DMSO)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse inner medullary collecting duct cells (mIMCD-3)
|
| Treatment protocol |
mIMCD-3 cells grown on 35 mm dishes and treatment protocols were as described before in "overall design"
|
| Growth protocol |
mIMCD-3 cells were routinely grown in DMEM-F12 containing penicillin (100 IU/ml), streptomycin (100 μg/ml) and amphotericin B (2.5 μg/ml), supplemented with 5% fetal calf serum, at 37C and 5% CO2. Cells were passaged at a ratio of 1:4-1:8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using QIAshredder spin column and Rneasy Mini Kit according to manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cDNA were prepared from 500 ng total RNA according to company's protocol (Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript (WT) Expression Arrays, edition 05/2009).
|
| |
|
| Hybridization protocol |
5.5 ug of cDNA were fargmented and labeled, and 2.3 ug of cDNA were hybridized on GeneChip Mouse Gene 1.0 ST arrays for 16 hr at 45 C, at a rotation of 60 rpm according to company's protocol (Affymetrix GeneChip WT Terminal Labelling and Hybridisation User Manual, Rev. 4). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to company's protocol (Affymetrix GeneChip Expression Wash, Stain and Scan User Manual for Cartridge Arrays, Rev. 3).
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip 3000 7G scanner.
|
| Description |
VEH_4
Gene expression data in mIMCD-3 cells treated with vehicle
|
| Data processing |
CEL files were generated using Affymetrix GeneChip Command Console software, and the data were analyzed and normalized using Robust Multichip Analysis (RMA) method with Affymetrix Expression Console software to generate CHP files. CHP files were then imported to Qlucore Omics Explorer to short-list target genes potentially regulated by AGN193109 and DEAB.
|
| |
|
| Submission date |
Nov 25, 2011 |
| Last update date |
Nov 26, 2011 |
| Contact name |
Qihe Xu |
| E-mail(s) |
[email protected]
|
| Organization name |
King's College London
|
| Street address |
123, Coldharbour Lane
|
| City |
London |
| ZIP/Postal code |
SE5 9NU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE33955 |
Gene expression regulated by AGN193109 and 4-diehtylaminobenzaldehyde (DEAB) in mIMCD-3 cells |
|
