|
| Status |
Public on Jun 19, 2012 |
| Title |
TGF-beta stimulated vs. control IEC-6 cell replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
IEC-6 cells treated with 50ng/ml TGF-beta
|
| Organism |
Rattus norvegicus |
| Characteristics |
passage: passage 4-passage 10 at 1:4 passage ratio, cells are used within 14 times population doubling upon received from ATCC
sample type: rat small intestinal crypt cell line IEC-6
cell line: IEC-6
treatment protocol: 50ng/ml TGF-beta (R&D Systems)
growth protocol: IEC-6 cells were grown in growth media (DMEM with 4 mM L-glutamine adjusted to contain 1.5 g/L sodium bicarbonate and 4.5 g/L glucose and supplemented with 0.1 Unit/ml bovine insulin, 90%; fetal bovine serum, 10%; and maintained at 37.0°C, 5% CO2.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with miRNeasy Mini Kit (Qiangen) according to the manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
300 ng of each sample was labeled with Cy5/Cy3 using miRCURY LNA microRNA array Power Labeling kit (Exiqon).
|
| |
|
| Channel 2 |
| Source name |
IEC-6 cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
passage: passage 4-passage 10 at 1:4 passage ratio, cells are used within 14 times population doubling upon received from ATCC
sample type: rat small intestinal crypt cell line IEC-6
cell line: IEC-6
treatment protocol: untreated
growth protocol: IEC-6 cells were grown in growth media (DMEM with 4 mM L-glutamine adjusted to contain 1.5 g/L sodium bicarbonate and 4.5 g/L glucose and supplemented with 0.1 Unit/ml bovine insulin, 90%; fetal bovine serum, 10%; and maintained at 37.0°C, 5% CO2.)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted with miRNeasy Mini Kit (Qiangen) according to the manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
300 ng of each sample was labeled with Cy5/Cy3 using miRCURY LNA microRNA array Power Labeling kit (Exiqon).
|
| |
|
| |
| Hybridization protocol |
Hybridization SureHyb chamber kit and Gasket slide kit (Agilent) were used to hybridize the labeled RNA for 18 h to Exiqon miRCURY LNA miRNA array V.11.0 (miRBase Sequence Database, http://microrna.sanger.ac.uk/sequences, release 11.0).
|
| Scan protocol |
Arrays were scanned on an Axon GenePix 4000B scanner
|
| Data processing |
GPR files containing fluorescent ratios (sample/control) were generated using GenePix Pro 6.0 software. GPR files were read into R/Bioconductor [19] using the marray package. GenePix flagged spots were removed from subsequent analysis, and only unflagged human, mouse and rat probes were used for normalization and subsequent analysis. M (log2 ratios) of Cy5 to Cy3 signals were calculated for each array, and normalized by print tip loess normalization using only unflagged spots.
|
| |
|
| Submission date |
Mar 19, 2010 |
| Last update date |
Jun 19, 2012 |
| Contact name |
Bo Lonnerdal |
| E-mail(s) |
bllonnerdal@ucdavis.edu
|
| Organization name |
University of California, Davis
|
| Department |
Nutrition
|
| Lab |
3329 Meyer Hall
|
| Street address |
1 Shields Ave.
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL7723 |
| Series (1) |
| GSE20982 |
Murine small intestinal crypt cell line IEC-6: control vs. TGF-beta stimulated |
|
