|
| Status |
Public on Nov 29, 2007 |
| Title |
ICC-MY, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
BALB/c mice aged 6-9-days, small intestine
|
| Organism |
Mus musculus |
| Characteristics |
ICC-MY cells were isolated from the tunica muscularis tissues by fluorescence-activated cell sorting .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated and purified using Trizol (Invitrogen, Carlsbad, CA) and the RNeasy Mini kit (Qiagen, Valencia, CA) respectively per manufacturers' instructions. RNA was quantified and its quality was tested by Agilent Bioanalyser (Agilent Technologies, Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
Total RNA from each sample was used to prepare biotinylated target RNA, according to the manufacturers' instructions. Briefly, about 50 ng of total RNA was used to generate first strand cDNA by using a T7-linked oligo(dT) primer. After second-strand synthesis, in vitro transcription was performed with unlabelled ribonucleotides (Ambion, PN AM1333). A second round of cDNA synthesis was then performed with random primers, followed by in vitro transcription with biotinylated UTP and CTP resulting in a final yield of more than 40ug cRNA.
|
| |
|
| Hybridization protocol |
Target cDNA generated from each sample were then processed as per manufacturer's recommendation using an Affymetrix GeneChip 3000 System Spike controls were added to 15 µg fragmented cRNA before overnight hybridization. Arrays were then washed and stained with streptavidin-phycoerythrin.
|
| Scan protocol |
The sample was scanned on an Affymetrix GeneChip 3000 system.
|
| Description |
Gene expression data from ICC-MY cells
|
| Data processing |
Analysis was performed using publicly available software Bioconductor. Simpleaffy was used to preprocess individual probe intensities from CEL files into expression values from which fold changes were derived using Limma. Robust MultiArray Analysis (RMA), which uses quantile normalization for cross-chip normalization, was used to preprocess the data.
|
| |
|
| Submission date |
May 15, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Hui Chen |
| Organization name |
University of Nevada, Reno
|
| Department |
Physiology and Cell Biology
|
| Street address |
1664 N Virginia St
|
| City |
Reno |
| State/province |
NV |
| ZIP/Postal code |
89557 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE7809 |
Transcriptional expression of ICC-DMP and ICC-MY in murine small intestine |
|
| Relations |
| Reanalyzed by |
GSE119085 |
