|
| Status |
Public on May 05, 2009 |
| Title |
Chimpanzee liver, biological rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
chimpanzee liver
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: liver, Gender: male, Age: 37 years
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer's instructions. RNA was quantified (A260) using a Nanodrop-1000 spectrophotometer (Nanodrop Technologies).
|
| Label |
biotin
|
| Label protocol |
Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854). Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).
|
| |
|
| Hybridization protocol |
The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Human Exon 1.0 ST Arrays (exon arrays) according to manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility.
|
| Scan protocol |
Hybridized Affymetrix Human Exon 1.0 ST Arrays (exon arrays) were scanned following the manufacturer’s protocols at the Stanford Protein and Nucleic Acid Facility.
|
| Description |
none
|
| Data processing |
Raw image files were processed using Affymetrix GCOS software to generate CEL data files. The GeneBASE algorithm (Kapur et al., 2007, Genome Biol 8:R82) was used to produce the expression values, with minor modifications. Exon array expression indexes were calculated by the JETTA program using perfect-match probes shared between human and chimpanzee genomes.
|
| |
|
| Submission date |
Apr 10, 2009 |
| Last update date |
May 05, 2009 |
| Contact name |
Yi Xing |
| E-mail(s) |
[email protected]
|
| Phone |
319-384-3099
|
| Fax |
319-384-3150
|
| Organization name |
University of Iowa
|
| Department |
Internal Medicine, Biomedical Engineering
|
| Street address |
3294 CBRB, 285 Newton Rd
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE15626 |
Using high-density exon arrays to profile gene expression in closely related species (Exon 1.0 ST) |
| GSE15666 |
Using high-density exon arrays to profile gene expression in closely related species |
|
