|
| Status |
Public on Oct 07, 2008 |
| Title |
MU reference technical replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Universal Human Reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
Universal Human Reference RNA
catalog no. 740000
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted
|
| Label |
Biotin
|
| Label protocol |
Biotin-labelled target for the microarray experiment were prepared using 1µg of total RNA. The RNA was subjected to a rRNA removal procedure with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen) and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Human Exon 1.0 ST array (Affymetrix) at 45˚C for 16-20 hours. Following hybridization, non-specifically bound material was removed by washing and detection of specifically bound target was performed using the GeneChip® Hybridization, Wash and Stain kit, and the GeneChip® Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
The arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).
|
| Description |
Meta-probeset expression data (transcript cluster ids)
apt-probeset-summarize -p ../../LIBRARY_FILES/HuEx-1_0-st-v2.pgf -c ../../LIBRARY_FILES/HuEx-1_0-st-v2.clf -b ../../LIBRARY_FILES/antigenomic.bgp -a plier-gcbg-sketch -a dabg --use-feat-effect plier-gcbg-sketch.feature-response.txt --rm-probes probe_mask_list_maqc2_2SD.txt --probeset-ids meta-probeset.core.txt.mask
|
| Data processing |
The Affymetrix Power Tools software package (Affymetrix) was used to quantile normalize the probe fluorescence intensities and to summarize the probe set (representing exon expression) and meta-probe set (representing gene expression) intensities.
|
| |
|
| Submission date |
Oct 06, 2008 |
| Last update date |
Jan 04, 2012 |
| Contact name |
Amandine Bemmo |
| Organization name |
McGill University
|
| Department |
Human Genetics
|
| Lab |
McGill University and Genome Quebec Innovation Center
|
| Street address |
740, Dr Penfield Avenue
|
| City |
Montréal |
| State/province |
Québec |
| ZIP/Postal code |
H3A 1A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE13066 |
Gene Expression and Isoform Variation: Gene-level Analysis |
| GSE13072 |
Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays |
|
