|
| Status |
Public on Aug 23, 2013 |
| Title |
Endometrium_Asoprisnil_25_20 |
| Sample type |
RNA |
| |
|
| Source name |
Endometrium_Asoprisnil_25_20
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Endometrium
gender: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from endometrial samples, collected from women exposed to asoprisnil, as previously described (Henderson et al 2003; J. Clin. Endocrinol. Metab. 88: 440-449). Quality and integrity of each RNA sample was checked with the Agilent 2100 Bioanalyser (Agilent Inc, Santa Clara, CA, USA) according to manufacturer's instructions and the RNA Integrity Number (RIN) determined. Only samples with a RIN > 8.5 were processed for further analysis. Prior to full array analysis, RNA was subjected to the Affymetrix Test3 Array (Affymetrix Inc, Santa Clara, CA, USA) to exclude degraded samples with insufficient target.
|
| Label |
biotin
|
| Label protocol |
Biotin-labelled cRNA was synthesised from 10 ug total RNA. cDNA synthesis, second strand synthesis, in-vitro transcription amplification, biotin-labelling and purification were performed according to the Affymetrix Gene Chip Expression 'Eukaryotic Sample and Array Processing' manual.
|
| |
|
| Hybridization protocol |
Chapter 3 in http://media.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf Table 3.2 Array format 49 = 200ul volume. Step 11 hybridise for 16 hrs, proceed to 'GeneChip Expression Wash, Stain and Scan User Manual' P/N 702731: http://media.affymetrix.com/support/downloads/manuals/wash_stain_scan_cartridge_arrays_manual.pdf Chapter 1. Fluidics station 450. Table 1.1 49 format = 250ul volume. Fluidics protocol FS450_0001.
|
| Scan protocol |
Chapter 3 http://media.affymetrix.com/support/downloads/manuals/wash_stain_scan_cartridge_arrays_manual.pdf
|
| Description |
Endometrium, asoprisnil-exposed
|
| Data processing |
1. RMA normalisation, 2. Removal of sample Endo_50Rex for quality reasons, 3. Non-specific filtering by variation (gene's Inter-Quartile-Range has to be above Inter-Quartile-Range median of all genes), 4. Statistical testing through eBayes moderated t tests between placebo group and each of the Asoprisnil dose groups. P-value adjustment for multiple testing was done with Benjamini-Yekutieli method. Software: R/Bioconductor
|
| |
|
| Submission date |
May 31, 2013 |
| Last update date |
Sep 25, 2013 |
| Contact name |
Hilary Critchley |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Edinburgh
|
| Department |
MRC Centre for Reproductive Health
|
| Lab |
The Queen's Medical Research Institute
|
| Street address |
47 Little France Crescent
|
| City |
Edinburgh |
| ZIP/Postal code |
EH16 4TJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE47577 |
Regulation of endometrial bleeding by uNK cells |
|
