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Sample GSM1152636 Query DataSets for GSM1152636
Status Public on Aug 23, 2013
Title Endometrium_Asoprisnil_10_23
Sample type RNA
 
Source name Endometrium_Asoprisnil_10_23
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

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
1007_s_at 8.713846515
1053_at 5.136364257
117_at 3.612072381
121_at 7.531119982
1255_g_at 1.783223461
1294_at 6.071845179
1316_at 3.503194587
1320_at 3.1659368
1405_i_at 7.324757285
1431_at 2.76943668
1438_at 5.241758359
1487_at 5.410957949
1494_f_at 2.421032326
1552256_a_at 6.56477643
1552257_a_at 5.663677154
1552258_at 2.37354683
1552261_at 6.662510529
1552263_at 3.164997856
1552264_a_at 5.912734194
1552266_at 2.887704034

Total number of rows: 54675

Table truncated, full table size 1211 Kbytes.




Supplementary file Size Download File type/resource
GSM1152636_TAP_ENDO_23_HG-U133plus2_031105.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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