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Sample GSM436442 Query DataSets for GSM436442
Status Public on Dec 19, 2009
Title Stroma_Endo_control_rep3
Sample type RNA
 
Source name Stromal culture, endometriosis, control
Organism Homo sapiens
Characteristics tissue: endometrial stromal culture cell
cell type: stromal cell fibroblasts
disease status: endometriosis
treatment group: control
Growth protocol Endometrial tissue biopsies were obtained from 14 reproductive age women. Six subjects had endometriosis (n=1 minimal, n=2 mild, n=1 moderate-severe, n=2 severe), on visualization of lesions during laparoscopy and their histologic evaluation (Table 1). Staging of endometriosis was according to the revised American Fertility Society classification system (19). Participating subjects with endometriosis were 22-46 years old (mean 33.5+/-3.0), not pregnant, and did not use hormonal medications within 3 months before surgery. Controls were eight cycling subjects (37-49 years old, mean 44.4+/-.7) undergoing endometrial biopsy or hysterectomy for benign reasons such as fibroids, pelvic organ prolapse, pelvic pain or endometrial polyps. Controls had regular menstrual cycles (25-35 days), were documented not to be pregnant, had no history of endometriosis and no evidence of endometriosis at laparoscopy and had not been on hormonal therapies for at least 3 months before tissue sampling.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from hESF from subjects without (n=4) and with (n=4) endometriosis and purified using Qiagen RNeasy Plus Mini kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Samples were stored in RNase-free H2O, quantified by spectroscopy, and purity was analyzed using the 260/280 absorbance ratio. RNA quality and integrity were assessed using Agilent Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA) with all samples demonstrating high quality (RIN=9.7-10).
Label biotin
Label protocol Hybridization was performed using Affymetrix Human Gene 1.0 ST arrays (Affymetrix, Inc, Santa Clara, CA). Briefly, for each sample 100 ng of total RNA were reverse transcribed to cDNA using 500 ng of T7-(N6) primers and SuperScript II. A second strand of DNA was generated using DNA Polymerase, followed by overnight in vitro transcription to generate cRNA. After processing through cRNA cleanup spin columns, 10 μg of cRNA was reverse transcribed using random primers and SuperScript II. Mixtures were digested with RNase H, and the cDNA purified by the cDNA clean-up spin columns. Finally, 5.5 μg of sense cDNA was fragmented and labeled using the geneChip WT terminal labeling kit. Quality of cDNA and fragmented cDNA was assessed using an Agilent bioanalyzer.
 
Hybridization protocol Microarrays were hybridized, washed, stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007).
Scan protocol According to manufacturer's instruction.
Description No additional information
Data processing To minimize technical (non-biological) variability among arrays, densitometry values between arrays were normalized using the RMA function and further transformed to the logarithmic scale (log2). Probes with a corresponding GenBank accession ID were selected for functional analysis. Statistically significant differences between groups were determined using SAM and RankProd methods using the Bioconductor (http://www.bioconductor.org/) packages Siggene and RankProd, respectively, both run under R software (http://www.r-project.org/).
 
Submission date Aug 05, 2009
Last update date Aug 10, 2009
Contact name Jose Antonio Martinez-Conejero
E-mail(s) josn.mc@gmail.com
Organization name iGenomix
Street address C/ Guadassuar 1, bajo
City Valencia
ZIP/Postal code 46015
Country Spain
 
Platform ID GPL6244
Series (1)
GSE17504 The PKA Pathway of Endometrial Stromal Fibroblasts Reveals Differentiation and Proliferative Potential in Endometriosis

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
7892501 7.404261
7892502 4.387825
7892503 3.792199
7892504 10.17672
7892505 3.965256
7892506 4.08097
7892507 4.53863
7892508 3.716363
7892509 11.71419
7892510 3.834983
7892511 4.981182
7892512 8.885581
7892513 5.104922
7892514 11.92296
7892515 10.17454
7892516 5.362817
7892517 6.154192
7892518 3.123682
7892519 6.14739
7892520 10.29446

Total number of rows: 33297

Table truncated, full table size 549 Kbytes.




Supplementary file Size Download File type/resource
GSM436442.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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