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Sample GSM850536 Query DataSets for GSM850536
Status Public on Nov 06, 2012
Title PCOS, biological rep 7
Sample type RNA
 
Source name PCOS, biological rep 7
Organism Homo sapiens
Characteristics cell type: granulosa cells
disease: Polycystic ovary Syndrome
Treatment protocol Normal and PCOS women were treated with FSH after pituitary downregulation until E2 levels reached 300 pg/mL per dominant follicles. hCG was then administered followed by transvaginal oocyte retrieval.
Growth protocol Ovarian aspirates were collected after oocyte retrieval from the consented normal and PCOS patients in the operating room and processed immediately for granulosa cell isolation and RNA extraction to minimize RNA degradation. RNA was stored at -80┬░C until use.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.The precipitated product was further purified using RNeasy Mini Kit (Qiagen, CA).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45 C on the HG-133 Plus 2 Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using GeneChip® Scanner 7G by Affymetrix.
Description Gene expression using RMA method
Data processing The CEL files from the two Affymetrix series were combined using the matchprobes package in the R programming environment. Thereafter, the RMA method in the R affy package was used to obtain probe set expression summaries.
 
Submission date Dec 19, 2011
Last update date Nov 06, 2012
Contact name Rita Singh
E-mail(s) ghrika_s@yahoo.com
Organization name University of Delhi
Department Department of Zoology
Lab Molecular Reproduction
Street address Department of Zoology
City Delhi
ZIP/Postal code 110007
Country India
 
Platform ID GPL570
Series (1)
GSE34526 Differential Gene Expression in Granulosa Cells from Polycystic Ovary Syndrome Patients with and without Insulin Resistance: Identification of Susceptibility Gene Sets through Network Analysis

Data table header descriptions
ID_REF
VALUE Robust multiarray average (RMA)

Data table
ID_REF VALUE
1007_s_at 1240.258758
1053_at 428.0155604
117_at 2293.982326
121_at 356.2949015
1255_g_at 73.08098005
1294_at 2468.926575
1316_at 155.0398659
1320_at 178.0050671
1405_i_at 3352.54266
1431_at 24.98531145
1438_at 19.52821214
1487_at 730.0815377
1494_f_at 448.0326483
1552256_a_at 26004.38778
1552257_a_at 1351.349225
1552258_at 184.5818274
1552261_at 48.27375982
1552263_at 743.2964248
1552264_a_at 1894.152461
1552266_at 63.9354961

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM850536_RSN-5.CEL.gz 3.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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