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Sample GSM850532 Query DataSets for GSM850532
Status Public on Nov 06, 2012
Title PCOS, biological rep 3
Sample type RNA
 
Source name PCOS, biological rep 3
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 3103.043886
1053_at 319.0360586
117_at 1241.071653
121_at 663.8713022
1255_g_at 47.13286209
1294_at 939.6160591
1316_at 123.2635557
1320_at 88.72889521
1405_i_at 4727.8227
1431_at 67.01559635
1438_at 47.74472598
1487_at 485.4836681
1494_f_at 176.5722758
1552256_a_at 6414.151044
1552257_a_at 631.1932169
1552258_at 190.0219921
1552261_at 25.70736199
1552263_at 638.7575758
1552264_a_at 1205.959647
1552266_at 47.29317751

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM850532_RSN-16.CEL.gz 4.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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