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Sample GSM850529 Query DataSets for GSM850529
Status Public on Nov 06, 2012
Title Normal, biological rep 3
Sample type RNA
 
Source name Normal, biological rep 3
Organism Homo sapiens
Characteristics cell type: granulosa cells
disease: normal
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 3528.268069
1053_at 308.8496858
117_at 505.4982142
121_at 535.265823
1255_g_at 92.87307145
1294_at 583.5557978
1316_at 109.4130345
1320_at 153.3692657
1405_i_at 5937.467234
1431_at 60.75560422
1438_at 15.77842071
1487_at 319.7901779
1494_f_at 154.80149
1552256_a_at 15883.84551
1552257_a_at 2034.115312
1552258_at 138.7005447
1552261_at 32.56503259
1552263_at 504.084438
1552264_a_at 650.5678319
1552266_at 101.751585

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM850529_RSN-13.CEL.gz 4.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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