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Sample GSM850530 Query DataSets for GSM850530
Status Public on Nov 06, 2012
Title PCOS, biological rep 1
Sample type RNA
Source name PCOS, biological rep 1
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
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
VALUE Robust multiarray average (RMA)

Data table
1007_s_at 2697.704327
1053_at 266.3510626
117_at 693.4075445
121_at 631.6009607
1255_g_at 44.93576697
1294_at 547.969892
1316_at 149.7369868
1320_at 106.5038094
1405_i_at 4367.224285
1431_at 21.75080315
1438_at 34.00998272
1487_at 525.0456438
1494_f_at 228.8974554
1552256_a_at 3346.873878
1552257_a_at 354.4910281
1552258_at 165.3488088
1552261_at 5.301016383
1552263_at 938.9073314
1552264_a_at 646.6727471
1552266_at 107.836518

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM850530_RSN-10.CEL.gz 4.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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