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Sample GSM573679 Query DataSets for GSM573679
Status Public on Jul 29, 2011
Title mRNA CEPI 551
Sample type RNA
Source name Laser Capture Microdissected Serous Ovarian Cancer Epithelia
Organism Homo sapiens
Characteristics tumor stage/grade: IIIc/IV/3
age at surgery: 59
Treatment protocol Following pathological verification, a serous papillary epithelial cancer sample was embedded in cryomatrix (Shandon). Seven micron frozen sections were cut and attached to uncharged microscope slides for each sample. Immediately following dehydration and staining (HistoGene, LCM Frozen Section Staining Kit, Arcturus), slides were processed in an Autopix‘ instrument (Arcturus) for laser capture microdissection (LCM) of cells to CapSure Macro LCM Caps. Approximately 30,000 epithelia were collected from each cancer sample.
Extracted molecule total RNA
Extraction protocol RNA was isolated with Trizol (Invitrogen) and purified with PicoPure RNA Isolation Kit (Arcturus). RNA quality was verified on the Bioanalyzer RNA Pico Chip (Agilent Technologies).
Label biotin
Label protocol Total RNA from the above extractions was processed using the RiboAmp OA or HS kit (Arcturus) in conjunction with the IVT Labeling Kit from Affymetrix, to produce an amplified, biotin-labeled mRNA suitable for hybridizing to GeneChip Probe Arrays (Affymetrix).
Hybridization protocol Labeled mRNA was hybridized to GeneChip Human Genome U133 Plus 2.0 Arrays in the GeneChip Hybridization oven 640, further processed with the GeneChip Fluidics Station 450 and scanned with the GeneChip Scanner 3000.
Scan protocol as per manufacturer's protocol using GeneChip Scanner 3000.
Description Serous ovarian tumor tissues were placed in cryotubes and immediately (<1 minute) frozen in liquid nitrogen following resection.
Data processing MAS 5.0 via Affymetrix Expression Console (TM) Software Version 1.1
Submission date Aug 03, 2010
Last update date Jul 29, 2011
Contact name Shubin Shahab
Organization name Georgia Institute of Technology
Department Biology
Lab McDonald
Street address 310 Ferst Drive
City Atlanta
State/province GA
ZIP/Postal code 30332
Country USA
Platform ID GPL570
Series (2)
GSE23391 miRNAs in ovarian cancer: A systems approach (mRNA data)
GSE23392 miRNAs in ovarian cancer: A systems approach

Data table header descriptions
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 2741.42 P 0.00179591
AFFX-BioB-M_at 3969.7 P 5.16732e-05
AFFX-BioB-3_at 2519.58 P 0.000126798
AFFX-BioC-5_at 6549.44 P 4.42873e-05
AFFX-BioC-3_at 7790.08 P 4.42873e-05
AFFX-BioDn-5_at 15948.5 P 4.42873e-05
AFFX-BioDn-3_at 22675 P 0.000224668
AFFX-CreX-5_at 74405.6 P 5.16732e-05
AFFX-CreX-3_at 71866.6 P 4.42873e-05
AFFX-DapX-5_at 179.473 A 0.327079
AFFX-DapX-M_at 26.5623 A 0.916408
AFFX-DapX-3_at 27.4851 A 0.852061
AFFX-LysX-5_at 291.353 A 0.313723
AFFX-LysX-M_at 150.268 A 0.425962
AFFX-LysX-3_at 79.7089 A 0.440646
AFFX-PheX-5_at 43.148 A 0.58862
AFFX-PheX-M_at 50.7511 A 0.686277
AFFX-PheX-3_at 357.413 A 0.39692
AFFX-ThrX-5_at 31.883 A 0.891021
AFFX-ThrX-M_at 43.5998 A 0.814869

Total number of rows: 54675

Table truncated, full table size 1597 Kbytes.

Supplementary file Size Download File type/resource
GSM573679.CEL.gz 5.5 Mb (ftp)(http) CEL
GSM573679.CHP.gz 492.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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