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Sample GSM1358718 Query DataSets for GSM1358718
Status Public on May 01, 2014
Title 532137_A04
Sample type RNA
 
Source name Cervical tissue
Organism Homo sapiens
Characteristics disease state: Locally advanced cervical cancer
carcinoma type: Squamous cell carcinomas
Stage: IIA
Growth protocol Biopsies were frozen in liquid nitrogen until nucleic acid extractionThe population under study included 89 patients prospectively enrolled into the National Cancer Institute of Mexico. All patients included signed informed consent; the protocol was approved by institutional ethics and scientific committees. Immediately after surgical excision, tumor biopsies were analyzed for pathological confirmation and frozen in liquid nitrogen until nucleic acid extraction.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the MagNAPure Compact Instrument following manufacturer recommendations (Roche Diagnostics GmbH Roche Applied Science Mannheim, Germany). RNA quality was determined by by means of 18S:28S ratio. Hybridization targets were prepared from 250 ng of total RNA and amplified with whole transcriptome amplification kit 2 (Sigma Aldrich, St Louis, MO)
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems One Color Llabeling kit (Nimblegen Roche, Mannheim, Germany), following their standard operating protocol. See www.nimblegen.com. (Nimblegen Roche, Mannheim, Germany).
 
Hybridization protocol Hybridization was performed by NimbleGen Systems (Nimblegen Roche, Mannheim, Germany), following their standard operating protocol. See www.nimblegen.com. After standard washes, arrays were scanned.
Scan protocol Scanning was performed byNimblegen MS200 microarray scanner. Nimblegen Roche, Mannheim, Germany, following their standard operating protocol. Scanned images were gridded by using the NimbleScan v2.6 Software (Nimblegen Roche, Mannheim, Germany).
Description SAMPLE 69
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Mar 27, 2014
Last update date May 01, 2014
Contact name JORGE FERNANDEZ-RETANA
E-mail(s) ritepjorge.mivado@gmail.com
Phone 52(55)56280400
Organization name INSTITUTO NACIONAL DE CANCEROLOGIA
Department INVESTIGACION BASICA
Lab ONCOGENOMICA
Street address AV. SAN FERNANDO No22 COL SECCION XVI
City MEXICO, D.F.
State/province D.F.
ZIP/Postal code 14080
Country Mexico
 
Platform ID GPL16025
Series (1)
GSE56303 Genome wide expression profile in cervical cancer patients (staged, locally advanced)

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000409 1282.627679
AB000463 520.8203479
AB000781 435.2985118
AB001328 15.32459644
AB002294 1562.624708
AB002308 3427.371242
AB002311 352.4902484
AB002313 5115.984163
AB002360 85.07958691
AB002377 1606.371676
AB002381 698.4566737
AB002382 3810.750343
AB002384 109.5761435
AB003177 1459.112441
AB003333 4557.212253
AB006589 402.9021323
AB006590 445.6495271
AB006621 14.66332119
AB006625 22.53759249
AB007457 1563.342563

Total number of rows: 45033

Table truncated, full table size 951 Kbytes.




Supplementary file Size Download File type/resource
GSM1358718_532137A04_532.pair.gz 1.8 Mb (ftp)(http) PAIR
Processed data included within Sample table

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