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Sample GSM937056 Query DataSets for GSM937056
Status Public on Jan 16, 2013
Title vulvar normal tissue 1102-0405 expression
Sample type RNA
Source name normal tissue
Organism Homo sapiens
Characteristics differentiation: normal tissue
individual: 1102-0405
tissue: normal vulva
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent. Using the Illumina TotalPrep RNA Amplification Kit, 500ng were reversely transcribed, amplified and Biotin-16-UTP-labeled. The amount and quality of labeled CDNA were measured using both a NanoDrop spectrophotometer and an Agilent 2100 Bioanalyzer.
Label biotin
Label protocol Using the Illumina TotalPrep RNA Amplification Kit, 500ng were reversely transcribed, amplified and Biotin-16-UTP-labeled.
Hybridization protocol 750 ng of biotin-labeled cRNA was hibridized to the HumanHT-12 v.4 Illumina Sentrix BeadCHip according to the manufacturer's instructions.
Scan protocol Standard Illumina scanning protocol
Data processing Bead summary data was imported into GenomeStudio to remove control probes and to produce a text file containing the signal and detection p-values per probe for all samples, as well as imputing missing data using the k-nearest neighbor algorithm (Tech note: Inputing HumanHT-12 Expression BeadChip Data; Illumina, Inc.). The text file was imported into J-Express Pro 2011, and signal intensity values were quantile normalized (Bolstad et al. 2003) and log transformed (base 2). Significance Analysis of Microarrays (SAM) was used to look for differentially expressed genes. To obtain manageable datasets, differentially expressed genes were defined by a fold change ≥2 and q-value = 0.
Submission date May 24, 2012
Last update date Jan 16, 2013
Contact name Francesca Micci
Organization name Oslo Universitetssykehus
Department Institute for medical informatics
Lab cancer cytogenetics
Street address Ullernchausseen 70
City oslo
ZIP/Postal code 0310
Country Norway
Platform ID GPL10558
Series (2)
GSE38228 Expression analysis of 13 squamous cell carcinomas arising in the vulva
GSE38230 SCC of the vulva

Data table header descriptions
VALUE quantile normalized, log2 transformed, 5 missing probes imputed. Sample “03-4” not used.

Data table
ILMN_1762337 6.496898651
ILMN_2055271 6.360818386
ILMN_1736007 6.214481354
ILMN_2383229 6.213380814
ILMN_1806310 5.932033062
ILMN_1779670 5.821489811
ILMN_1653355 5.948548794
ILMN_1717783 5.312627792
ILMN_1705025 6.327153683
ILMN_1814316 6.052877426
ILMN_2359168 5.792095661
ILMN_1731507 5.322663307
ILMN_1787689 5.606553555
ILMN_3241953 6.450998306
ILMN_1745607 8.290931702
ILMN_2136495 11.50115299
ILMN_1668111 6.04854393
ILMN_2295559 6.061113834
ILMN_1735045 7.137971401
ILMN_1680754 6.104025841

Total number of rows: 47323

Table truncated, full table size 1150 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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