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Sample GSM937044 Query DataSets for GSM937044
Status Public on Jan 16, 2013
Title SCC of the vulva 02-869 expression
Sample type RNA
Source name tumor
Organism Homo sapiens
Characteristics differentiation: well, moderately and poorly differentiated
individual: 02-869
tissue: squamous cell carcinoma tumor
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 6.5387187
ILMN_2055271 6.361776352
ILMN_1736007 6.28494978
ILMN_2383229 6.333239079
ILMN_1806310 6.195868015
ILMN_1779670 5.811348438
ILMN_1653355 6.254420757
ILMN_1717783 5.330737114
ILMN_1705025 6.126557827
ILMN_1814316 6.121301651
ILMN_2359168 5.788776398
ILMN_1731507 5.482938767
ILMN_1787689 5.812903404
ILMN_3241953 6.687285423
ILMN_1745607 8.796033859
ILMN_2136495 10.78763962
ILMN_1668111 6.075947762
ILMN_2295559 6.320771217
ILMN_1735045 6.791571617
ILMN_1680754 6.272311688

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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