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Sample GSM937048 Query DataSets for GSM937048
Status Public on Jan 16, 2013
Title SCC of the vulva 03-1011 expression
Sample type RNA
Source name tumor
Organism Homo sapiens
Characteristics differentiation: moderately and well differentiated
individual: 03-1011
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 6.235315323
ILMN_2055271 6.520298004
ILMN_1736007 6.279314518
ILMN_2383229 6.172480583
ILMN_1806310 6.089206696
ILMN_1779670 5.756976128
ILMN_1653355 6.179759026
ILMN_1717783 5.454534054
ILMN_1705025 6.282916546
ILMN_1814316 6.155958653
ILMN_2359168 5.683338642
ILMN_1731507 5.378445149
ILMN_1787689 5.673115253
ILMN_3241953 6.57049036
ILMN_1745607 8.776738167
ILMN_2136495 7.946657658
ILMN_1668111 6.083768368
ILMN_2295559 6.117465496
ILMN_1735045 6.681044102
ILMN_1680754 6.01085043

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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