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Sample GSM937043 Query DataSets for GSM937043
Status Public on Jan 16, 2013
Title SCC of the vulva 02-848 expression
Sample type RNA
Source name tumor
Organism Homo sapiens
Characteristics differentiation: moderately differentiated
individual: 02-848
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 6.113464832
ILMN_2055271 6.362961292
ILMN_1736007 6.252027035
ILMN_2383229 6.165399075
ILMN_1806310 6.151587009
ILMN_1779670 5.658126831
ILMN_1653355 5.989352226
ILMN_1717783 5.207074165
ILMN_1705025 6.29007864
ILMN_1814316 6.024563313
ILMN_2359168 5.789268017
ILMN_1731507 5.603197575
ILMN_1787689 5.744293213
ILMN_3241953 6.894334316
ILMN_1745607 9.557971954
ILMN_2136495 7.795330048
ILMN_1668111 6.125506401
ILMN_2295559 6.040291786
ILMN_1735045 7.400047779
ILMN_1680754 6.045321465

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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