NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM937057 Query DataSets for GSM937057
Status Public on Jan 16, 2013
Title vulvar normal tissue 1102-0395 expression
Sample type RNA
 
Source name normal tissue
Organism Homo sapiens
Characteristics differentiation: normal tissue
individual: 1102-0395
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
E-mail(s) francesca.micci@medisin.uio.no
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
ID_REF
VALUE quantile normalized, log2 transformed, 5 missing probes imputed. Sample “03-4” not used.

Data table
ID_REF VALUE
ILMN_1762337 6.952773094
ILMN_2055271 6.376785278
ILMN_1736007 6.411174774
ILMN_2383229 6.115947247
ILMN_1806310 6.142068863
ILMN_1779670 5.719501019
ILMN_1653355 6.174255371
ILMN_1717783 5.47995615
ILMN_1705025 6.110470772
ILMN_1814316 6.227871418
ILMN_2359168 5.711645603
ILMN_1731507 5.367766857
ILMN_1787689 5.483451843
ILMN_3241953 6.812539101
ILMN_1745607 8.080916405
ILMN_2136495 11.097085
ILMN_1668111 6.080022812
ILMN_2295559 6.172264576
ILMN_1735045 8.836841583
ILMN_1680754 6.022534847

Total number of rows: 47323

Table truncated, full table size 1150 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap