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SAMPLES (12)

mace:id
Technology # Array version
Species
Organ
Tissue
Physiopathology
Type
Name

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User name	Arndt Benecke
Email	arndt@ihes.fr
Phone / Fax number	+33160926665 / +33160926609
Location	Institut des Hautes Etudes Scientifiques (Integrative Biology) - 35, route de Chartres - 91440 Bures sur Yvette, France

Scientific description

Follicular thyroid tumours were investigated using global gene expression analysis. Aim of this study was the identification of new markers for follicular thyroid carcinoma.

Technical description

Sample type 	RNA
  	
Source Name 	follicular thyroid adenoma
Organism(s) 	Homo sapiens
Characteristics 	tumor: follicular thyroid adenoma
age: 34
gender: Female
Extracted molecule 	total RNA
Extraction protocol 	Total RNA was extracted from 5-10 10Âµm slices of snap frozen material using the Qiagen RNeasy Mini kit according to manufacturer's instructions.
Label 	Digoxigenin
Label protocol 	1 microgram of total RNA was reverse transcribed, amplified and digoxigenin (DIG)-labeled using the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit V.2.0 according to manufacturer's instructions (Part Number 4363142 Rev.A).
  	
Hybridization protocol 	10Âµg of DIG-labeled cRNA were hybridized to the Applied Biosystems Human Genome Survey Microarray V.2.0 using the Applied Biosystems Chemiluminescence Detection Kit according manufacturer's instructions (Part Number 4346875D).
Scan protocol 	The chemiluminescent signal detection, image acquisition and image preprocessing of the microarrays were performed on the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer using the provided Applied Biosystems Expression Array System Software v 1.1.

Data processing 	Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems Expression Array System Software v 1.1. Further statistical analysis was performed with the statistical computing environment R. Additional software packages (ab1700, rma, multtest) were taken from the Bioconductor project. Probe level normalization was conducted using the quantile normalization method. Probeset summarization was calculated using the robust median polish method on the normalized data. For each probeset an additive robust additive model on the logarithmic scale (base 2) was fitted across the arrays, considering the different affinities of the probes via the probe effect. A global filter was used: the signal intensity of a probe set had to be above 100 in at least 25 percent of the samples, if the group size is equal. Also a variance filter was used: the interquartile range of log2 intensities had to be at least 0.5. p-Values were calculated applying the two sample t-test (assuming equal variances in both groups) to identify differentially expressed genes between the two groups. False Discovery Rate (FDR) was used to account for multiple testing. Also Fold Changes (FC) between the two groups were calculated for each gene. Differentially expressed genes were determined with p-value, FDR and FC criteria.

References

* Hinsch N, Frank M, DÃ¶ring C, VorlÃ¤nder C et al. QPRT: a potential marker for follicular thyroid carcinoma including minimal invasive variant; a gene expression, RNA and immunohistochemical study. BMC Cancer 2009 Mar 26;9:93.

Pubmed : http://www.ncbi.nlm.nih.gov/pubmed/19321014

Dataset was originally published as GSE15045 in the NCBI/GEO database.