GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1331404 Query DataSets for GSM1331404
Status Public on Feb 21, 2014
Title sem-lymph-met_4
Sample type RNA
Source name lymphogen metastasis
Organism Homo sapiens
Characteristics tissue: biopsy taken from lymphogen metastasis
gender: male
Extracted molecule total RNA
Extraction protocol Not provided
Label Cyanine-3-labeled cRNA
Label protocol 100 ng total RNA per sample were introduced into a reverse transcription with subsequent in vitro transcription (RT-IVT) reaction. Prior to RT-IVT, the total RNA samples were spiked with in vitro synthesized polyadenylated transcripts (One-Color RNA Spike-In Mix, Agilent Technologies) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reverse transcribed into cDNA and then converted into Cyanine-3 labeled cRNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies).
Hybridization protocol Following cRNA clean-up and quantification 600 ng of each Cyanine-3-labeled cRNA sample was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labeled cRNA samples were hybridized at 65°C for 17 hrs on separate Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarrays (AMADID 039494). Afterwards, microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies) followed by drying with acetonitrile (SIGMA).
Scan protocol Fluorescent signal intensities were detected with Scan Control A.8.4.1 software (Agilent Technologies) on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction software (Agilent Technologies).
Description RS-315_0004
Data processing The quantile normalized, log2 transformed data were averaged across replicates, resulting in the columns group # (normalized). A pairwise comparison was analyzed. Group lymphogen was used as reference group and RNA expression of group occult was compared to this baseline.
To filter for genes with a robust differential expression between two compared groups, several parameters are taken into account:
Robust detection:
A probe is only considered if it is reliably detectable (“Detected” call, flag information from the Feature Extraction software) in all samples of one of the two compared groups. Specifically, if filtering for induction in group x compared to group y, the probe must be called “Detected” in all samples of group x. If filtering for repression, it must be called “Detected” in all samples of the reference group y.
Statistical significance:
Two filtering approaches were used that apply different stringency levels to the data set:
a) Stringent filtering:
A probe is only classified as induced in a specific comparison if its corrected p-value is ≤ 0.05 and if it has a Fold Change value ≥ 1.5 and 2, respectively. Analogously, a probe is classified as repressed if its corrected p-value is ≤ 0.05 and its Fold Change is ≤ -1.5 and -2, respectively. By using this stringent filtering, the multiple testing error is taken into account, and the false discovery (FDR) rate is controlled at a maximum level of 5%.
b) Non-stringent filtering:
Stringency was reduced by using the non-corrected instead of the corrected p-value. Using this approach, a probe is only classified as induced in a specific comparison if its (non-corrected) p-value is ≤ 0.05, and if it has a Fold Change value ≥ 1.5 and 2, respectively. Analogously, a probe is classified as repressed if its (non-corrected) pvalue is ≤ 0.05 and its Fold Change is ≤ -1.5 and -2, respectively.
By using this non-stringent filtering, the multiple testing error is not taken into account. Finally, several analysis tools from the PANTHER website, release 8.1 (accessible through were applied for functional evaluation of differential regulation.
Submission date Feb 20, 2014
Last update date Feb 21, 2014
Contact name Michael Abend
Phone +49-89-992692- 2280
Organization name Bundeswehr Institute of Radiobiology
Street address Neuherbergstr. 11
City Munich
State/province Bavaria
ZIP/Postal code 80937
Country Germany
Platform ID GPL17077
Series (1)
GSE55198 Gene expression analysis of human seminoma samples

Data table header descriptions
VALUE quantile normalized, log2 transformed data

Data table
GE_BrightCorner 16.922878
A_23_P117082 11.727592
A_33_P3246448 5.5960813
A_33_P3236322 3.3431592
A_33_P3319925 5.03051
A_21_P0000509 18.679329
A_21_P0000744 9.520311
A_24_P215804 7.604678
A_23_P110167 9.902855
A_33_P3211513 7.721448
A_23_P103349 2.6131713
A_32_P61480 2.1115334
A_33_P3788124 5.226594
A_33_P3414202 6.654474
A_33_P3316686 7.534448
A_33_P3300975 6.682908
A_33_P3263061 10.201971
A_24_P278460 8.28911
A_21_P0014651 6.918147
A_24_P286898 8.298775

Total number of rows: 39211

Table truncated, full table size 879 Kbytes.

Supplementary file Size Download File type/resource
GSM1331404_RS-315_0004.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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