Comment[GEAAccession]	E-GEAD-913
MAGE-TAB Version	1.1
Investigation Title	Differentially expressed genes in RCC (CBX24)
Experiment Description	To examine the correlation of copy number aberrations (CNAs) with expression profiles, we performed on the same tumor samples of 22 cases of renal clear cell carcinoma, using oligonucleotide microarray. We extracted differentially expressed genes between cases with and without CNAs, and analysed theie chromosomal locations.
Experimental Design	disease state design
Experimental Factor Name	sample_name
Experimental Factor Type	sample_name
Person Last Name	CIBEX
Person First Name	DDBJ
Person Affiliation	Molecular Pathology,Faculty of Medicine,Oita University
Person Roles	submitter
Public Release Date	2025-01-27
PubMed ID	17922474
Protocol Name	P-GEAD-3594	P-GEAD-3595	P-GEAD-3596	P-GEAD-3597	P-GEAD-3598	P-GEAD-3599	P-GEAD-3600	P-GEAD-3601
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid labeling protocol	nucleic acid hybridization to array protocol	array scanning and feature extraction protocol	normalization data transformation protocol	growth protocol	treatment protocol
Protocol Description	Signal intensities were log transformed. For selection of differentially expressed genes by CNAs status, probe sets were assessed by ANOVA (Tukey t test) with Post-Hoc testing correction (P<0.05)., -80degree C	RNeasy Mini Kit (QIAGEN)	Low RNA Fluorescent Linear Amplification Kit (Agilent Technologies).	cRNA probes were hybridized to a microarray in Hybridization buffer (Agilent Technologies) at 60degree C for 17h.	A microarray was scanned using Microarray scanner (Agilent Technologies) at a pixel resolution size of 5microm., Whole Human Genomic Oligo Microarray 44K	Feature extraction V.9.1 (Agilent technologies), Probe set data were median normalized per chip. Then data were centered across the gene in 6 normal controls, followed by filtering based on having a signal intensity of 100 or greater and containing no flagged values, Signal intensities were log transformed. For selection of differentially expressed genes by grading status, probe sets were assessed by ANOVA (Tukey t test) with Post-Hoc testing correction (P<0.05).	none	none
SDRF File	E-GEAD-913.sdrf.txt
Comment[Number of channel]	single-channel
Comment[Array Design REF]	A-GEAD-118
Comment[AEExperimentType]	transcription profiling by array
Comment[SecondaryAccession]	CBX24
Comment[BioProject]	PRJDB20014
Comment[CIBEX Accept Date]	2007-05-25
Comment[CIBEX Public Release Date]	2007-10-11
Comment[Last Update Date]	2025-01-28