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Series GSE17753 Query DataSets for GSE17753
Status Public on Aug 19, 2010
Title Impact of RNA degradation on gene expression profiling
Organism Homo sapiens
Experiment type Expression profiling by array
Summary 1.) Background: Gene expression profiling is a highly sensitive technique which is used for profiling of tumor samples for medical prognosis. RNA quality and degradation influences the analysis results of gene expression profiles. The impact of this influence on the profiles and its medical impact is not fully understood. As patient samples are very valuable for clinical studies, it is necessary to establish criteria for the RNA quality to use these samples in later analysis. 2.) Methods: To investigate the effects of RNA integrity on gene expression profiling whole genome expression arrays were used. We therefore used tumor biopsies from patients diagnosed with locally advanced rectal cancer. To simulate degradation, the isolated total RNA of all patients was subjected to heat-induced degradation in a time-dependent manner. Expression profiling was then performed and data were analyzed bioinformatically to assess the differences. 3.) Results: The biological differences between the patients largely over-weighed the differences introduced by RNA degradation. Only a relatively small number of probes (275 out of 41000) show a significant effect due to degradation. The genes that show the strongest effect due to RNA degradation were especially those with short mRNAs and probe positions near the 5' end. 4.) Conclusions: RNA from tumor samples with differing realistic qualities (> 5) can still be used to perform gene expression analysis. A much higher biological variance between patients is observed compared to the effect that is imposed by degradation of RNA. Nevertheless there are genes that are prone to degradation, especially very short ones and those with the probe binding side close to the 5ยด-end. Therefore, these genes should be excluded from gene expression analysis when working with degradated RNA.
 
Overall design Biopsies were taken from 3 different patients with 4 time-points of degradation per patient. The resulting 12 samples were separately hybridised (OneColor Array Design).
 
Contributor(s) Opitz L, Salinas-Riester G, Grade M, Jung K, Ghadimi M, Beissbarth T, Gaedcke J
Citation(s) 21062371, 20696062
Submission date Aug 21, 2009
Last update date Aug 28, 2019
Contact name Gabriela Salinas
E-mail(s) Gabriela.Salinas-Riester@medizin.uni-goettingen.de
Organization name Universitaetsmedizin Goettingen
Department Department of Human Genetics
Lab NGS Integrative Genomics
Street address Justus-von-Liebig-Weg 11
City Goettingen
State/province Lower-Saxony
ZIP/Postal code 37077
Country Germany
 
Platforms (1)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Samples (12)
GSM443139 P159.195min
GSM443140 P159.150min
GSM443141 P159.105min
Relations
BioProject PRJNA118359

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17753_RAW.tar 113.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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