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Series GSE47888 Query DataSets for GSE47888
Status Public on Apr 01, 2015
Title Deciphering the RNA landscape by RNAome sequencing [Affymetrix]
Organism Mus musculus
Experiment type Expression profiling by array
Summary Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods.
 
Overall design 8 mouse embryonic stem cell samples, control and cisplatin treated, 4 replicates per group
 
Contributor(s) Derks K, Misovic B, van den Hout M, Kockx C, Payan Gomez C, Brouwer R, Vrieling H, Hoeijmakers J, van IJcken W, Pothof J
Citation(s) 25826412, 26484291
Submission date Jun 12, 2013
Last update date Apr 01, 2020
Contact name Kasper Derks
E-mail(s) kasper.derks@mumc.nl
Organization name Maastricht University Medical Center
Department Clinical Genetics
Street address P. Debyelaan 25
City Maastricht
State/province Limburg
ZIP/Postal code 6229 HX
Country Netherlands
 
Platforms (1)
GPL11180 [HT_MG-430_PM] Affymetrix HT MG-430 PM Array Plate
Samples (8)
GSM1161955 ES_cells_Cisplatin_8hours.3
GSM1161956 ES_cells_Cisplatin_8hours.4
GSM1161957 ES_cells_Cisplatin_8hours.5
This SubSeries is part of SuperSeries:
GSE48084 Deciphering the RNA landscape by RNAome sequencing
Relations
BioProject PRJNA208888

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
GSE47888_RAW.tar 16.4 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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