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Series GSE43335 Query DataSets for GSE43335
Status Public on Jul 07, 2013
Title Small RNA-seq of undiseased human brain
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary The surprising observation that virtually the entire human genome is transcribed means we know very little about the function of many emerging classes of RNAs, except their astounding diversity. Traditional RNA function prediction methods rely on sequence or alignment information, which are limited in their ability to classify classes of non-coding RNAs (ncRNAs). To address this, we developed CoRAL, a machine learning-based approach for classification of RNA molecules. CoRAL uses biologically interpretable features including fragment length, cleavage specificity, and antisense transcription to distinguish between different ncRNA classes. We evaluated CoRAL using genome-wide small RNA sequencing (smRNA-seq) datasets from two human tissue types (brain and skin [GSE31037]), and were able to classify six different types of RNA transcripts with 79~80% accuracy in cross-validation experiments, and with 71~73% accuracy when CoRAL uses one tissue type for training and the other as validation. Analysis by CoRAL revealed that long intergenic ncRNAs, small cytoplasmic RNAs, and small nuclear RNAs show more tissue specificity, while microRNAs, small nucleolar, and transposon-derived RNAs are highly discernible and consistent across the two tissue types. The ability to consistently annotate loci across tissue types demonstrates the potential of CoRAL to characterize ncRNAs using smRNA-seq data in less characterized organisms.
 
Overall design Four samples were sequenced, each one coming from frozen brain tissue (frontal cortex) of a deceased female human patient with no remarkable pathology.
 
Contributor(s) Wang L, Gregory BD
Citation(s) 24149843
Submission date Jan 08, 2013
Last update date May 15, 2019
Contact name Paul Ryvkin
Organization name University of Pennsylvania
Department Pathology
Lab Li-San Wang's Lab
Street address 423 Guardian Dr, 1404 Blockley Hall
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (4)
GSM1060654 Normal Brain 1
GSM1060655 Normal Brain 2
GSM1060656 Normal Brain 3
Relations
BioProject PRJNA185476
SRA SRP017809

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
GSE43335_RAW.tar 34.8 Mb (http)(custom) TAR (of TXT)
GSE43335_class_pri.txt.gz 275 b (ftp)(http) TXT
GSE43335_smrna_locus.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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