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Series GSE40053 Query DataSets for GSE40053
Status Public on Dec 22, 2012
Title C. elegans piRNAs are processed from capped-small RNAs transcribed at promoters throughout the genome
Organisms Caenorhabditis elegans; Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Piwi-interacting (pi) RNAs are a class of germline-expressed small RNAs that have been linked to epigenetic programming in metazoa. C. elegans piRNAs known as 21U-RNAs are defined by more than 15,000 genome-encoded species. To explore the origin of 21U-RNAs we employed methods to enrich the 5' ends of Pol II transcripts. We show that a species of capped-short (cs) RNA is frequently expressed bidirectionally at Pol II loci in C. elegans. Interestingly, at annotated 21U-RNA loci, csRNAs originate precisely 2 nt upstream of the mature piRNA species suggesting that csRNAs are piRNA precursors. In addition, we show that csRNAs associated with TS sites genome-wide define a previously overlooked class of 21U-RNA loci, and nearly double the number of piRNA species available for genome surveillance. Our methods should be of general utility in TS site identification and 5' anchored RNA-expression profiling.
Overall design Identification of capped RNA including capped small RNA and long capped RNA in C. elegans. The mouse data are independent data to test the CapSeq sequencing protocol.
Contributor(s) Lee H, Chaves D, Conte D
Citation(s) 23260138
Submission date Aug 10, 2012
Last update date May 15, 2019
Contact name Craig Mello
Organization name University of Massachusetts Medical School
Department Program in Molecular Medicine
Lab Craig Mello
Street address 368 Plantatoin Street, Suite AS5-2047
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
Platforms (3)
GPL9269 Illumina Genome Analyzer II (Caenorhabditis elegans)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL13657 Illumina HiSeq 2000 (Caenorhabditis elegans)
Samples (11)
GSM984426 CapSeq, insert size 100-130 nt L1
GSM984427 CapSeq, insert size 100-130 nt L2
GSM984428 CapSeq, insert size 100-130 nt YA
BioProject PRJNA172751
SRA SRP014826

Download family Format
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Supplementary file Size Download File type/resource
GSE40053_RAW.tar 267.3 Mb (http)(custom) TAR (of FA)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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