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Series GSE82128 Query DataSets for GSE82128
Status Public on Jun 01, 2017
Title Drosophila retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon (retroTn) mobility in Drosophila somatic cells. EsiRNAs are primarily generated from transposon and inverted repeat (hairpin) loci in Drosophila culture cells. After discovering a nucleus specific physical interaction between the essential esiRNA cleavage enzyme Dcr2 and Symplekin, a component of the core cleavage complex (CCC) required for 3’ end processing of mRNAs, we investigated cellular localization of esiRNA biogenesis and overlap between these pathways. We found that knockdown of CCC components perturbs esiRNA levels and that retroTn precursor transcripts are highly enriched in the nucleus while hairpin RNAs are predominantly cytoplasmic. Additionally, retroTn and hairpin-derived esiRNAs have distinct physical characteristics. Combined, these observations support a novel mechanism in which differences in localization of esiRNA precursors impacts esiRNA biogenesis; hairpin-derived esiRNAs are generated in the cytoplasm independent of Dcr2-Symplekin interactions, while retroTns are processed in the nucleus.
Overall design This submission includes 18 raw data files. Two samples (Blank control, Symplekin and CPSF73 RNAi-depleted) are represented by three technical triplicate raw data files. RNA-seq and small RNA-seq data are provided for each sample.
Contributor(s) Harrington AW, McKain MR, Michalski D, Bauer KM, Steiniger M
Citation(s) 28415970
Submission date Jun 01, 2016
Last update date May 15, 2019
Contact name Mindy Steiniger
Organization name University of Missouri-St. Louis
Street address 1 University Blvd.
City St. Louis
ZIP/Postal code 63121
Country USA
Platforms (2)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
Samples (18)
GSM2183918 Blank RNAi RNA-seq rep1
GSM2183919 Blank RNAi RNA-seq rep2
GSM2183920 Blank RNAi RNA-seq rep3
BioProject PRJNA324098
SRA SRP075974

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
GSE82128_RAW.tar 64.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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