Wessels et al. 2020 (PRJNA432508)

General Details

Title Global identification of functional microRNA-mRNA interactions in Drosophila
Organism
Number of Samples 12
Release Date 2018/02/01 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP131957
ENA SRP131957
GEO
BioProject PRJNA432508

Publication

Title
Authors Wessels HH,Lebedeva S,Hirsekorn A,Wurmus R,Akalin A,Mukherjee N,Ohler U
Journal Nature communications
Publication Date 2019 Apr 9
Abstract MicroRNAs (miRNAs) are key mediators of post-transcriptional gene expression silencing. So far, no comprehensive experimental annotation of functional miRNA target sites exists in Drosophila. Here, we generated a transcriptome-wide in vivo map of miRNA-mRNA interactions in Drosophila melanogaster, making use of single nucleotide resolution in Argonaute1 (AGO1) crosslinking and immunoprecipitation (CLIP) data. Absolute quantification of cellular miRNA levels presents the miRNA pool in Drosophila cell lines to be more diverse than previously reported. Benchmarking two CLIP approaches, we identify a similar predictive potential to unambiguously assign thousands of miRNA-mRNA pairs from AGO1 interaction data at unprecedented depth, achieving higher signal-to-noise ratios than with computational methods alone. Quantitative RNA-seq and sub-codon resolution ribosomal footprinting data upon AGO1 depletion enabled the determination of miRNA-mediated effects on target expression and translation. We thus provide the first comprehensive resource of miRNA target sites and their quantitative functional impact in Drosophila.
PMC PMC6456604
PMID 30967537
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR6661166 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661167 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661168 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661169 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661170 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661171 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661172 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661173 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661174 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661175 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661176 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
SRR6661177 PRJNA432508 Drosophila melanogaster S2 Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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