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Series GSE134516 Query DataSets for GSE134516
Status Public on Jul 01, 2020
Title A universal, benchtop, gel-free method for the rapid and simultaneous isolation of all known classes of functional small RNAs
Organisms Arabidopsis thaliana; Drosophila melanogaster; Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary All known silencing small (s)RNAs operate via ARGONAUTE(AGO)-family proteins within RNA-induced-silencing-complexes (RISCs). Based on AGOs conserved biochemical properties, we have developed a universal, 15-min benchtop extraction procedure allowing simultaneous purification of all classes of RISC-associated sRNAs known to date, without prior knowledge of the samples-intrinsic AGO repertoires. Optimized into a user-friendly kit, the method –coined “TraPR” for Trans-kingdom, rapid, affordable Purification of RISCs– operates irrespectively of the organism, tissue, cell type or bio-fluid of interest, including from minute amounts of input material. The method is highly suited for direct sRNA deep-sequencing, with TrAPR-generated libraries being qualitatively and quantitatively at least on-par with those obtained via gold-standard procedures involving tedious polyacrylamide gel excisions. TraPR considerably improves the quality and consistency of sRNA sample preparation including from notoriously difficult-to-handle tissues/bio-fluids such as starchy storage roots and mammalian plasma, and regardless of RNA contaminants or samples’ RNA-degradation status.
Overall design Trans-kingdom, rapid, affordable Purification of RISC (TraPR) protocol for sRNA isolation was compared to standard sRNA library preparation from total RNA. A variety of source tissue, like Arabidopsis flower buds, Drosophila ovaries and mouse livers and plasa were used for these comaparisons.
Contributor(s) Oberlin S, Grentzinger T, Handler D, Brennecke J, Voinnet O
Citation(s) 32496553
Submission date Jul 18, 2019
Last update date Jul 01, 2020
Contact name Stefan Oberlin
Organization name ETH Zürich
Department Department of Biology
Street address Universitätstrasse 2
City Zürich
ZIP/Postal code 8092
Country Switzerland
Platforms (4)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (49)
BioProject PRJNA555390
SRA SRP215328

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Supplementary file Size Download File type/resource
GSE134516_At_miRNA_counts.csv.gz 22.4 Kb (ftp)(http) CSV
GSE134516_Dm_miRNA_counts.csv.gz 20.1 Kb (ftp)(http) CSV
GSE134516_Mm_liver_miRNA_counts.csv.gz 66.7 Kb (ftp)(http) CSV
GSE134516_Mm_plasma_miRNA_counts.csv.gz 92.2 Kb (ftp)(http) CSV
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