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Series GSE88913 Query DataSets for GSE88913
Status Public on Feb 22, 2017
Title Small RNA sequencing of serum-derived RNA for the evaluation of 5' tRNA halves depletion protocols
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary 5' tRNA halves are abundantly present in small RNA libraries prepared from serum samples, thereby limiting the detection of other small RNA species. In this study, we developed and compared two protocols for the selective depletion of 5' tRNA halves in RNA isolated from murine serum samples. To evaluate the efficacy of both protocols on small RNA sequencing, we performed the two 5' tRNA halves depletion protocols on total RNA isolated from a serum pool collected from healthy mice. Each RNA sample was divided into three and the resulting fractions were either depleted using beads or RNase H, or used as a control. The experiment was performed in triplicate. Upon depletion, libraries were prepared using TruSeq Small RNA Library Preparation kit. For both protocols, very high depletion efficiencies were observed, with more than 99% of the targeted tRNA-types being depleted. This resulted in a more than 6-fold increase in mapped miRNA reads and 60% more detected mature miRNAs when performing small RNA sequencing on murine serum samples. Importantly, we observed no considerable effects on the relative expression values of miRNAs.
Overall design Serum samples from healthy mice were combined together into a total of 3 serum pools. The RNA extracted from each pool was divided into three and the resulting fractions were either depleted using beads or RNase H, or used as a control.
Contributor(s) Van Goethem A
Citation(s) 27901112
Submission date Oct 18, 2016
Last update date May 15, 2019
Contact name Alan Van Goethem
Organization name Ghent University
Street address De Pintelaan 185
City Ghent
ZIP/Postal code 9000
Country Belgium
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (9)
GSM2354256 Serum_Pool_A. tRNA_dep_Beads
GSM2354257 Serum_Pool_A. tRNA_dep_RNase_H
GSM2354258 Serum_Pool_A. tRNA_dep_None
This SubSeries is part of SuperSeries:
GSE88915 Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples
BioProject PRJNA349062
SRA SRP091725

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE88913_RAW.tar 380.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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