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Series GSE88728 Query DataSets for GSE88728
Status Public on Feb 22, 2017
Title Small RNA sequencing of serum collected from mice before and after manifestation of tumor
Organism Mus musculus
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary To investigate the effectiveness of performing 5' tRNA half depletion, we evaluated the association of tumor burden on circulating miRNAs present in mouse serum. Three nude mice (NCr) were orthotopically injected with SH-SY5Y human neuroblastoma cells. Serum samples were collected one week before cell injection and two weeks after injection, when mice had palpable tumors. We performed 5' tRNA half depletion using biotinylated probes and streptavidin beads and prepared small RNA libraries using the TruSeq Small RNA Library Prep kit. By depleting the 5' tRNA halves in the serum-derived RNA samples, we were able to detect 3 times more differentially expressed miRNAs when comparing serum from mice carrying orthotopically engrafted tumors with serum from healthy control mice. We detected 34 differentially expressed miRNAs, of which six are unique to humans, 13 unique to mice and 15 have complete conservation between the two species.
Overall design Serum samples from three mice were collected both before and two weeks after tumor cell injection. RNA from each serum sample was divided into two and either depleted for tRNA-halves or not.
Contributor(s) Van Goethem A
Citation(s) 27901112
Submission date Oct 13, 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 (12)
GSM2344861 NCr Mouse 1046. TimePoint 1.tRNA dep
GSM2344862 NCr Mouse 1046. TimePoint 1.tRNA undep
GSM2344863 NCr Mouse 1047. TimePoint 1.tRNA dep
This SubSeries is part of SuperSeries:
GSE88915 Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples
BioProject PRJNA348374
SRA SRP091518

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

Supplementary file Size Download File type/resource
GSE88728_RAW.tar 60.0 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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