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| 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
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| 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.
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| 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.
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| 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 |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (12)
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| This SubSeries is part of SuperSeries: |
| GSE88915 |
Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples |
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| Relations |
| BioProject |
PRJNA348374 |
| SRA |
SRP091518 |
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