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| Status |
Public on Sep 01, 2020 |
| Title |
Alteration of transcriptome by recombinant ncRNA agents |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Identify whether recombinant ncRNAs are recognized by mammalian cells and processed into mature microRNAs, thus leading to the alteration of downstream target genes. In addition, we also explored whether the alteration of known or novel target genes are Dicer dependent.
Methods: HEK293T (Dicer-WT) and 424 (Dicer-KO) cell lines were treated with 20nM of control tRNA (MSA), nCAR/miR-34a-5p, or nCAR/miR-34a-3p in triplicate.
Results: Read counts of known mRNAs were analyzed using a RSEM-EdgeR workflow. Sequence reads were mapped to the human reference genome (hg19) by BWA, read counts for individual genes were computed using RSEM, and EdgeR was used to analyze significant (log2FC > 1.2 or log2FC < 0.8. P-value < 0.05 and log2CPM > 5) differentially expressed mRNAs.
Conclusions: Upon transfection of recombinant RNA agents in mammalian cells, known and novel target genes were regulated in a Dicer dependent manner (nCAR/miR-34a-5p) and also in a Dicer independent manner (nCAR/miR-124a-3p).
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| Overall design |
A total of 18 samples were analyzed. Three biological replicates in each group were subjected to treatment with control tRNA (MSA), nCAR/miR-34a-5p, or nCAR/miR-124a-3p. Therefore, each cell line had a total of 9 samples and the transcriptome was explored in two different cell lines for a total of 18 samples.
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| Contributor(s) |
Ho P, Yu A, Hu Z |
| Citation missing |
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| |
| Submission date |
Sep 29, 2017 |
| Last update date |
Sep 01, 2020 |
| Contact name |
Pui Yan Ho |
| E-mail(s) |
[email protected]
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| Organization name |
UC Davis
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| Street address |
2700 Stockton Blvd., Rm2120B
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| City |
Sacramento |
| State/province |
CA |
| ZIP/Postal code |
95817 |
| Country |
USA |
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| Platforms (1) |
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| Samples (18)
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| This SubSeries is part of SuperSeries: |
| GSE104445 |
Alteration of miRNome and transcriptome by recombinant ncRNA agents |
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| Relations |
| BioProject |
PRJNA412648 |
| SRA |
SRP119157 |
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