|
| Status |
Public on Nov 08, 2019 |
| Title |
AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [Proximal Colon] |
| Organism |
Mus musculus |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
The goal of this study was to determine the state of the tRNA transcriptome in Proximal Colon tissue of Mus Musculus (Mouse). This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification states of these RNAs assessed using mismatching percentages from sequencing data.
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| |
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| Overall design |
Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male Proximal Colons. These experiments were performed in triplicate (biological) and subjected to NGS.
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| |
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| Contributor(s) |
Howard JM, Holmes AD, Chan PP, Lowe TM, Manning AC |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Nov 07, 2019 |
| Last update date |
Nov 10, 2019 |
| Contact name |
Todd Lowe |
| E-mail(s) |
aimannin@ucsc.edu
|
| Organization name |
University of California Santa Cruz
|
| Department |
Biomolecular Engineering and Bioinformatics
|
| Lab |
Lowe Lab
|
| Street address |
1156 High Street
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95064 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (12)
|
| GSM4154355 |
Mouse Proximal Colon M4 +AlkB ARM-seq |
| GSM4154356 |
Mouse Proximal Colon M5 +AlkB ARM-seq |
| GSM4154357 |
Mouse Proximal Colon M6 +AlkB ARM-seq |
| GSM4154358 |
Mouse Proximal Colon M4 -AlkB DM-tRNA-seq |
| GSM4154359 |
Mouse Proximal Colon M5 -AlkB DM-tRNA-seq |
| GSM4154360 |
Mouse Proximal Colon M6 -AlkB DM-tRNA-seq |
| GSM4154361 |
Mouse Proximal Colon M4 +AlkB DM-tRNA-seq |
| GSM4154362 |
Mouse Proximal Colon M5 +AlkB DM-tRNA-seq |
| GSM4154363 |
Mouse Proximal Colon M6 +AlkB DM-tRNA-seq |
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| This SubSeries is part of SuperSeries: |
| GSE140105 |
AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) |
|
| Relations |
| BioProject |
PRJNA588265 |
| SRA |
SRP229103 |
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