|
| Status |
Public on Nov 03, 2021 |
| Title |
KOF3_tRFseq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue type: Cortex
strain: Nsun2 floxed, Camk2a-Cre pos.
developmental stage: Adult
molecule: small RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5ug total DNase-treated RNA was used for pre-treatment and library prep. Pre-treatment of RNA, library preparation, next-generation sequencing, and some aspects of data analysis were performed by Arraystar, Inc.
total RNA was extracted from mouse cortex using Trizol extraction and quantity was measured on Qubit fluorometer. Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
tRF seq processed data.xlsx
KOF3_tRFseq
|
| Data processing |
Library strategy: tRF-seq
Reads were trimmed and aligned to mature tRNA reference sequences from GtRNAdb and mitotRNAdb allowing for 1 mismatch, and reads that did not map were then mapped to precursor tRNA sequences (pre-tRNAs) allowing for 1 mismatch with bowtie software. Expression of mapped tRNA fragments was reflected with CPM.
|
| |
|
| Submission date |
Nov 02, 2021 |
| Last update date |
Nov 03, 2021 |
| Contact name |
Jennifer Blaze |
| E-mail(s) |
jennifer.blaze@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Street address |
1470 Madison Ave 9-202
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE165202 |
Neuronal Nsun2 deficiency is associated with codon-specific epitranscriptomic dysregulation of Gly-tRNAs and corresponding proteomic shift impacting synaptic signaling and behavior |
|
| Relations |
| BioSample |
SAMN22836833 |
| SRA |
SRX12894594 |
