|
| Status |
Public on Nov 03, 2021 |
| Title |
WT2_HydrotRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Mouse cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue type: Cortex
strain: Nsun2 floxed, Camk2a-Cre neg.
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 |
HydrotRNAseq processed data.xlsx
4238_HydrotRNAseq
|
| Data processing |
Library strategy: HydrotRNA-seq
Raw sequencing read data that passed the Illumina chastity filter was used for further data analysis, including alignment of trimmed reads (cutadapt) to mature tRNA reference sequences from GtRNAdb and mitotRNAdb using BWA. For tRNA alignment, the maximum number of mismatches were 2. tRNA expression levels were measured with tag count and the multi-map-corrected number of reads overlapping the tRNA (mrcount) was then calculated. Normalized tRNA counts are shown as CPM for each sample.
|
| |
|
| 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 |
SAMN22836859 |
| SRA |
SRX12894589 |
