|
| Status |
Public on Nov 03, 2021 |
| Title |
KO1_YAMAT |
| Sample type |
SRA |
| |
|
| Source name |
Mouse cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue type: Cortex
strain: Nsun2 floxed, Camk2a-Cre pos.
developmental stage: Adult
molecule: mature tRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5ug total RNA was deacetylated to remove amino acids from 3’ ends and demethylated to remove m1A, m1C, and m3C modifications using a proprietary demethylation mix (Arraystar, Inc). 40um of YAMAT forked linkers (Y-3-AD_UMI: 5'-P-GTATCCAGTNNNNTGGAATTCTCGGGTGCCAAGG-3'-ddC; Y-5-AD_UMI: 5’-GTTCAGAGTTCTACAGTCCGACGATCNNNNACTGGATACTGrGrN-3’) were then incubated with pure demethylated and deacetylated RNA followed by addition of 10X annealing buffer (50 mM Tris HCl pH 8, 100 mM MgCl2, 5 mM EDTA) and then overnight incubation with T4 RNA ligase 2. Linker-ligated RNA was then incubated with RT Primer (TruSeq Small RNA Library Prep Kit, Illumina) and reverse transcription was performed with Superscript III RT (Invitrogen) followed by bead purification. Libraries were amplified using Phusion Hotstart II Polymerase (Thermo Scientific) with primers and indexes from the TruSeq Small RNA kit (Illumina) for 11 PCR cycles. Amplified libraries were then bead-purified and run on the Agilent Bioanalyzer for confirmation of library size and quantified with the Qubit Fluorometer (Invitrogen).
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 MiSeq |
| |
|
| Description |
YAMATseq processed data.xlsx
4217_YAMAT
|
| Data processing |
Library strategy: YAMAT-seq
Raw sequencing reads were processed using cutadapt to trim adaptor sequences and UMItools to extract UMIs from reads and perform deduplication. Paired end reads were merged using Pear and differential expression analysis was performed using Deseq2, providing normalized counts 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 |
GPL16417 |
| 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 |
SAMN22836777 |
| SRA |
SRX12894660 |
