|
| Status |
Public on Jul 01, 2021 |
| Title |
wild type 2- cortex |
| Sample type |
SRA |
| |
|
| Source name |
Mouse cortex
|
| Organism |
Mus musculus |
| Characteristics |
tissue type: Cortex
strain: Nsun2 floxed, Camk2a-Cre neg.
developmental stage: Adult
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from Nsun2 KO or WT cortex using the Directzol RNA MiniPrep Kit (Zymo Research) including on-column DNase treatment and quantity was measured on Qubit fluorometer. Quality of total RNA was checked on the Agilent Bioanalyzer using the RNA 6000 Pico Kit
5ug of total RNA was rRNA depleted using the Illumina RiboZero Gold rRNA depletion kit according to manufacturer’s instructions. We then used 40-50ng rRNA-depleted RNA samples as input for the Smartr Stranded RNAseq kit (Takara Biosystems) following the manufacturer’s instructions for library prepraration and amplifying libraries with 11 PCR cycles. 4 libraries (2 KO, 2 WT) were then pooled at equimolar concentrations in one lane for sequencing on the Illumina HiSeq at the New York Genome Center
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
After paired-end sequencing, samples were mapped to mouse (GRCm38.p5_M13) with STAR (v2.5.3a) using a two-method step protocol following tool specifications
Genome_build: GRCm38.p5_M13
Supplementary_files_format_and_content: tdf
|
| |
|
| Submission date |
Jan 20, 2021 |
| Last update date |
Nov 02, 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 |
GPL17021 |
| 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 |
SAMN17390587 |
| SRA |
SRX9903800 |
