|
| Status |
Public on Nov 07, 2022 |
| Title |
Antisense1 Small RNA |
| Sample type |
SRA |
| |
|
| Source name |
Primary Hippocampal neurons
|
| Organism |
Mus musculus |
| Characteristics |
cell type: DIV 16 neurons from P0 pups
|
| Growth protocol |
Hippocampi were cultured from P0 mice for generating RNA at DIV 16.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using DirectZol RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
All samples were processed and sequenced on a NextSeq 500. The quality of the reads overall was quite high with no decrease in quality over the course of sequencing.
After quality control, the reads were mapped to the mouse transcriptome using Salmon using paired end settings (Salmon reference was made using Ensembl: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz)
Differential analysis was performed using DEseq
Genome_build: N/A
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes
|
| |
|
| Submission date |
Jul 20, 2021 |
| Last update date |
Nov 07, 2022 |
| Contact name |
Sathyanarayanan V Puthanveettil |
| E-mail(s) |
sputhanv@scripps.edu
|
| Phone |
561-228-2243
|
| Organization name |
Scripps Florida
|
| Department |
Neuroscience
|
| Lab |
Puthanveettil
|
| Street address |
130 Scripps Way
|
| City |
Jupiter |
| State/province |
Florida |
| ZIP/Postal code |
33458 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE180503 |
Gas5 Pulldown Total and small RNAseq |
|
| Relations |
| BioSample |
SAMN20331477 |
| SRA |
SRX11509273 |
