|
| Status |
Public on Nov 07, 2022 |
| Title |
DHPG_miRNA_3 |
| Sample type |
SRA |
| |
|
| Source name |
Primary Hippocampal neurons
|
| Organism |
Mus musculus |
| Characteristics |
tissue: DIV 16 neurons
developmental stage: P0 pups
agent: DHPG
|
| Growth protocol |
Hippocampi were cultured from P0 mice for generating RNA at DIV 16.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using traditional Trizol/chloroform extraction method
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded Total RNA Sample Prep
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
DHPG_miRNA_3
|
| 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: ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.abinitio.fa.gz
Supplementary_files_format_and_content: Excel file contaiining gene counts and differentially expressed genes
|
| |
|
| Submission date |
Nov 09, 2020 |
| 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) |
| GSE161071 |
cAMP and mGluR1/5 dependent expression of mRNA, lncRNA, and miRNA in mouse hippocampal neurons |
|
| Relations |
| BioSample |
SAMN16708841 |
| SRA |
SRX9461205 |
