|
| Status |
Public on Mar 31, 2024 |
| Title |
2_Scr-siRNA-Naïve |
| Sample type |
SRA |
| |
|
| Source name |
Brain-dCA1
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: Brain-dCA1
Sex: Male
cell type: All brain cell types
genotype: WT
treatment: Scr-siRNA-Naive
|
| Treatment protocol |
Streotaxic injection of siRNAs into dorsal CA1 area of the hippocampus
|
| Growth protocol |
Frozen brain tissue, from 8-9 week old Sprague Dawley rats
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted usin Rneasy mini plus kit (Qiagen)
Illumina TruSeq Stranded mRNA HT Sample Prep Kit, enriched by 14 cycles of PCR, validated using Agilent TapeStation and quantified by qPCR
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Group1_2
|
| Data processing |
Sequence read is trimmed using trimgalore (--paired --phred33 --fastqc --illumina -q 30 --length 30)
Trimmed sequence is mapped to Rat genome (Rattus_norvegicus.Rnor_6.0.99)
featureCounts v2.0.1 is used to quantify the mapping results (featureCounts" "-T" "32" "-p" "-t" "exon" "-g" "gene_id" "-a) and generate count matrix
Assembly: Rattus_norvegicus.Rnor_6.0.99
Supplementary files format and content: comma-separated values file includes the raw count for each sample
Supplementary files format and content: comma-separated values file includes the DESeq2 normalized count for each sample
|
| |
|
| Submission date |
Jun 22, 2023 |
| Last update date |
Mar 31, 2024 |
| Contact name |
Timothy Jarome |
| E-mail(s) |
tjjarome@vt.edu
|
| Organization name |
Virginia Polytechnic Institute and State University
|
| Street address |
175 W Campus Dr
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE235611 |
Monoubiquitination of histone H2B is a master regulator of the transcriptome during memory formation |
|
| Relations |
| BioSample |
SAMN35847091 |
| SRA |
SRX20755600 |
