|
| Status |
Public on Feb 26, 2024 |
| Title |
SKA2-sh1-W2-17 |
| Sample type |
SRA |
| |
|
| Source name |
hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
Sex: male
tissue: hippocampus
condition: SKA2-sh1
time point: 2 weeks
|
| Treatment protocol |
Male mice (8 weeks of age) received bilateral viral infusions of pAAV9-U6-shRNA[Ska2#1]-PGK-mCherry (SKA2-knockdown-AAV) or pAAV9-U6-shRNA[SCR]-PGK-mCherry (Ctrl-AAV) into the dorsal hippocampus. Mice were sacrificed two or four weeks after viral-mediated knockdown of SKA2. Brains were removed, snap-frozen in isopentane at -40 °C, and stored at -80 °C until further processing. Tissue punches of hippocampus were collected.
|
| Growth protocol |
Mice were kept under standard laboratory conditions and were maintained on a 12 h light–dark cycle (lights on from 0700 to 1900 h), with food and water provided ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the Agilent absolutely RNA miniprep kit. Samples were processed by mRNA enrichment and rRNA removal.
The cDNA library was sequenced using the BGISEQ-500 platform by BGI (Hong Kong, China). Sequencing was done with a 100-bp paired-end sequencing and yielded on average 49.3 million raw reads of which on average 48.3 million (98%) is mapped to the M. musculus (GRC38/mm10) genome using STAR and Salmon was used to quantify the expression of the transcripts (Dobin et al., 2013; Patro et al., 2017).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
X12
|
| Data processing |
The quality control (QC) of the raw reads was carried out to determine whether the sequencing data was suitable for subsequent analysis (Ewels et al., 2016). No reads were discarded. For additional QC and downstream analyses, the bcbioRNASeq R package was used (Steinbaugh et al., 2018).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.csv: Comma-separated matrix table with raw gene counts for every gene and every sample.
|
| |
|
| Submission date |
Jul 30, 2021 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Joy Otten |
| E-mail(s) |
jotten@mclean.harvard.edu
|
| Organization name |
McLean Hospital
|
| Street address |
115 Mill Street
|
| City |
Belmont |
| State/province |
Massachusetts |
| ZIP/Postal code |
MA 02478 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE181203 |
SKA2 regulated hyperactive secretory autophagy drives neuroinflammation-induced neurodegeneration |
|
| Relations |
| BioSample |
SAMN20504433 |
| SRA |
SRX11610346 |
