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| Status |
Public on Feb 26, 2024 |
| Title |
SKA2 regulated hyperactive secretory autophagy drives neuroinflammation-induced neurodegeneration |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We used RNA sequencing of mouse hippocampal tissue two and four weeks after viral-mediated knockdown of SKA2, in order to examine if transcriptional changes might be associated with a hyperactivated secretory autophagy pathway.
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| Overall design |
Mice 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 and 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. 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). 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).
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| Web link |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10963788/
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| Contributor(s) |
Otten J, Klengel T, Hartmann J |
| Citation(s) |
37066393 |
| |
| Submission date |
Jul 30, 2021 |
| Last update date |
May 28, 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 |
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| Platforms (1) |
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| Samples (32)
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| Relations |
| BioProject |
PRJNA751049 |
| SRA |
SRP330567 |
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