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Sample GSM5492371 Query DataSets for GSM5492371
Status Public on Feb 26, 2024
Title SKA2-sh1-W2-3
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 X2
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 SAMN20504426
SRA SRX11610326

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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