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Sample GSM8307465 Query DataSets for GSM8307465
Status Public on Aug 01, 2024
Title brain, tMCAO, rep2
Sample type SRA
 
Source name brain
Organism Mus musculus
Characteristics tissue: brain
cell type: microglia
genotype: WT
treatment: tMCAO
Treatment protocol Perform Sham and tMCAO modeling on WT mice.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the tissue using TRIzol reagent (Takara, Kyoto, Japan) according to the manufacturer’s instructions. RNA purity was tested using the Nano Photometer spectrophotometer (IMPLEN, Westlake Village, USA).
cDNA libraries were constructed from 1 μg of total RNA by using a cDNA-PCR Sequencing Kit (SQK-PCS109) according to the protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model PromethION
 
Description ONT_BMK210615-AK695-01O0005
M-2
Data processing The reverse transcriptase was used to enrich full-length cDNAs and added defined PCR adapters to both ends of the first-strand of cDNA and following cDNA PCR for 14 circles with LongAmp Tag DNA polymerase (New England Biolabs, Ipswich, MA, USA) (8 min for elongation time).
Agencourt XP beads (Beckman Coulter, Brea, USA) were used for DNA purification. The final cDNA libraries were subjected to FLO- MIN109 flow cells and analyzed on a PromethION platform at Biomarker Technology Company (Beijing, China).
The PCR products were then subjected to ONT adaptor ligation using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA).
Agencourt XP beads (Beckman Coulter, Brea, USA) were used for DNA purification.
The final cDNA libraries were subjected to FLO-MIN109 flow cells and analyzed on a PromethION platform at Biomarker TechnologyCompany (Beijing, China).
Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp.
Ribosomal RNA were discarded after mapping to rRNA database.
Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads.
Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Assembly: Consensus sequences were mapped to reference genome using minimap2
Supplementary files format and content: Tab-delimited text file includes raw counts and CPM of each sample
 
Submission date Jun 05, 2024
Last update date Aug 01, 2024
Contact name wan hanxi
E-mail(s) wanhanxi@tongji.edu.cn
Phone 18701875905
Organization name tongji university
Street address shanghai
City shanghai
State/province 上海
ZIP/Postal code 210000
Country China
 
Platform ID GPL26624
Series (1)
GSE269173 The gene expression of microglia in the brain after ischemic stroke
Relations
BioSample SAMN41694212
SRA SRX24816332

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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