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Status |
Public on Aug 01, 2024 |
Title |
brain, tMCAO, rep2 |
Sample type |
SRA |
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Source name |
brain
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Organism |
Mus musculus |
Characteristics |
tissue: brain cell type: microglia genotype: WT treatment: tMCAO
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Treatment protocol |
Perform Sham and tMCAO modeling on WT mice.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
PromethION |
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Description |
ONT_BMK210615-AK695-01O0005 M-2
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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
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Submission date |
Jun 05, 2024 |
Last update date |
Aug 01, 2024 |
Contact name |
wan hanxi |
E-mail(s) |
wanhanxi@tongji.edu.cn
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Phone |
18701875905
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Organization name |
tongji university
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Street address |
shanghai
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City |
shanghai |
State/province |
上海 |
ZIP/Postal code |
210000 |
Country |
China |
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Platform ID |
GPL26624 |
Series (1) |
GSE269173 |
The gene expression of microglia in the brain after ischemic stroke |
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Relations |
BioSample |
SAMN41694212 |
SRA |
SRX24816332 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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