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Sample GSM7730189 Query DataSets for GSM7730189
Status Public on Nov 27, 2023
Sample type SRA
Source name hippocampus
Organism Mus musculus
Characteristics tissue: hippocampus
condition: Photothrombosis (PT) model of cerebral ischemia
treatment: 1 m after PT+LEV (infarcted side)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the whole mouse hippocampus using the Maxwell 16 LEV simpleyRNA Tissue Kit (Promega).
The cDNAs were synthesized from total RNA using random primers. The ribose diols in the 5’ cap structures of RNAs were oxidized, and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (cap-trapping). After RNA digestion by RNaseONE/H and adaptor ligation to both ends of cDNA, double-stranded cDNA libraries (CAGE libraries) were constructed.
Library strategy RNA-Seq
Library source transcriptomic
Library selection CAGE
Instrument model Illumina NextSeq 500
Description Gene_expression-HP_cpm
Data processing CAGE libraries were sequenced using single end reads of 75nt on a NextSeq 500 instrument (Illumina).
Obtained reads (CAGE tags) were mapped to the mouse GRCm38 genome using BWA (version 0.7.17). Unmapped reads were then mapped by HISAT2 (version 2.0.5).
CAGE tag count data were clustered using the CAGEr (Haberle et al., Nucleic Acids Research 2015, 30:e51) using Paraclu algorithm (Frith et al., Genome Research 2007 18:1-12) with default parameters. Clusters with count per million (CPM) < 0.2 were discarded.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
For motif analysis, the genomic DNA sequence of the region from 200bp upstream to 50bp downstream of differentially expressed CAGE peaks were subjected to de novo motif discovery tools: AMD, GLAM2, DREME and Weeder. The occurrences of the motifs were examined by FIMO. The similarity of consensus motifs and the motifs in database JASPAR CORE 2020 vertebrates were evaluated by Tomtom.
The list of differentially expressed genes detected by RECLU with false discovery rate (FDR) ≤ 0.05 were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes CPM values for each sample.
Submission date Aug 23, 2023
Last update date Nov 27, 2023
Contact name Rie Komori
Organization name Tokushima Bunri University
Department Kagawa School of Pharmaceutical Sciences
Street address 1314-1, Shido
City Sanuki
ZIP/Postal code 769-2193
Country Japan
Platform ID GPL19057
Series (1)
GSE241525 Levetiracetam normalized E/I imbalance in the hippocampus after cortical stroke in aged mice
BioSample SAMN37123953
SRA SRX21466456

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

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