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Sample GSM7730194

Query DataSets for GSM7730194

Status

Public on Nov 27, 2023

Title

PT7d.HP.R

Sample type

SRA

Source name

hippocampus

Organism

Mus musculus

Characteristics

tissue: hippocampus
condition: Photothrombosis (PT) model of cerebral ischemia
treatment: 7 d after PT (non-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

E-mail(s)

komorir@kph.bunri-u.ac.jp

Organization name

Tokushima Bunri University

Department

Kagawa School of Pharmaceutical Sciences