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Sample GSM7937628

Query DataSets for GSM7937628

Status

Public on Nov 28, 2024

Title

sprague-Dawley,Cx43-wt,Day7_w4

Sample type

SRA

Source name

myocardium

Organism

Rattus norvegicus

Characteristics

tissue: myocardium
strain: sprague-Dawley

Extracted molecule

total RNA

Extraction protocol

①RNA degradation and contamination was monitored on 1% agarose gels. ② RNA purity was checked using the NanoPhotometer ®spectrophotometer(IMPLEN, CA, USA) . ③ RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system(Agilent Technologies, CA, USA）.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Quality control, Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Novel transcripts prediction.The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package
GO and KEGG enrichment analysis of differentially expressed genes
Assembly: Rattus_norvegicus.Rnor_6.0.97
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

Submission date

Dec 05, 2023

Last update date

Nov 28, 2024

Contact name

min wang

E-mail(s)

[email protected]

Organization name

Affiliated Suzhou Hospital of Nanjing Medical University

Street address

242 Guangji Road