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Sample GSM5739334 Query DataSets for GSM5739334
Status Public on Feb 08, 2024
Title S3
Sample type SRA
 
Source name Heart
Organism Mus musculus
Characteristics srain: C57BL/6
tissue: heart
gender: female
genotype: wild type
Extracted molecule total RNA
Extraction protocol Hearts were removed, flash fronzen in liquid nitrogen and RNA was extracted using Trizol reagant.
A total amount of 1.5 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample. MRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library preparations were sequenced on an Illumina HiSeq 4000 platform by Shanghai Life Genes Biotech Co. Ltd (Shanghai, China), and 150 bp paired-end reads were generated.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.6.1p2 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. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz.
Differential expression analysis of two conditions was performed using the DESeq2 R package (v1.26.0). Pvalue < 0.05 and absolute log2 (fold change) > 0.58 were set as the threshold for significantly differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample
 
Submission date Dec 17, 2021
Last update date Feb 08, 2024
Contact name Shujia Lin
E-mail(s) linshujia96@sjtu.edu.cn
Organization name Shanghai Children’s Hospital
Street address No. 355 Luding Road, Shanghai, China
City Shanghai
ZIP/Postal code 200062
Country China
 
Platform ID GPL21103
Series (1)
GSE191112 RNA-sequencing analysis reveals the different gene expression in male and female wild type and TECRL knockout mice.
Relations
BioSample SAMN24155268
SRA SRX13435919

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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