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Sample GSM5739333

Query DataSets for GSM5739333

Status

Public on Feb 08, 2024

Title

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