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Sample GSM6481270

Query DataSets for GSM6481270

Status

Public on Apr 19, 2023

Title

HC biol rep3

Sample type

SRA

Source name

Heart

Organism

Mus musculus

Characteristics

strain: CD-1 (ICR)
tissue: Heart
developmental stage: adult offspring
treatment: derived from natural pregnancy

Treatment protocol

The control group was natural pregnancy. The ART group included the following operations: ovulation induction, vitrification and thawing, in vitro fertilization, embryo in vitro culture and transfer. The zygotes were cultured in KSOM medium for 24 hours, and the cleaved embryos were used for embryo transfer. The cleaved embryos were transferred into the fallopian tubes of pseudopregnant female mice by operation. Twenty embryos were transplanted into each female mouse and raised normally until the offspring mice were born.

Growth protocol

For both the control group and the ART group, the feeding environment of mice was 12 h/12 h light/dark, the temperature was 25℃, and the humidity was 50%. Their offspring were raised to adulthood (8 weeks old) after birth. The feeding, management, and use of mice complied with the ‘3Rs’ of animal ethics.

Extracted molecule

total RNA

Extraction protocol

The offspring mice were raised to adulthood (8W) after birth. After being killed by cervical dislocation, the liver and kidney tissues were retrieved and thoroughly washed with normal saline to remove the blood. Then, the tissue block was cut 0.5 cm×0.5 cm in size with sterile RNase-free surgical scissors, ground into a powder after adding liquid nitrogen, and collected in a sterile RNase-free EP tube. After TRIzol was added and fully lysed, the total RNA in the tissues was obtained for sequencing according to the conventional RNA extraction steps.
The library was built according to standard Illumina protocols, which mainly include the steps of rRNA removal, mRNA isolation and fragmentation, cDNA double-strand synthesis and purification, cDNA terminal repair, 3’ end plus A, adaptor ligation, screening cDNA fragments of around 200 bp, PCR library enrichment and purification, etc.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Data processing

Firstly, Fastp (version 0.18.0) was used to remove the adaptor sequence and low-quality bases to obtain clean reads.
Bowtie2 (version 2.2.8) was used to remove ribosome RNA (rRNA) reads.
Then, mapped reads were obtained by comparing clean reads to the reference genome through Hisat2 (version 2.4).
The FPKM value of gene expression (fragment per kilobase of transcript per million mapped reads) was calculated by StringTie (version 1.3.1).
DEseq2 analyzed the gene expression differences between samples. The screening criteria for differential genes were the following: the FPKM in at least one group was greater than 1; the differential fold change (FC) was greater than 2.5; and the false discovery rate (FDR) was less than 0.05.
Assembly: Ensembl_release100 (GRCm39)
Supplementary files format and content: gene_expression_anno.xls including FPKM values for each sample

Submission date

Aug 18, 2022

Last update date

Apr 19, 2023

Contact name

Lei Zhang

E-mail(s)

zlei@nwafu.edu.cn

Phone

0371-65580512

Organization name

Henan Provincial People’s Hospital