GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM4131026

Query DataSets for GSM4131026

Status

Public on Oct 20, 2020

Title

cattle_adipose_2

Sample type

SRA

Source name

high IMF

Organism

Bos taurus

Characteristics

intramuscular fat: high IMF
tissue: adipose

Treatment protocol

Animals were weaned at three months of age, castrated at six months of age, started to fatten at 18 months of age, and slaughtered at 30 months of age.

Growth protocol

Three Xinyang buffalo and three Nanyang cattle were raised in the breeding farm of Xinyang Buffalo (Guangshan, Henan province, P.R. China) and the breeding center of Nanyang cattle (Nanyang, Henan province, P.R. China), respectively, with equivalent forage and feeding management conditions.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using TRIzol reagent (Invitrogen, USA). The quality and concentration of total RNA were determined by the NanoDrop 2,000 (Nanodrop, Wilmington, DE) and 1% agarose gel.
Approximately 2 μg total RNA per sample was used for library construction according to protocol of the TruSeq® RNA LT Sample Prep Kit v2 (Illumina, USA).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 3000

Data processing

Low-quality reads and those containing adapters were removed to obtain clean reads using Trim Galore. High-quality data were used for the subsequent analysis. Each read was aligned to the reference genome using STAR. Mapped reads were assembled using Cufflinks v2.2.1. These assemblies were merged to the reference gene model annotation by Cuffmerge.
For mRNAs and lncRNAs, fragments per kilobase of transcript per million mapped reads (FPKM) was used as index to calculate the expression level of each transcript in every library using Cuffdiff program.
For circRNA prediction, the CIRCexplorer2 was employed to identify the back-spliced junction of circRNAs. To calculate the expression levels of circRNAs, back-spliced reads per million mapped reads (BSRP) was used.
Genome_build: UMD3.1
Supplementary_files_format_and_content: (1) Tab-delimited text files include FPKM values (mRNAs and lncRNAs) or BSRP values (circRNAs) for each sample. (2) The .fa files include sequences of lncRNAs and circRNAs predicted in this study.

Submission date

Oct 18, 2019

Last update date

Oct 20, 2020

Contact name

Huang JiePing

E-mail(s)

[email protected]

Organization name

Guangxi University

Street address

Xixiangtang District