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Sample GSM3082821

Query DataSets for GSM3082821

Status

Public on Aug 21, 2019

Title

Thirtymonth 1

Sample type

SRA

Source name

thirtymonth adipose tissue

Organism

Bubalus bubalis

Characteristics

tissue: adipose tissue
age: thirty months

Growth protocol

Six adipose samples from Xinyang buffalo of two developmental states (6Month and 30Month old) were collected from Benniu abattoir, a local slaughterhouse of Xinayang, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

Extracted molecule

total RNA

Extraction protocol

Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer. The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries.
Then the rRNA depleted RNA samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.
Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with a Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) and sequenced by Illumina HiSeq 3000 (LC Sciences, USA) on a 125 bp paired-end run.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 3000

Description

mRNA、lncRNA、circRNA

Data processing

From the raw FASTQ files, adapter was removed using Trim Galore and filtered data were aligned to the Bos taurus reference genome (bosTau7) from UCSC (http://genome.ucsc.edu/) with TopHat2 (version 2.0.14)
Linear transcripts assembly and abundance estimation were performed using CuffLinks analyzed by LC-Bio (Hangzhou, China). The assembled transcripts were mapped to the reference annotation using a program named Cuffcompare in the Cufflinks site to derive novel genes.
The transcript abundances were normalized as the number of uniquely mapped fragments per kilobase of exon per million fragments mapped (FPKM).
Supplementary_files_format_and_content: FPKM

Submission date

Apr 05, 2018

Last update date

Oct 18, 2019

Contact name

Yun Ma

E-mail(s)

[email protected]

Organization name

Xinyang Normal University

Street address

Shihe