GSM3082823: Thirtymonth 3; Bubalus bubalis; RNA-Seq - SRA

SRX3892937: GSM3082823: Thirtymonth 3; Bubalus bubalis; RNA-Seq
1 ILLUMINA (Illumina HiSeq 3000) run: 66.6M spots, 20.1G bases, 8.2Gb downloads

Submitted by: NCBI (GEO)

Study: Transcriptome Analysis of Fat Deposition in Buffalo at Different Stages

PRJNA448902 • SRP137711 • All experiments • All runs

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Background: Background: In bovines, the development and growth of adipose involves many physiological processes and plays an extremely important role in the quality of beef, however, the regulatory mechanisms underlying the differences in meat quality are largely unknown. Therefore, a buffalo adipose transcriptome analysis was performed to compare gene expression profiles between different growth stages. Results: Finally, a total of 21,693 mRNAs were obtained, of which 2506 were significantly differentially expressed mRNAs in the two groups, 9494 lncRNAs, a total of 281 lncRNAs and 2506 mRNAs showed significant differential expression patterns and 14990 between the two buffaloes CircRNA, 252 circRNAs were significantly differentially expressed between young and adult buffalo. Overall design: 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.

Sample: Thirtymonth 3

SAMN08871710 • SRS3130740 • All experiments • All runs

Organism: Bubalus bubalis

Library:

Instrument: Illumina HiSeq 3000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction 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.

Experiment attributes:

GEO Accession: GSM3082823

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 66.6M spots, 20.1G bases, 8.2Gb

Run	# of Spots	# of Bases	Size	Published
SRR6949372	66,608,360	20.1G	8.2Gb	2019-08-27

ID:: 5346601

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