Selection and validation of differentially expressed metabolic and immune genes in weaned Ghurrah versus crossbred piglets.

Tropical Animal Health and Production
A KarthikeyanB P Mishra

Abstract

In the present investigation, differentially expressed genes (DEGs) were studied using RNA sequencing (RNA-seq) technique in porcine peripheral blood mononuclear cells (PBMC) of weaned Ghurrah and crossbred piglets at 3-month age. Transcriptomic analysis was done using three different packages, namely, EBSeq, DESeq2, and edgeR, to identify the DEGs between Ghurrah and crossbred piglets. Total 7717 DEGs were commonly identified by all three packages, out of which 4151 genes found to be up-regulated, and 3566 genes were down-regulated. Functional annotation of these DEGs indicated metabolism as the most commonly enriched category followed by the immune response. Genes related to metabolism and growth were up-regulated in crossbred piglets as compared with Ghurrah piglets, whereas immunity-related genes were up-regulated in Ghurrah piglets elucidating the disease resistance nature of this indigenous breed over crossbred counterparts. Further, eight DEGs, namely, LRP-1, ADCY4, ERRFI1, LDHD, ARG1, OASL, MGARP, and S100A8, were validated by qRT-PCR in a separate set of biological samples and found to be in concordance with RNA-seq results. Finding in the present study provides insight into genes and their molecular mechanisms governi...Continue Reading

References

Feb 16, 2002·Methods : a Companion to Methods in Enzymology·K J Livak, T D Schmittgen
Mar 1, 2006·The Journal of Laboratory and Clinical Medicine·Choong-Chin LiewAdam A Dempsey
Jul 29, 2006·BMC Bioinformatics·Silpa SuthramTrey Ideker
Aug 22, 2009·Cutaneous and Ocular Toxicology·Jennifer A PriceJohn S Graham
Mar 4, 2010·Genome Biology·Mark D Robinson, Alicia Oshlack
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Nov 13, 2010·Nucleic Acids Research·Chris StarkMike Tyers
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Feb 23, 2013·Bioinformatics·Ning LengChristina Kendziorski
Jun 20, 2018·International Journal of Molecular Sciences·Virginia Actis Dato, Gustavo Alberto Chiabrando
Aug 20, 2018·Cellular Physiology and Biochemistry : International Journal of Experimental Cellular Physiology, Biochemistry, and Pharmacology·Shengjuan WeiPeishi Yan

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Citations

Jul 27, 2021·Physiology and Molecular Biology of Plants : an International Journal of Functional Plant Biology·Aman DabralManeesh S Bhandari

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Methods Mentioned

BETA
biopsy
RNA-seq
Profiler
PCR
electrophoresis

Software Mentioned

EdgeR
VENNY
EBSeq
Primer3
Cytoscape
ggplot2
DESeq2
RSEM calculate expression
FASTQC
Bowtie

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