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Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome profiling of liver and white adipose tissue of male SD rats and CRISPR/Cas-9-mediated heterozygous knockout SD-Nme7+/- male rats

ABSTRACT: We aimed to compare the transcriptome of liver and white adipose tissue of adult male SD rats and the novel CRISPR/Cas-9-mediated heterozygous knockout SD-Nme7+/- adult male rats using Affymetrix Rat Gene 2.1 ST Array Strip. Total RNA was isolated from the liver and visceral adipose tissue (RNeasy Mini Kit, Qiagen) of SD and SDNme7+/- rats. The quality and integrity of the total RNA was evaluated on the Agilent 2100 Bioanalyzer system (Agilent, Palo Alto, CA). Microarray experiments were performed using the Rat Gene 2.1 ST Array Strip. The whole hybridization procedure was performed using the Affymetrix GeneAtlas® system according to the manufacturer's instructions. The quality control of the chips was performed using Affymetrix Expression Console. After applying quality filters and data normalization by the Robust Multichip Average (RMA) algorithm implemented in Affymetrix Expression Console, the set of obtained differentially expressed probesets was filtered by the false discovery rate (FDR) method implemented in PARTEK Genomics Suite 7 (Partek, St. Louis, Missouri). Transcriptomic data were then processed by a standardized sequence of analyses (hierarchical clustering and principal component analysis, gene ontology, gene set enrichment, Upstream Regulator Analysis, Mechanistic Networks, Causal Network Analysis, and Downstream Effects Analysis) using Ingenuity Pathway Analysis.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Ondřej Seda

PROVIDER: E-MTAB-10011 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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