Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Barcoded mRNA-seq of murine brown preadipocytes (IBA) upon transcriptomic perturbation

ABSTRACT: Loss of function assays were performed in differentiating IBAs using short hairpin RNAs (shRNAs) against a set of candidate transcription factors: NFIA, DBP, HOXA4, ZFP467, SOX18, ELF3, YBX2 and PPARa. Gene expression profiles of the perturbed and non perturbed (controls including non transduced cells, cells transduced with scrambled and GFP constructs) transcriptomes were measured at Day 6 of differentiation using a novel multiplex, bulk mRNA-seq barcoding method which employs a 3' sequencing approach. This method allowed the measurement of the deviation of the perturbed transcriptome from the non-perturbed transcriptome.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Rachana Pradhan

PROVIDER: E-MTAB-5161 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dissecting the brown adipogenic regulatory network using integrative genomics.

Pradhan Rachana N RN Bues Johannes J JJ Gardeux Vincent V Schwalie Petra C PC Alpern Daniel D Chen Wanze W Russeil Julie J Raghav Sunil K SK Deplancke Bart B

Scientific reports 20170209

Brown adipocytes regulate energy expenditure via mitochondrial uncoupling, which makes them attractive therapeutic targets to tackle obesity. However, the regulatory mechanisms underlying brown adipogenesis are still poorly understood. To address this, we profiled the transcriptome and chromatin state during mouse brown fat cell differentiation, revealing extensive gene expression changes and chromatin remodeling, especially during the first day post-differentiation. To identify putatively causa ...[more]

PMID: 28181539

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Project description:Hydroxylated polychlorinated biphenyls are the metabolites produced from polychlorinated biphenyls (PCBs) by drug-metabolizing enzyme cytochrome P450 1A1. These compounds are bound to transthyretin, a major plasma thyroid hormone-binding protein in amphibian tadpoles. The compounds-transthyretin complexes are transferred into the brain across the blood brain barrier in mammals. Thus these compounds are suspected to disrupt neural development in brain. We studied about the effects of hydroxylated PCBs on the thyroid system in brain using metamorphosing tadpoles of African clawed toad, Xenopus laevis. The metamorphosis assay revealed that these compounds had inhibitory effects on the thyroid hormone-induced metamorphosis. This in vivo assay was a powerful tool to detect thyroid-disrupting activities, because we were not able to detect the inhibitory effects of these compounds using thyroid hormone-responsive reporter gene assay in a cultured Xenopus cell line. A genome-wide gene expression analysis in brain following short-term exposure to these compounds demonstrated that the delay of metamorphosis and the morphological thyroid-disrupting changes could be caused partially by disruption of the thyroid hormone-induced gene expression by hydroxylated PCBs. Furthermore, we associated functional ontology terms with the transcripts whose expression were altered by thyroid hormone alone, or thyroid hormone and hydroxylated PCBs. We suggested that these approachs using a technique of bioinformatics revealed molecular mechanism of thyroid-disrupting activities in vivo. Thyroid hormones induce amphibian metamorphosis and alter a lot of thyroid hormone-responsive gene expression. We studied about the effects of hydroxylated PCBs on TH-induced gene expression. Premetamorphic tadpoles were treated with 500 nM hydroxylated PCBs in the presence of 1 nM thyroid hormone for 4 days. After exposure period total RNA was extracted from brain. Study included at least three replicate of each treatment.

Dataset Information

Barcoded mRNA-seq of murine brown preadipocytes (IBA) upon transcriptomic perturbation

Publications

Dissecting the brown adipogenic regulatory network using integrative genomics.

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