Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Long non-coding RNAs regulate adipogenesis

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Cole Trapnell

PROVIDER: E-GEOD-29899 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Long noncoding RNAs regulate adipogenesis.

Sun Lei L Goff Loyal A LA Trapnell Cole C Alexander Ryan R Lo Kinyui Alice KA Hacisuleyman Ezgi E Sauvageau Martin M Sauvageau Martin M Tazon-Vega Barbara B Kelley David R DR Hendrickson David G DG Yuan Bingbing B Kellis Manolis M Lodish Harvey F HF Rinn John L JL

Proceedings of the National Academy of Sciences of the United States of America 20130211 9

The prevalence of obesity has led to a surge of interest in understanding the detailed mechanisms underlying adipocyte development. Many protein-coding genes, mRNAs, and microRNAs have been implicated in adipocyte development, but the global expression patterns and functional contributions of long noncoding RNA (lncRNA) during adipogenesis have not been explored. Here we profiled the transcriptome of primary brown and white adipocytes, preadipocytes, and cultured adipocytes and identified 175 ln ...[more]

PMID: 23401553

Similar Datasets

Long non-coding RNAs regulate adipogenesis (Illumina RNA-Seq)

2013-02-15 | E-GEOD-29898 | biostudies-arrayexpress

Long non-coding RNAs regulate adipogenesis (Affymetrix)

Project description:Adipogenesis involves the regulation of hundreds of genes by several well-studied proteins, but the role of long, noncoding RNAs in this process has not been defined. We track the regulation of hundreds of lncRNAs during adipocyte differentiation, and find several that are essential for this process. We profiled knockdown of lncRNAs that are upregulated during mouse adipocyte development We compared adipocytes differentiated in vitro after knockdown of 10 lncRNAs against control adipocytes and pre-adipocytes using Affymetrix expression microarrays. When cultured primary-preadipytes reached 70-80% confluence, we transfected siRNAs against each lincRNA. 24 hours after transfection, cells were recovered in full culture media and grown to confluence for differentiation. Total RNA was collected from control pre-adipocytes (D0) prior to differentation. Four days after recovery, total RNA was collected from each knockdown, a scramble control, and an untransfected control (D4).

2013-02-15 | E-GEOD-29897 | biostudies-arrayexpress

Influenza infection rewires energy metabolism and induces browning features in adipose cells and tissues

Project description:Influenza A viruses cause epidemics and pandemics with damaging health and economic impacts. Alike any obligate intracellular pathogen, IAVs hijack host cell machinery and energetic resources to multiply within, and eventually exit, the host. Increased fatty acid and cholesterol synthesis, as well as increased glucose metabolism have been identified as the major metabolic changes induced by infection. Besides these effects on metabolism, IAV infection also triggers a variety of innate defense mechanisms within the host cell. Although mainly defined as a virus of the respiratory tract, with airway epithelial cells being its prime cellular habitat, complications outside the site of infection have also been reported. However, whether influenza on its own may impact on endocrine tissues and, thereby, lead to metabolic complications, has never been investigated. Here, we compared the response of preadipocytes and adipocytes to IAV infection, in terms of transcriptomic profiles and bioenergetics. The results showed that IAV triggers a browning adipogenesis process, leading to metabolic reprogramming of the adipose tissue resulting in long-lasting alterations of body metabolism. We conclude that the adipose tissue might be an undervalued organ in influenza pathophysiology.

2019-07-20 | E-MTAB-6646 | biostudies-arrayexpress

ChIP-seq based genome wide profiling of the histone mark H3K27ac and transcription factor Nuclear Factor 1 (NFI) in a differentiating murine brown preadipocyte cell line (IBA)

Project description:ChIP sequencing was used to generate genome-wide maps of the histone mark H3K27ac during in vitro differentiation of a murine brown preadipocyte cell line (IBA) at five different time points, in two biological replicates: Day 0 (confluence), 2h (post induction), Day 1, Day 2 and Day 4 (mature brown adipocytes). Additionally, transcription factor (TF) localisation maps of the Nuclear Factor 1 (NFI) were generated using ChIP sequencing at two time points: Day 0 and Day 4.

2017-09-21 | E-MTAB-5159 | biostudies-arrayexpress

MicroRNAs are required for the feature maintenance and differentiation of brown adipocytes

Project description:Brown adipose tissue is specialized to burn lipids for heat generation as a natural defense against cold and obesity. Previous studies established microRNAs as essential regulators of brown adipocyte differentiation, but it remains unknown whether microRNAs are required for the feature maintenance of mature brown adipocytes. To address this question, we ablated Dgcr8, a key regulator of the microRNA biogenesis pathway, in mature brown as well as white adipocytes. The adipose tissue -specific Dgcr8 knockout mice displayed enlarged but pale interscapular brown fat with decreased expression of genes characteristic of brown fat, and the mice were intolerant to cold exposure. In vitro primary brown adipocyte cultures confirmed that microRNAs are required for marker gene expression in mature brown adipocytes. We also demonstrated that microRNAs are essential for the browning of subcutaneous white adipocyte both in vitro and in vivo. Using this animal model, we performed microRNA expression profiling analysis and identified a set of BAT-specific microRNAs that are up-regulated during brown adipocyte differentiation and enriched in brown fat compared to other organs. We identified miR-182 and miR-203 as new regulators of brown adipocyte development. Taken together, our study demonstrates an essential role of microRNAs in the maintenance as well as the differentiation of brown adipocytes. TotalRNAs were extracted using a Qiagen kit, and 5 M-NM-<g of total RNAs for each sample were used to prepare the mRNA- Seq library according to the manufacturerM-bM-^@M-^Ys instruction (NEB). cDNA libraries were prepared and sequenced by Hi-seq in Whitehead Genome Core. 2 replicates of each treatment were analyzed.

2014-08-07 | E-GEOD-60165 | biostudies-arrayexpress

RNA-seq of brown adipocyte mouse cells treated with different concentrations of DNA origami structures with organized insulin molecules or free insulin molecules against untreated controls

Project description:Insulin binds the insulin receptor (IR), which in turn has showed to form nanoclusters at the cell membrane. Trying to exploit the nanoscale spatial organization of IR, we developed rod-like insulin-DNA-origami nanostructures carrying different numbers of insulin molecules. These structures (referred to as NanoRods, or NR) were then utilized to investigate receptor activity to spatial distribution of insulin molecules. One part of this investigation was to study the transcriptional response of brown adipocytes treated with NR bound to one insulin (NR-1) and NR bound to seven insulin (NR-7), and compare to untreated controls. Furthermore, free insulin was also used to ensure that similar pathways were activated when using NR-bound insulin.

2023-07-03 | E-MTAB-12160 | biostudies-arrayexpress

De novo Reconstruction of Adipose Tissue Transcriptomes Reveals Novel Long Non-coding RNAs that Regulate Brown Adipocyte Development

Project description:Brown adipose tissue (BAT) protects against obesity by promoting energy expenditure via uncoupled respiration. To uncover BAT-specific long non-coding RNAs (lncRNAs), we used RNA-seq to reconstruct de novo transcriptomes of mouse brown, inguinal white, and epididymal white fat and identified ~1500 lncRNAs, including 127 BAT-restricted loci induced during differentiation and often targeted by key regulators PPARγ, C/EBPα and C/EBPβ. One of them, lnc-BATE1, is required for establishment and maintenance of BAT identity and thermogenic capacity. lnc-BATE1 inhibition impairs concurrent activation of brown fat and repression of white fat genes, and is partially rescued by exogenous lnc-BATE1 with mutated siRNA-targeting sites, demonstrating a function in trans. We show that lnc-BATE1 binds heterogeneous nuclear ribonucleoprotein U and that both are required for brown adipogenesis. Our work provides an annotated catalog for the study of fat depot-selective lncRNAs, available online, and establishes lnc-BATE1 as a novel regulator of BAT development and physiology. Total RNA profiles of BAT, iWAT and eWAT samples were sequenced on the Illumina HiSeq2000 platform

2015-04-23 | E-GEOD-66686 | biostudies-arrayexpress

Clarion GO screen assay to assess gene expression responses of human mature adipocytes under control and IL-1B induced conditions in response to herbal extracts of Sage (S. offinicalis) and Chamomile (C. nobile).

Project description:Chronic inflammation plays a critical role in the initiation and development of various human illnesses. The use of steroidal anti-inflammatory drugs (SAIDs) or non-steroidal anti-inflammatory drugs (NSAIDs) is now much more frequent and presents a number of unwanted side effects. For example long- or short-term usage of SAIDs presents multiple negative side effects such as stomach irritation, thinning of the skin, immune defence regression, weight gain and even sometimes a cortico-dependence, and NSAIDs have been linked to a higher risk of strokes, heart attacks, and heart-related deaths. In parallel, there has been renewed interest in alternative medicines and natural therapies and thousands of potential medicinal plants, including sage and chamomile. This study assesses the gene expression responses of human mature adipopcytes (differentiated from fibroblastic pre-adipocytes [PromoCell, Germany; Catalogue #C-12730]), pre-treated with aqueous ethanol extract of sage (Salvia officinalis) or Roman chamomile (Chamaemelum nobile), following 4h or 24h treatment with IL-1B versus control conditions.

2020-10-05 | E-MTAB-9609 | biostudies-arrayexpress

Next generation sequencing analysis of microRNAs in brown preadipocytes and in vitro differentiated mature brown fat cells

Project description:We performed a genome-wide deep sequencing analysis of the microRNAs abundant in mesenchymal stem cells (MSCs) derived from murine brown adipose tissue and in in vitro differentiated mature brown adipocytes. Several microRNAs were identified as differentially regulated when comparing datasets from MSCs vs. mature fat cells. These microRNAs may have an implication in the regulation of adipogenesis as well as thermogenesis in brown adipose tissue (BAT). Examination of BAT-derived MSCs (BAT-MSC; 1 sample) and in vitro differentiated mature brown fat cells (BAT-DIFF; 1 sample) vertis biotechnologie AG, D-85354 Freising, Germany (library construction and sequencing)

2013-05-28 | E-GEOD-45499 | biostudies-arrayexpress

Thermogenic differentiation of adipocyte progenitors

Project description:FACS-purified adipocyte progenitors from murine subcutaneous adipose tissue were cultured under conditions promoting general adipogenic differentiation or beige/brite adipocyte differentiation (treatment with cPGI2). Time course expression profiling was performed during differentiation. In addition, some cultures of differentiated adipocytes were stimulated with norepinephrine for 3 hours. In parallel, differentiation and norepinephrine stimulation of progenitors from interscapular brown fat was performed and profiled.

2015-08-20 | E-MTAB-3693 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data