Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide identification and analysis of long noncodingRNAs in porcine preadipocytes treated with TGF-β1

ABSTRACT: Several studies have revealed thatTGF-β1 may play a key role in epithelial-mesenchymal transition (EMT); however, little is known about the effects of TGF-β1 treatment on porcine preadipocytes. To identify the key lncRNAregulator, two libraries were constructed from porcine preadipocytes were treated with or without 10 ng/mL human recombinant TGF-β1 for 48 h by using the Illumina HiSeqXten platform. RT-qPCR was used to detect the expression of ten differentially expressed lncRNAs, andthe results were consistent with the sequencing results. In addition, the lncRNATargets platform was used to construct an interaction network of lncRNAs and the Smad7 gene.A total of 39 lncRNA transcripts, including 28 upregulated and 11 downregulated transcripts, were significantly differentially expressed in the TGF-β1 group compared with the control group. Functional annotation and enrichment analysisof the host genes revealed that the differentially expressed lncRNAs were related to single-organism process, cell part and cellular process.We constituted the lncRNA/mRNAco-expression network in the TGF-βsignaling pathway.In our study, we systematically investigated the lncRNA contents in porcine preadipocytes were treated with or without 10 ng/mL human recombinant TGF-β1. A total of 8158 lncRNA transcripts were identified, and 39 of these transcripts were significantly differentially expressed between two libraries.

ORGANISM(S): Sus scrofa

PROVIDER: GSE132049 | GEO | 2019/06/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Identificaion of long noncoding RNAs related to TGF-β signaling in human cultured tubular epithelial cells

Project description:To identify differentially expressed long noncoding RNAs (lncRNAs) upon TGF-β stimulation in human cultured tubular epithelial cells HK2 and HKC8, we have employed long noncoding RNA microarray expression profiling as a discovery platform to find differentially expressed lncRNAs with TGF-β stimulation in these cells. Cultured human tubular epithelial cells HK2 and HKC8 were stimulated with PBS or TGF-β1. After incubation with TGF-β1 (10ng/ml) for 24 hours, 86 overlapping lncRNAs were upregulated and 47 overlapping lncRNAs were downregulated more than 2 fold vesus cells treated with PBS in these two epithelial cell lines. Expression of ENST00000429588 from this result was quantified in the same RNA samples by real-time PCR, confirming the upregulation upon TGF-β stimulation is repeatable.

2018-08-15 | GSE108554 | GEO

Genome-wide transcript profiling for native porcine valvular interstitial cells and those cultured on TCPS and treated with TGF-β1

Project description:Fibrotic diseases have significant health impact and have been associated with differentiation of the resident fibroblasts into myofibroblasts. In particular, stiffened extracellular matrix and TGF-β1 in fibrotic lesions have been shown to promote pathogenic myofibroblast activation and progression of fibrosis in various tissues. To better understand the roles of mechanical and chemical cues on myofibroblast differentiation and how they may crosstalk, we cultured primary valvular interstitial cells (VICs) isolated from porcine aortic valves and studied how traditional TCPS culture, which presents a non-physiologically stiff environment, and TGF-β1 affect native VIC phenotypes. We carried out gene expression profiling using porcine genome microarrays from Affymetrix and found that traditional TCPS culture induces major changes in gene expression of native VICs, rendering these cells more activated and similar to cells treated with TGF-β1. We also monitored time-dependent effects induced by TGF-β1 by examining gene expression changes induced by TGF-β1 at 8 hours and 24 hours. Porcine aortic VICs were isolated and cultured with or without TGF-β1 treatment for RNA extraction and hybridization on Affymetrix microarrays. We included 3 biological replicates for each condition. P0 VICs were freshly isolated cells which had not been cultured. P2 VICs were cells that had been passaged 2 times and cultured on plastic plates in low serum media. Some of the P2 VICs were treated with TGF-β1 at 5ng/ml for 8 hours or 24 hours. All the control and TGF-β1-treated conditions were collected at the same time on day 3 of culture.

2013-09-02 | E-GEOD-48839 | biostudies-arrayexpress

Novel long non‐coding RNA 005620 induces epirubicin resistance of triple-negative breast cancer via regulating ITGB1 expression

Project description:In this study, a total of 12 differentially expressed lncRNAs were established through lncRNA sequencing analysis. Lnc005620 is one of the novel intronic lncRNAs which is highly expressed in Epi-R MDA-MB-231. Lnc005620 is an important lncRNA that leads to the resistance of Epirubicin in triple negative breast cancer by integrin β1.

2021-03-02 | GSE152003 | GEO

Oncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [HT-seq]

Project description:Most cancer genomics papers to date have focused on aberrations in genomic DNA and protein-coding transcripts. However, around 50% of transcripts have no coding potential and may exist as non-coding RNA. We performed RNA-seq in BRAFv600e melanoma skin cancer and on melanocytes over-expressing oncogenic BRAF to catalog transcriptome remodeling. We discovered that BRAF regulates expression of 1027 protein coding transcripts, 39 annotated lncRNAs and 70 novel transcripts. Many of the novel transcripts are lncRNAs. We used an indepenedent dataset to interrogate our novel transcripts and found that the novel lncRNA BANCR is a BRAF-regulated lncRNA recurrently upregulated in melanoma. Knockdown of BANCR impairs melanoma cell migration. Whole transcriptome RNA-seq followed assembly to Refseq/Gencode and de novo transcript assembly. RNA-seq performed on: 2 BRAFv600e melanomas, melanocytes+RFP control and melanocytes + BRAFv600e. We discovered protein-coding transcripts, annotated ncRNAs and novel transcripts (including lncRNAs) regulated by BRAFv600e also coordinately expressed in melanoma.

2012-04-28 | E-GEOD-33092 | biostudies-arrayexpress

Global identification of growth-related long non-coding RNAs in breast muscle of chicken

Project description:Long non-coding RNAs (lncRNAs) can have potential roles in development of tissues and organs. We selected breast muscle of fast-growing White Recessive Rock chicken (WRR) and slow-growing Xing Hua chicken (XH) to identify lncRNA transcripts by LncRNA-Seq. This study identified 21,993 novel lncRNAs. Among 7,339 differentially expressed lncRNAs, 723 up-regulated and 6,616 down-regulated lncRNAs were found in WRR compared with XH. Of them, five novel lncRNA were antisense transcripts for growth-related genes CACNA1D (unigene 14689_all), IL4I1 (unigene 15355_all), LEF-1 (unigene 19525_all) and FABP1 (unigenes 17536_all and 17537_all) respectively. Meanwhile, 12 other novel lncRNAs were found in the intron or downstream of some known growth-related genes (IGF1, IGF2BP2, IGF2BP3, CACNA1D, IL4I1, LEF-1 and FABP1). In addition, 4,043 SSRs and 200,049 SNPs were identified. Our data revealed the global lncRNA expression pattern in muscle tissue, and contributed a useful genomic resource towards studying the effects of lncRNAs in regulating chicken growth. Two RNA pool for WRR and XH strains

2014-06-24 | E-GEOD-58755 | biostudies-arrayexpress

Expression of lncRNAs between buffalo and yellow cattle muscle

Project description:Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.

2019-12-20 | GSE123869 | GEO

The long noncoding RNA expression profile of hepatocellular carcinoma identified by microarray analysis

Project description:To explore the potential involvement of lncRNAs in hepatocellular carcinoma (HCC) oncogenesis, we conducted lncRNA and mRNA profiling in 3 pairs of human HCC and adjacent normal tissue (NT) by microarray. With abundant probes accounting for 33,045 lncRNAs and 30,215 coding transcripts in our microarray, the number of lncRNAs and coding transcripts that could be detected here is 10,149 and 14,944, respectively. From the data, thousands of lncRNAs and mRNAs were found to bedifferentially expressed (Fold Change≥2.0) in HCC tissues compared with NT and identified 624 lncRNAs and 1050 mRNAs were differentially expressed in all three HCC tissues.Bioinformatic analysis (gene ontology, pathway and network analysis) was performed for further study of these differentially expressed mRNAs.By qRT-PCR analysis in nineteen pairs HCC and adjacent normal tissues, we found that eightl ncRNAs were aberrantly expressed in HCC compared with corresponding NT, which is consistent with microarray data. Additionally, change trends of seven lncRNAs were basically identical to their nearby coding genes. In this study, to explore the potential involvement of lncRNAs in hepatocellular carcinoma (HCC) oncogenesis, we conducted lncRNA and mRNA profiling in 3 pairs of human HCC and adjacent normal tissue (NT) by microarray.

2014-02-21 | E-GEOD-55191 | biostudies-arrayexpress

Transcriptome analysis of a PRRSV-infected and control PAMs

Project description:Transcriptomes analysis of long noncoding RNA (lncRNA) and mRNA expression profiles of the porcine alveolar macrophages (PAMs) after porcine reproductive and respiratory syndrome virus (PRRSV) infection in vitro. We obtained 105,627,026 clean reads from 109,443,286 raw reads. A total of 951 annotated and 751 novel lncRNAs were identified. PAMs showed distinct transcriptome profiles after PRRSV infection. It was observed that 126 lncRNAs and 753 mRNAs were differentially expressed between PRRSV-infected and control group PAMs.

2019-06-20 | GSE132735 | GEO

Genome-wide transcript profiling for native porcine valvular interstitial cells and those cultured on TCPS and treated with TGF-β1

2013-09-02 | GSE48839 | GEO

lncRNA and mRNA profiles show difference in Tetralogy of Fallot

Project description:In this study,compared with normal group, there were 94 differentially expressed lncRNAs and 83 mRNA transcripts in TOF (P<0.05). Correlation analysis between lncRNA and mRNA further showed that differentially expressed lncRNA can be linked to mRNAs, suggesting the regulator role of lncRNA in mRNA expression

2022-11-23 | GSE184905 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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