Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Human adipose transcriptome reveals primate-specific long intergenic noncoding RNAs that modulate adipocyte metabolic function

ABSTRACT: Through deep RNA-seq in human subcutaneous adipose bioposies and established long noncoding RNAs (lincRNAs) annotations, we identified human lincRNAs expressed in all subjects, including subsets of lincRNAs that exhibit differential expression by sex and race. Our comprehensive profiling on subcutaneous adipose lincRNA transcriptome provides great resource to advance novel understanding of genetic regulation in adipose biology.

ORGANISM(S): Homo sapiens

PROVIDER: GSE76404 | GEO | 2017/08/30

SECONDARY ACCESSION(S): PRJNA307250

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

Project description:Long intergenic noncoding RNAs (lincRNA) transcribed from intergenic regions of eukaryotic genomes play important roles in key biological processes; yet, plant lincRNAs remain poorly characterized. Here we profiled lincRNA expression in inflorescences, leaves and roots using ATH lincRNA v1 array. we found 92% lincRNAs could be detected in at least 2 ATH lincRNA v1 arrays and majority of the lincRNAs were expressed at levels higher than those of pri-miRNAs but lower than those of mRNAs.Using a cut-off of 2-fold change, we identified 149 lincRNAs preferentially expressed in inflorescences, 232 in leaves and 164 in roots.

2011-08-06 | GSE30394 | GEO

Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

2011-08-05 | E-GEOD-30394 | biostudies-arrayexpress

Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

Project description:Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions play important roles in key biological processes.Analysis of published transcriptom datasets suggested some lincRNAs may be regulated by SERRATE,CBP20 and CBP80 in Arabidopsis. To further investigate the regulation, we use Arabidopsis lincRNA arrays v1 to detect lincRNA expression in se-2 and cbp20/80 double mutants.We found the expression levels of 940 lincRNAs (20%) out of the 4,634 lincRNAs with probes in array were significantly alerted in all mutants (P-value of eBays ANOVA < 0.05 & fold change of signal intensity > 2). This group included 525 up-regulated and 415 down-regulated lincRNAs.

2012-09-29 | GSE35963 | GEO

Human Long Intergenic Noncoding RNA Linc-ADAL Knockdown in Mature Adipocytes using Lentiviral ShRNA

Project description:Thousands of human long intergenic noncoding RNAs (lincRNAs) have been detected in human adipose tissue. Here we characterized the function of one human adipse lincRNA, linc-ADAL (chr5:115292235-115296985) in mature adipcoytes through loss-of-function studies. Our results indicate that knockdown of linc-ADAL in differentiated adipocytes modulated expression of lipid metabolism genes.

2019-02-13 | GSE95173 | GEO

Long Intergenic Noncoding RNAs regulated by SERRATE, CBP20 and CBP80

2012-09-29 | E-GEOD-35963 | biostudies-arrayexpress

A large intergenic non-coding RNA induced by p53 mediates global gene repression in the p53 transcriptional response

Project description:Recently, more than a thousand large intergenic non-coding RNAs (lincRNAs) have been reported. These RNAs are evolutionarily conserved in mammalian genomes and thus presumably function in diverse biological processes. Here, we report the identification of lincRNAs that are regulated by p53. One of these lincRNAs (lincRNA-p21) serves as a repressor in p53-dependent transcriptional responses. Inhibition of lincRNA-p21 affects the expression of hundreds of gene targets enriched for genes normally repressed by p53. The observed transcriptional repression by lincRNA-p21 is mediated through the physical association with hnRNP-K. This interaction is required for proper genomic localization of hnRNP-K at repressed genes and regulation of p53 mediated apoptosis. We propose a model whereby transcription factors activate lincRNAs that serve as key repressors by physically associating with repressive complexes and modulating their localization to sets of previously active genes.

2010-08-09 | GSE21761 | GEO

Identification of Arabidopsis Long Intergenic Noncoding RNA regulated by RNA-dependent RNA polymerase 2 (RDR2)

Project description:RNA-dependent RNA polymerase 2 (RDR2) is a crucial regulator of RNA-directed DNA methylation (RdDM). Recentily RDR2 was reported to regulate expression of long intergenic noncoding RNAs. Here we used ATH lincRNA v1 expression arrays to compare lincRNA expression in inflorescence tissues of rdr2-1 and WT. Among the 4,634 lincRNAs detected we found that more than 34% of them were differentially expressed, including 676 lincRNAs that were up-regulated and 890 down-regulated in rdr2-1.

2011-08-06 | GSE30395 | GEO

Identification of Arabidopsis Long Intergenic Noncoding RNA regulated by RNA-dependent RNA polymerase 2 (RDR2)

2011-08-05 | E-GEOD-30395 | biostudies-arrayexpress

Systematic Analysis of Long Intergenic Non-Coding RNAs in C. elegans Germline Uncovers Roles in Somatic Growth

Project description:Long intergenic non-coding RNAs (lincRNAs) are transcripts longer than 200 nucleotides that are transcribed from non-coding loci yet undergo biosynthesis similar to coding mRNAs. The disproportional number of lincRNAs expressed in testes suggests that lincRNAs are important during gametogenesis, but experimental evidence has implicated very few lincRNAs in this process. We took advantage of the relatively limited number of lincRNAs in the genome of the nematode Caenorhabditis elegans to systematically analyse the functions of lincRNAs during meiosis. We deleted six lincRNA genes that are highly and dynamically expressed in the C. elegans gonad and tested the effects on central meiotic processes. Surprisingly, whereas the lincRNA deletions did not strongly impact fertility, germline apoptosis, crossovers, or synapsis, linc-4 was required for somatic growth. Slower growth was observed in linc-4-deletion mutants and in worms depleted of linc-4 using RNAi, indicating that linc-4 transcripts are required for this post-embryonic process. Unexpectedly, analysis of worms depleted of linc-4 in soma versus germline showed that the somatic role stems from linc-4 expression in germline cells. This unique feature suggests that some lincRNAs, like some small non-coding RNAs, are required for germ-soma interactions

2021-07-31 | GSE154322 | GEO

Integrative Annotation of Human Large Intergenic Non-Coding RNAs Reveals Global Properties and Specific Subclasses

Project description:Large intergenic non-coding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-Seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalogue of over 8,000 human lincRNAs. Our catalogue unifies previously existing annotation sources with transcripts we assembled from RNA-Seq data collected from ~4 billion RNA-Seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of more than 30 properties, including sequence, structural, transcriptional, and orthology features. We find that lincRNA expression is strikingly tissue specific compared to coding genes, and that they are typically co-expressed with their neighboring genes, albeit to a similar extent to that of pairs of neighboring protein-coding genes. We distinguish an additional sub-set of transcripts that have high evolutionary conservation but may include short open reading frames, and may serve either as lincRNAs or as small peptides. Our integrated, comprehensive, yet conservative reference catalogue of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes. We extracted profiled the transcriptome expression polyadenylated mRNA-Seq. We then used these to reconstruct the transcriptome using de-novo assemblers and identify long non coding RNAs and their expression.

2011-08-27 | E-GEOD-30554 | biostudies-arrayexpress

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