Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation

ABSTRACT: LincRNA-EPS is a long noncoding RNA that is expressed in macrophages and downregulated upon exposure to diverse microbial products. Analysis of macrophages from lincRNA-EPS-deficient mice revealed a specific role for this lincRNA in restraining immune response gene (IRG) expression. Mechanistically, lincRNA-EPS associates with chromatin at regulatory regions of IRGs to repress their transcription. To gain insight into the molecular function of lincRNA-EPS on chromatin, we generated ATAC-Seq libraries from wildtype and lincRNA-EPS-deficient macrophages stimulated with LPS.

ORGANISM(S): Mus musculus

PROVIDER: GSE78873 | GEO | 2016/05/08

SECONDARY ACCESSION(S): PRJNA314247

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation

Project description:RNA-seq was performed in biological replicates (2 mice per group) of wild-type and lincRNA-EPS-/- BMDMs at 0, 2, and 6 hours after LPS treatment (100 ng/ml). RNA-seq libraries were prepared as described (Heyer et al., 2015). Briefly, ribosomal RNA (rRNA) was depleted using the Ribozero rRNA removal kit (Epicentre). Purified mRNAs were fragmented with RNA fragmentation reagent (Life Technologies) for 4 minutes and 30 seconds at 70C to obtain 100-150 nt long RNA fragments. After ethanol precipitation and washing, RNAs were re-suspended in 5 l of water and the 3 ends dephosphorylated using PNK (New England BioLabs) for 1 hr at 37C. RNA fragments with a 3 OH were then ligated to a preadenylated DNA adaptor using T4 RNA ligase 2, truncated K227Q (NEB). Following this, ligated RNAs were reverse-transcribed with Superscript III (Invitrogen) using a bar-coded reverse-transcription primer that anneals to the preadenylated adaptor. After reverse-transcription, gel purified cDNAs were circularized using CircLigase I (Epicentre) and PCR amplified using paired-end primers PE1.0 and PE2.0 (Illumina) for 14 cycles. PCR amplicons were gel purified and submitted for sequencing on the Illumina Hiseq2000. Tophat version 2.0.12 was used to align single sequence reads to version 73 of the Ensembl mouse genome (mm10) with options: --library-type fr-firststrand -g 1 -x 1 --read-mismatches 2. Cufflinks version 2.1.1 was used to estimate RNA abundances with Ensembl version 73 GTF and the --library-type fr-firststrand option. The Cuffdiff program was used to perform differential expression analysis between wild-type BMDMs and lincRNA-EPS-/- BMDMs at each corresponding time (0,2, and 6 hours after LPS treatment). To compute fold-change values for genes/transcripts with FPKM values of zero, a pseudocount of 1 was added to all FPKM values first.

2016-07-29 | E-MTAB-4088 | biostudies-arrayexpress

WT and lincRNA-EPS knockout iBMMs that knocked down PKR or not

Project description:Test transcripts in control and siPKR WT and lincRNA-EPS knockout iBMMs

2022-01-12 | GSE193325 | GEO

WT and lincRNA-EPS knockout iBMMs that infected with VSV or not

Project description:Test transcripts in mock and VSV infected WT and lincRNA-EPS knockout iBMMs

2022-01-12 | GSE193324 | GEO

A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation.

Project description: Not available

| S-EPMC5289747 | biostudies-literature

A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation

Project description:A long noncoding RNA lincRNA-EPS acts as a transcriptional brake to restrain inflammation

| PRJEB11889 | ENA

WT and lincRNA-EPS knockout iBMMs that infected with VSV or not

Project description:WT and lincRNA-EPS knockout iBMMs that infected with VSV or not

| PRJNA795791 | ENA

WT and lincRNA-EPS knockout iBMMs that knocked down PKR or not

Project description:WT and lincRNA-EPS knockout iBMMs that knocked down PKR or not

| PRJNA795804 | ENA

LincRNA-EPS negatively regulates host antiviral immunity by antagonizing viral RNA interacting with PKR

Project description:LincRNA-EPS negatively regulates host antiviral immunity by antagonizing viral RNA interacting with PKR

| PRJNA795796 | ENA

Transcriptome analyses of in vitro exercise by EPS and adrenaline

Project description:To evaluate transcriptomic changes induced by in vitro exercise, we established two in vitro exercise models; EPS (electrical pulse stimulation and clenbuterol treatment). As for clen-buterol treatment, differentiated C2C12 myotubes were treated by 30 ng/ml clenbuterol for 1 hour and control and clenbuterol treated C2C12 myotubes were analyzed by RNA-sequencing. As for an EPS model, EPS was applied to differentiated C2C12 myotubes for 24 hours and control and EPS applied C2C12 myotubes were analyzed by RNA-sequencing.

2021-11-06 | GSE183159 | GEO

Gene expression changes induced in Rice (Oryza sativa) leaves following treatment with any one of the following: wild type Xoo, lipopolysaccharide (LPS) and exopolysaccaride (EPS) deficient Xoo mutant; LPS proficient but EPS deficient Xoo mutant

Project description:Lipopolysaccharide is a Microbe Associated Molecular Pattern (MAMP) that is known to induce defense responses in plants. In rice we have shown that Xoo LPS induce callose deposition, reactive oxygen production and induced resistance response. The exopolysaccaride (EPS) secreted by Xoo might be involved in supressing these defense responses. We have performed transcriptional profiling of rice leaf gene expression changes after treatment with Xoo strains BXO1003 (LPS-, EPS-), BXO1002 (LPS+ EPS-) and BXO43 (wild type) along with milliQ treated leaves to identify the genes that are differentially expressed. RNA was isolated from mid veins of rice leaves 15 hours after injecting them with Xoo strains BXO1003 (LPS-, EPS-), BXO1002 (EPS-), BXO43 (wild type) or milli-Q water. The rice gene expression in each of the treatment was normalized based on the gene expression in the milli-Q treatment.

2015-06-30 | E-GEOD-61833 | 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