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

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

PROVIDER: PRJNA795804 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17514841_1.fastq.gz	Fastqsanger.gz
	SRR17514841_2.fastq.gz	Fastqsanger.gz
	SRR17514842_1.fastq.gz	Fastqsanger.gz
	SRR17514842_2.fastq.gz	Fastqsanger.gz
	SRR17514843_1.fastq.gz	Fastqsanger.gz

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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

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

Project description: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.

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LincRNA-EPS regulates iron metabolism and osteoclastogenesis under inflammatory micro-environment

Project description:This study aims to investigate the impact of LincRNA-EPS on osteoclast lineage differentiation. We established LincRNA-EPS gene knockout mice on the C57BL/6 background and isolated bone marrow-derived macrophages (BMDMs) from both knockout and wild-type mice. These BMDMs were induced with RANKL in vitro for 2 days to generate pre-osteoclast cells. Transcriptome sequencing was performed on these cells, followed by further analysis of differentially expressed genes to explore the effects of LincRNA-EPS deficiency on osteoclast differentiation in BMDMs. In this study, we found that dysregulated osteoclastogenesis and iron homeostasis without lincRNA-EPS, represented by up-regulated gene Lcn2.

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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

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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

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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

LincRNA-EPS impairs host antiviral immunity by antagonizing viral RNA-PKR interaction.

Project description:LincRNA-EPS is an important regulator in inflammation. However, the role of lincRNA-EPS in the host response against viral infection is unexplored. Here, we show that lincRNA-EPS is downregulated in macrophages infected with different viruses including VSV, SeV, and HSV-1. Overexpression of lincRNA-EPS facilitates viral infection, while deficiency of lincRNA-EPS protects the host against viral infection in vitro and in vivo. LincRNA-EPS-/- macrophages show elevated expression of antiviral interferon-stimulated genes (ISGs) such as Mx1, Oas2, and Ifit2 at both basal and inducible levels. However, IFN-β, the key upstream inducer of these ISGs, is downregulated in lincRNA-EPS-/- macrophages compared with control cells. RNA pulldown and mass spectrometry results indicate that lincRNA-EPS binds to PKR and antagonizes the viral RNA-PKR interaction. PKR activates STAT1 and induces antiviral ISGs independent of IFN-I induction. LincRNA-EPS inhibits PKR-STAT1-ISGs signaling and thus facilitates viral infection. Our study outlines an alternative antiviral pathway, with downregulation of lincRNA-EPS promoting the induction of PKR-STAT1-dependent ISGs, and reveals a potential therapeutic target for viral infectious diseases.

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LincRNA-EPS regulates iron metabolism and osteoclastogenesis under inflammatory micro-environment

Project description:LincRNA-EPS regulates iron metabolism and osteoclastogenesis under inflammatory micro-environment

| PRJNA1305314 | 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

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RNA-seq analysis about MuERVL knocked down samples

Project description:RNA-seq analysis about MuERVL knocked down samples

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