Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA expression profiles in the BMDM of C57BL/6J wild type and lncRNA AK085865 knock-out mice

ABSTRACT: Long non-coding RNAs (lncRNAs) play key roles in various biological processes. However, the roles of lncRNAs in macrophage polarization remain largely unexplored. Our study have found that lncRNA AK085865 play a vital role in macrophage polarization and specific bind to ILF2 protein and further influence the miRNA processing process. The miRNA expression profiles in the BMDM of C57BL/6J wild type and lncRNA AK085865 knock-out mice were obtained using microarray analysis. Based on the threshold of fold-change ≥2.0 and a p-value ≤ 0.05, we screened a total of 24 miRNAs, of which 11 were upregulated and 13 were downregulated in KO compared to that in WT BMDMs.This study provides new insights into the role of lncRNA AK085865 regulating miRNAs expression in the mice BMDMs.

ORGANISM(S): Mus musculus

PROVIDER: GSE125574 | GEO | 2020/07/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Expression analysis of microRNAs in INT-HA-induced M2-like macrophages and untreated macrophages (M0)

Project description:Using the highly sensitive miRNA microarray, we screened 107 up-regulated microRNAs and 33 down-regulated microRNAs in the INT-HA-induced M2-like macrophages and we explored the functions of these miRNAs in macrophage polarization. The enrichment results indicated that these miRNAs might participate in the process of macrophage polarization. Furthermore, the quantitative real-time polymerase chain reaction results showed that miR-935 may play an important role in M2 macrophage polarization which was activated by INT-HA.

2021-02-08 | GSE110339 | GEO

miRNA-seq in human lung cancer tissues

Project description:we conducted transcriptome and small RNA sequencing to identify differentially expressed genes (DEGs), miRNAs (DEMs), and lncRNAs (DELs). Function analysis on DEM-target genes can explain the regulatory roles of miRNAs in LC. The lncRNA-miRNA pairs, miRNA-mRNA pairs, and lncRNA-mRNA pairs were identified, which were then combined to construct the interplay of lncRNAs/miRNAs/mRNAs. And we used the online databases to verify the selected DEMs, DELs, and DEGs. Our study identified 2509 DEGs, 34 DEMs, and 432 DELs in LC patients. miRNA-mRNA pairs, including 1 miRNA (hsa-miR-21-5p) and 5 targeted genes (RECK, TIMP3, EHD1, RASGRP1 and ERG), were figured out. We finally found the hub subnetwork (LINC00632/has-miR-21-5p/TIMP3) by combining lncRNA-miRNA pairs, miRNA-mRNA pairs and lncRNA-mRNA pairs.

2022-01-27 | GSE194300 | GEO

lncRNA-seq in human lung cancer tissues

Project description:We conducted transcriptome and small RNA sequencing to identify differentially expressed genes (DEGs), miRNAs (DEMs), and lncRNAs (DELs). Function analysis on DEM-target genes can explain the regulatory roles of miRNAs in LC. The lncRNA-miRNA pairs, miRNA-mRNA pairs, and lncRNA-mRNA pairs were identified, which were then combined to construct the interplay of lncRNAs/miRNAs/mRNAs. And we used the online databases to verify the selected DEMs, DELs, and DEGs. Our study identified 2509 DEGs, 34 DEMs, and 432 DELs in LC patients. miRNA-mRNA pairs, including 1 miRNA (hsa-miR-21-5p) and 5 targeted genes (RECK, TIMP3, EHD1, RASGRP1 and ERG), were figured out. We finally found the hub subnetwork (LINC00632/has-miR-21-5p/TIMP3) by combining lncRNA-miRNA pairs, miRNA-mRNA pairs and lncRNA-mRNA pairs.

2022-01-27 | GSE194299 | GEO

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs

Project description:Long noncoding RNAs (lncRNAs) are important regulators of cell fate, and their mis-expression has been implicated in many diseases. While distinct polymerases generate messenger vs. noncoding ribosomal or tRNAs3, little is known about distinct mechanisms controlling lncRNA expression. Here we show that transcription of lncRNAs is quantitatively different from that of messenger RNAs (mRNAs)--as revealed by deficiency of Dicer (Dcr), a key ribonuclease that generates microRNAs (miRNAs). Loss of Dcr in mouse embryonic stem cells (mESCs) led surprisingly to decreased level of the majority of lncRNAs. The canonical Dgcr8-Dcr-miRNA pathway is required for robust lncRNA expression, at the level of transcriptional initiation and elongation of lncRNA genes rather than at the level of their stability. cMyc, an oncogenic transcription factor, whose expression is indirectly regulated by Dcr-miRNA in mESCs, is partly responsible for lncRNA transcription. Loss of cMyc led to a more dramatic decrease of lncRNAs than mRNAs, and cMyc overexpression rescues lncRNA expression in Dcr KO cells. A quantitative metric of “mRNA-lncRNA decoupling” revealed that Dcr and cMyc differentially regulate lncRNAs vs. mRNAs in diverse cell types and in vivo, as evidenced by hundreds of microarray experiments. Thus, Dcr and cMyc may allow numerous lncRNAs to be activated or deactivated as a class, implicating lncRNAs to potential regulatory roles in development and disease states where Dcr and cMyc have been associated with. RNA was sequenced from WT and Dcr KO mESCs and the expression of lncRNAs and mRNAs are compared between WT and Dcr KO mESCs.

2014-06-15 | E-GEOD-55338 | biostudies-arrayexpress

miRNA regulated by Notch signaling in macrophage

Project description:This two-color miRNA chip was perfored to identify the downstream miRNAs regulated by Notch signaling in macrophage polarization. To identify the downstream miRNAs mediated by Notch signaling during macrophage polarization regulating, RNA was isolated from bone marrow drived macrophages (BMDMs) of Notch signaling deletion and wild type mice as experiment samples. Three control (+/-) and three experiment (-/-) samples were detected.

2015-03-28 | E-GEOD-67364 | biostudies-arrayexpress

RNA Immunoprecipitation in macrophages using NLRC4 and Caspase11 and high-throughput sequencing of isolated lncRNA

Project description:At the epigenetic level, lncRNAs play important roles in cell differentiation and function. We identified novel long-stranded non-coding RNA (GM1082) in BMDMs, which may play an important role in macrophage differentiation and function.To confirm the interaction between LNCRNA and NLRC4 and Caspase11, we performed RNA immunoprecipitation using NLRC4 and Caspase11 antibodies, and high-throughput sequencing of the obtained RNA.

2021-04-28 | GSE173399 | GEO

miRNA regulated by Notch signaling in macrophage

Project description:This two-color miRNA chip was perfored to identify the downstream miRNAs regulated by Notch signaling in macrophage polarization.

2015-03-28 | GSE67364 | GEO

LncRNA-mRNA expression profiles and functional networks of hyposalivation in the submandibular gland in hypertension

Project description:Hyposalivation is a complication of hypertension. Although the lncRNA have recently been identified to play a role in the pathogenesis of hypertension, the specific effects of lncRNAs on hyposalivation caused by hypertension remain unclear. The aim of the current study was to construct and systematically analyze the lncRNA-miRNA-mRNA network and reveal its potential roles in hyposalivation.

2020-08-24 | GSE144438 | GEO

LncRNA/mRNA expression profiling for THP-1 macrophages and THP-1 macrophage-derived foam cells

Project description:By identifying differentially expressed LncRNAs/mRNAs in THP-1 macrophages and THP-1 macrophage-derived foam cells, we select some differentially expressed LncRNAs and explore their roles in atherosclerosis process. We already find that some LncRNA can effect cholesterol metabolism and level of inflammation factor, which may influence atherosclerosis process. In the study presented here, 6 human samples were used to acquire expression profiles, which provide futher insight into the pathologies of atherosclerosis

2014-05-20 | E-GEOD-54039 | biostudies-arrayexpress

In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (30 PCL lncRNA data sets)

Project description:The identification of deregulated microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in multiple myeloma (MM) has progressively added a further level of complexity to MM biology. In addition, the cross-regulation between lncRNAs and miRNAs has begun to emerge, and theoretical and experimental studies have demonstrated the competing endogenous RNAs (ceRNAs) activity of lncRNAs as natural miRNA decoys in pathophysiological conditions, including cancer. Currently, information concerning lncRNA and miRNA interplay in MM is virtually absent. Herein, we investigated in silico the lncRNA and miRNA relationship in a representative datasets encompassing 95 MM and 30 plasma cell leukemia patients at diagnosis and in four normal controls, whose expression profiles were generated by a custom annotation pipeline to detect specific lncRNAs. We applied target prediction analysis based on miRanda and RNA22 algorithms to 235 lncRNAs and 459 miRNAs selected with a potential pivotal role in the pathology of MM. Among pairs that showed significant correlation between lncRNA and miRNA expression levels, we identified 10 lncRNA-miRNA relationships suggestive of novel ceRNA network with relevance in MM.

2017-11-09 | GSE106745 | 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