Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MeRIP-seq profiling of m⁶A modifications in Alkbh5-KO and control bone marrow-derived macrophages following M1 polarization

ABSTRACT: We performed MeRIP-seq combined with RNA-seq to identify downstream targets of the m⁶A demethylase ALKBH5 in macrophages. Bone marrow-derived macrophages from myeloid-specific Alkbh5 knockout and Alkbh5-fl/fl littermate control mice were polarized to the M1 phenotype with LPS and IFN-γ. m⁶A-enriched RNA was immunoprecipitated using an anti-m⁶A antibody and sequenced on an Illumina NovaSeq 6000 platform. Altered m⁶A peaks in Alkbh5-KO cells were predominantly located within coding sequences, 3′ untranslated regions, and regions near stop codons. Integrative analysis with RNA-seq identified genes with both altered m⁶A methylation and differential expression, revealing the m⁶A epitranscriptomic landscape regulated by ALKBH5 in M1-polarized macrophages.

ORGANISM(S): Mus musculus

PROVIDER: GSE337112 | GEO | 2026/09/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

MeRIP-seq of Alkbh5/Mettl3 knockout Bone marrow-derived macrophages

Project description:Alkbh5/Mettl3loxp/loxp mice were crossed with Lyz2-Cre mice to generate macrophage-specific conditional knockout mice for Alkbh5/Mettl3. Bone marrow-derived macrophages (BMDMs) were isolated from these mice, and MeRIP-seq was performed to investigate the impact of the knockout on RNA N6-Methyladenosine

2025-07-16 | GSE274791 | GEO

GS1 Cytokine Array Analysis of Primary Human Macrophages Polarized to M0, M1, M2, 14P-TAM, and 14P-RT TAM states

Project description:A comparative analysis of 20 analytes from matched primary macrophages polarized to various states was performed to characterize a novel polarization method and compare it to classically polarized M0, M1, and M2 macrophages. Macrophages polarized by the xenoline JX14P and its matched in vivo radiation-selected variant, JX14P-RT, exhibited cytokine expression profiles distinct from M0, M1, and M2 macrophages. Furthermore, macrophages polarized by JX14P exhibit distinct cytokine profiles compared to those polarized by the matched RT-selected xenoline JX14P-RT.

2025-12-31 | E-MTAB-15227 | biostudies-arrayexpress

Transcription profiling of human monocytes cultured in the presence of M-CSF for 7 days and polarized to M1 or M2 cells to characterize human monocyte-to-macrophage differentiation and polarization

Project description:Monocytes mature to macrophages in the presence of the lineage determining cytokine M-CSF. They can be further polarized into M1 or M2 macrophages with distinct functional properties. We used microarrays to detail the global programme of gene expression underlying macrophage maturation and polarization and identified distinct classes of up-regulated genes during this process. Experiment Overall Design: Freshly isolated monocytes were cultured in the presence of M-CSF for 7 days, and then polarized to M1 or M2 cells. The study includes Monocytes at day 0, macrophages at day 3 and 7, M1 and m2 polarized macrophages.

2007-11-02 | E-GEOD-5099 | biostudies-arrayexpress

ALKBH5 is a New Mammalian RNA Demethylase

Project description:N6-methyladenosine (m6A) is the most prevalent internal modification of messenger RNA (mRNA) in higher eukaryotes. Here we report ALKBH5 as a new mammalian demethylase that oxidatively removes the m6A modification in mRNA in vitro and inside cells. This demethylation activity of ALKBH5 significantly affects mRNA export and RNA metabolism as well as the assembly of mRNA processing factors in nuclear speckles. Alkbh5-deficient male mice are characterized by impaired fertility resulting from apoptosis that affects meiotic metaphase-stage spermatocytes. In accordance with this defect, we have identified in mouse testes 1552 differentially expressed genes which cover broad functional categories and include spermatogenesis-related mRNAs involved in the p53 functional interaction network. We show that Alkbh5-deficiency impacts the expression levels of some of these mRNAs, supporting the observed phenotype. The discovery of this new RNA demethylase strongly suggests that the reversible m6A modification plays fundamental and broad functions in mammalian cells. RNA-seq in two cell types

2013-02-15 | E-GEOD-40132 | biostudies-arrayexpress

MeRIP-seq comparison of Alkbh5 knockout AT2 cells

Project description:We performed RNA sequencing on FACS-purified alveolar type II (AT2) cells isolated from Alkbh5 conditional knockout mice and littermate controls. AT2 cells were collected 14 days after bleomycin-induced lung injury. The MeRIP-seq dataset captures transcriptional changes associated with Alkbh5 deletion in AT2 cells, including the observed upregulation of Amphiregulin (Areg). These data provide a resource for analyzing gene expression programs in regenerating alveolar epithelium.

2026-04-29 | GSE312382 | GEO

MeRIP-seq profiling of m⁶A modifications in Alkbh5-KO and control bone marrow-derived macrophages following M1 polarization

Project description:MeRIP-seq profiling of m⁶A modifications in Alkbh5-KO and control bone marrow-derived macrophages following M1 polarization

| PRJNA1484068 | ENA

Microarray of non-polarized and M1- and M2-polarized canine macrophages in vitro

Project description:Unstimulated (M0), M1-polarized (GM-CSF, LPS, IFNÎ³-stimulated), and M2-polarized (M-CSF, IL-4-stimulated) canine blood-derived macrophages were generated in vitro and investigated for differences in their transcriptome to create a basis for future investigations upon the role of macrophage polarization in dogs, a species, which has emerging importance for translational research.

2017-08-10 | E-MTAB-5458 | biostudies-arrayexpress

Identification of ALKBH5 targets in osteosarcoma by methyl RNA immunoprecipitation [MeRIP-seq]

Project description:To identify potential target mRNAs that are demethylated by ALKBH5, meRIP-seq with a m6A antibody was conducted in 143B osteosarcoma cells transfected with scrambled or ALKBH5-siRNA.

2022-06-28 | GSE154529 | GEO

RNA-seq analysis identifies regulators of macrophage reprogramming from M2 to M1-like phenotype

Project description:We analyzed expression profiles of thioglyolate elicted peritoneal exudate cells (peritoneal macrophages). Peritoneal macrophages were polarized into M1 and M2 macrophages by activation with IFNgamma+ LPS and Il4, respectively. We predicted a gene-regulatory network, which consists of four transcription factors (E2f1,Myc, Stat6, Pparg) regulating metabolic genes, M1 and M2-associated genes. The predicted regulators were all active in M2 macrophages. We hypothesized that these transcription factors are essential regulators to maintain M2 phenotype. To further validate our findings, we treated M2-polarized macrophages with siRNA-pools targeting E2f1, Myc, Stat6 and Pparg. In this study, we observed a switch towards an M1-like phenotype after transfection of siRNA-pools. In addition, Inflammatory pathways were upreguated while fatty acid metabolism was down regulated.

2020-01-27 | GSE129253 | GEO

Identification of downregulated microRNA in a gastric cancer cell line co-cultured with M1- or M2-polarized macrophage

Project description:We showed that co-culture with TAMs triggered Bmi1 expression in gastrointestinal cancer cell lines. miRNAs have been found to target various oncogenes and tumor suppressors. We therefore hypothesized that the regulation of Bmi1 expression in gastrointestinal cancer cells may be mediated by miRNAs using miRNA microarray analysis. THP-1 cells were seeded in the transwell inserts (3540, Corning) for 6-well plates (1 M-CM-^W 106 cells/well). For preparation of M1-polarized THP-1 macrophages, 320 nM phorbol myristate acetate (PMA) was added to THP-1 cells for 6 h, followed by PMA plus 20 ng/ml interferon (IFN)-M-NM-3 and 100 ng/ml lipopolysaccharide for the following 18 h. For preparation of M2-polarized THP-1 macrophages, 320 nM PMA was added to THP-1 cells for 6 h, followed by PMA plus 20 ng/ml interleukin (IL)-4/IL-13 for the following 18 h. After three washes to remove cytokines, M1- or M2-polarized THP-1 macrophages were co-cultured in upper inserts with AGS cells in 6-well plates (1 M-CM-^W 105 cells/well) without direct contact, in each medium without 10% FBS as described above. After 24 h of co-culture, the upper inserts containing macrophages were discarded. AGS cells were collected and analyzed to identify downregulated microRNA in a gastric cancer cell line co-cultured with M1- or M2-polarized macrophage.

2013-09-05 | E-GEOD-50601 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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