Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide EGR1 chromatin occupancy in wild-type C57BL/6J bone-marrow–derived macrophages measured by CUT-taq

ABSTRACT: This study generated CUT-taq (tagmentation-based in situ ChIP; CUT&Tag-like) sequencing data to profile genome-wide EGR1 chromatin binding in mouse bone-marrow–derived macrophages (BMDMs). BMDMs were differentiated from wild-type C57BL/6J bone marrow in GM-CSF for 7 days, harvested at 4.0 × 10^5 cells per sample, and processed using the Hyperactive™ In-Situ ChIP Library Prep Kit for Illumina (Vazyme TD901–TD902). Cells were immobilized on concanavalin A beads, permeabilized with digitonin, incubated with anti-EGR1 primary and secondary antibodies (Thermo), and tagmented with Hyperactive pA-Tn5 (Vazyme). Libraries were PCR-amplified with P5/P7 primers, quality-checked on an Agilent 2100 Bioanalyzer, and sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp). Raw sequencing files (FASTQ) and processed data files are provided to enable reuse and reanalysis of EGR1 binding profiles in GM-CSF–differentiated macrophages.

ORGANISM(S): Mus musculus

PROVIDER: GSE318298 | GEO | 2026/02/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

EGR1 is a gatekeeper of inflammatory enhancers in human macrophages

Project description:We investigated the function of EGR1 in macrophage differentiation and activation. We generated EGR1 CHIP-seq and CUT-and-RUN data during GM-CSF induced macrophage differentiation, paired with ATAC-seq. We performed RNA-seq and CHIP-seq for H3K27ac in EGR1-depleted differentiated macrophages. Finally we generated RNA-seq data in activated macrophages with EGR1 overexpression.

2020-01-01 | GSE136216 | GEO

Mouse bone marrow derived macrophages

Project description:Bone marrow cells (BM) were isolated and primed with M-CSF (M BMDM) or GM-CSF (GM BMDM) for 7 days. M-BMDMs were treated with IL6 (20 ng/ml) for 3 h or 24 h while GM-BMDMs were treated for 3 h. The difference between BM, M-BMDM, and GM-BMDM were analyzed to describe the phenotye and function of each population. Moreover, by RNA-seq analysis, the influence of IL6 treatment on GM-BMDMs and M-BMDMs were analyzed.

2022-10-31 | GSE179637 | GEO

Integrated transcriptomic and metabolomic analysis reveals the metabolic programming of GM-CSF-and M-CSF-differentiated mouse macrophages

Project description:Macrophages play a critical role in the inflammatory response and tumor development. Macrophages are primarily divided into pro-inflammatory M1-like and anti-inflammatory M2-like macrophages based on their activation status and functions. In vitro macrophage models could be derived from mouse bone marrow cells stimulated with two types of differentiation factors: GM-CSF (GM-BMDMs) and M-CSF (M-BMDMs), to represent M1-and M2-like macrophages, respectively. Since macrophage differentiation requires coordinated metabolic reprogramming and transcriptional rewiring in order to fulfill their distinct roles, we combined both transcriptome and metabolome analysis, coupled with experimental validation, to gain insight into the metabolic status of GM-and M-BMDMs. The data revealed higher levels of the tricarboxylic acid cycle (TCA cycle), oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO), and urea and ornithine production from arginine in GM-BMDMs, and a preference for glycolysis, fatty acid storage, bile acid metabolism, and citrulline and nitric oxide (NO) production from arginine in M-BMDMs. Correlation analysis with the proteomic data showed high consistency in the mRNA and protein levels of metabolic genes. Similar results were also obtained when compared to RNA-seq data of human monocyte derived macrophages from the GEO database. Furthermore, canonical macrophage functions such as inflammatory response and phagocytosis were tightly associated with the representative metabolic pathways. In the current study, we identified the core metabolites, metabolic genes, and functional terms of the two distinct mouse macrophage populations. We also distinguished the metabolic influences of the differentiation factors GM-CSF and M-CSF, and wish to provide valuable information for in vitro macrophage studies.

2023-09-19 | MTBLS6502 | MetaboLights

RNAseq analysis of GM-CSF and M-CSF polarized bone marrow derived macrophages cultured on TC or noTC dishes

Project description:Bone marrow cells were isolated, primed with M-CSF (M BMDM) or GM-CSF (GM BMDM) and cultured on tissue culture dishes (TC) or low adherent dishes (noTC) for 7 days. BMDMs were treated with LPS (100 ng/ml) for 3 hours. The difference between TC- and noTC-cultured BMDMs were analyzed to describe the phenotye and function of each population. Moreover, the influence of LPS treatment on GM-BMDMs and M-BMDMs were analyzed.

2022-06-10 | GSE198821 | GEO

CUT&Tag analysis of H3K4me3 and Paxip1 in CRISPR/Cas9-mediated Paxip1 knockout KPC1199 murine PDAC cell line

Project description:To gain mechanistic insight into how Epigenetic factors reprogramming metabolism in response to DON treatment. we performed CUT&Tag sequencing in murine PDAC cells. sgPaxip1 cells were treated in Cont group or DON group , and harvested after 72 hours. CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme). DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme).

2025-03-05 | GSE246545 | GEO

CUT&Tag analysis of H3K4me3, H3K27Ac,H2A119Ub, H3K27me3 and H3K36me3 in KPC1199 murine PDAC cell line

Project description:To gain mechanistic insight into how Epigenetic factors reprogramming metabolism in response to glutamine starvation. we performed CUT&Tag sequencing in murine PDAC cells. KPC1199 cells were treated in Cont group or Low Gln group , and harvested after 72 hours. CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme). DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme).

2024-12-31 | GSE229903 | GEO

Project description:GM-CSF receptor-β deficient (Csf2rb–/– or KO) mice develop a lung disease identical to hereditary pulmonary alveolar proteinosis (hPAP) in humans with recessive CSF2RA or CSF2RB mutations that impair GM-CSF receptor function. We performed pulmonary macrophage transplantation (PMT) of bone marrow derived macrophages (BMDMs) without myeloablation in Csf2rb–/–mice. BMDMs were administered by endotracheal instillation into 2 month-old Csf2rb–/– mice. Results demonstrated that PMT therapeutic of hPAP in Csf2rb–/– mice was highly efficacious and durable. Alveolar macrophages were isolated by bronchoalveolar lavage one year after administration subjected to microarray analysis to determine the effects of PMT therapy on the global gene expression profile.

2014-10-01 | GSE60528 | GEO

CUT&Tag analysis of H3K36me3 and H3K27me3, in Setd2-WT and -KO murine PDAC cell line

Project description:To gain mechanistic insight into how Setd2 loss promotes activation of AKT signaling, we performed CUT&Tag sequencing in PDAC cells (KPC1199) with Setd2-KO and Setd2-WT). Setd2-WT and -KO murine PDAC cells were cultured and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K36me3 and H3K27me3 were employed. Trueprep index kit v2 and v3 for illumina were used to establish DNA library.

2023-02-06 | GSE176013 | GEO

Macrophages heterogeneity in human atherosclerotic plaques

Project description:This study aims to characterize the transcriptional profile of Granulocyte-macrophage colony-stimulating factor induced macrophages (GM-MÃ) and M-CSF macrophages (M-MÃ) and to investigate in situ a subset of genes and their products specific to each phenotype in human atherosclerosis plaques 18 RNG/MRC two-colour oligonucleotide microarrays (Le Brigand et al. 2006) were used to generate global mRNA expression profiles for GM-CSF-induced, M-CSF-induced, and peritoneal macrophages. The microarray experiments were conducted either as a common reference (peritoneal-like macrophages) design or using a direct design by hybridizing Granulocyte-macrophage colony-stimulating factor (GM-CSF)-induced human monocyte-derived macrophage (GM-MÃ) and CSF-induced human monocyte-derived macrophages(M-MÃ) on the same arrays

2010-05-16 | E-GEOD-18275 | biostudies-arrayexpress

CUT&Tag sequencing in PDAC cells with Setd2-KO and Setd2-WT sorted from orthotopic PDAC tumor

Project description:To gain mechanistic insight into how Setd2 loss reprogramming tumor cell metabolism, we performed CUT&Tag sequencing in PDAC cells with Setd2-KO and Setd2-WT sorted from orthotopic PDAC tumor. Setd2-WT and -KO murine PDAC cells were sorted with DAPI-CD45.2-Pdpn-Epcam+ or cultured, and freshly collected as soon as possible. Hyperactive pA-Tn5 Transposase for CUT&Tag kit from Vazyme (TD901), and antibodies against H3K36me3, H3K27Ac and H3K27me3 were employed. Trueprep index kit v2 and v3 for illumina were used to establish DNA library.

2024-08-07 | GSE196241 | GEO

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