Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ubiquitination Proteome of heat-killed MTB stimulated Thp-1-derived macrophages

ABSTRACT: This project analyzed the ubiquitination proteome of heat-killed MTB stimulated and unstimulated macrophages.

ORGANISM(S): Homo Sapiens

SUBMITTER: Binwu Ying

PROVIDER: PXD039906 | iProX | Tue Feb 07 00:00:00 GMT 2023

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

From tuberculosis bedside to bench: UBE2B splicing as a potential biomarker and its regulatory mechanism.

Lyu Mengyuan M Zhou Jian J Zhou Yanbing Y Chong Weelic W Xu Wei W Lai Hongli H Niu Lu L Hai Yang Y Yao Xiaojun X Gong Sheng S Wang Qinglan Q Chen Yi Y Wang Yili Y Chen Liyu L Zengwanggema Zeng Jiongjiong J Wang Chengdi C Ying Binwu B

Signal transduction and targeted therapy 20230224 1

Alternative splicing (AS) is an important approach for pathogens and hosts to remodel transcriptome. However, tuberculosis (TB)-related AS has not been sufficiently explored. Here we presented the first landscape of TB-related AS by long-read sequencing, and screened four AS events (S100A8-intron1-retention intron, RPS20-exon1-alternaitve promoter, KIF13B-exon4-skipping exon (SE) and UBE2B-exon7-SE) as potential biomarkers in an in-house cohort-1. The validations in an in-house cohort-2 (2274 sa ...[more]

PMID: 36828823

Similar Datasets

Nascent-protein ubiquitination is required for heat shock-induced gene downregulation in human cells.

Project description:Proteotoxic stress such as heat shock causes heat-shock factor (HSF)-dependent transcriptional upregulation of chaperones. Heat shock also leads to a rapid and reversible downregulation of many genes, a process we term stress-induced transcriptional attenuation (SITA). The mechanism underlying this conserved phenomenon is unknown. Here we report that enhanced recruitment of negative transcription elongation factors to gene promoters in human cell lines induces SITA. A chemical inhibitor screen showed that active translation and protein ubiquitination are required for the response. We further find that proteins translated during heat shock are subjected to ubiquitination and that p38 kinase signaling connects cytosolic translation with gene downregulation. Notably, brain samples of subjects with Huntington's disease also show transcriptional attenuation, which is recapitulated in cellular models of protein aggregation similar to heat shock. Thus our work identifies an HSF-independent mechanism that links nascent-protein ubiquitination to transcriptional downregulation during heat shock, with potential ramifications in neurodegenerative diseases.

2019-02-07 | GSE112379 | GEO

Expression data from mouse bone marrow derived macrophages

Project description:To understand the effect of LPS on macrophages, macrophages were stimulated with LPS and the gene expressions were analyzed by microarray.

2022-11-01 | GSE167853 | GEO

Transcription profiling of human macrophages from Crohns disease patients or healthy control individuals, either unstimulated or stimulated with heat killed E. coli;

Project description:Comparison of gene expression in macrophages from Crohn's disease patients or healthy control individuals, either unstimulated or stimulated with heat killed E. coli

2009-08-03 | E-TABM-733 | biostudies-arrayexpress

Transcription profiling of human macrophages from ulcerative colitis patients or healthy control individuals, either unstimulated or stimulated with heat killed E. coli

Project description:Comparison of gene expression in macrophages from ulcerative colitis patients or healthy control individuals, either unstimulated or stimulated with heat killed E. coli

2009-08-03 | E-TABM-734 | biostudies-arrayexpress

Gene expression from bone-marrow derived macrophages.

Project description:Gene expression from WT and NFAT5 KO primary macrophage cultures. Keywords: Bone-marrow derived macrophages. We analyzed 4 arrays from each condition: unstimulated WT BMDMs, LPS stimulated WT BMDMs, unstimulated KO BMDMs, LPS stimulated KO BMDMs.

2012-01-20 | E-GEOD-26343 | biostudies-arrayexpress

Transcription profiling of human monocyte-derived macrophages treated with IFN alpha

Project description:To study effects of IFNalpha treatment on monocyte-derived macrophages which may influence susceptibility or resistance to HIV. Experiment Overall Design: Human monocyte-derived macrophages were stimulated with IFNalpha and analyzed for global gene expression.

2009-07-05 | E-GEOD-16755 | biostudies-arrayexpress

Ubiquitination-proteomics in mouse primary macrophages

Project description:To determine all ubiquitination modified proteins and corresponding ubiquitinated sites, we performed di-Gly LC/MS in mouse primary macrophages (MG132-treated).

2023-10-06 | PXD045946 | iProX

RNA-seq of M-CSF differentiated human peripheral monocyte-derived macrophages (MDMs) - Validation macIDR

Project description:Macrophages represent multifunctional leukocytes defined by their stimulus-specific transcriptional reprogramming. As in vivo macrophages are often difficult to obtain, in vitro macrophage models are often used. We aggregated public expression data to define consensus expression profiles for eight commonly-used in vitro macrophage models and built the classifier macIDR, capable of distinguishing macrophage subsets with high accuracy (>0.95). Classification of in vivo macrophages suggested that alveolar macrophages resembled interleukin-10 activated macrophages in general whereas chronic obstructive pulmonary disease patients displayed decreased similarity to interferon-γ stimulated macrophages. Adipose tissue-derived macrophages were classified as unstimulated macrophages, but would resemble LPS-stimulated macrophages more in diabetic-obese patients. Rheumatoid arthritic synovial macrophages were similar to macrophages stimulated with interleukin-10 or interferon-γ. Altogether, our results suggest that macIDR is capable of identifying in vitro macrophages. By projecting in vivo macrophages onto the in vitro macrophages, we were capable of elucidating macrophage-specific changes as a result of tissue and disease.

| EGAS00001003451 | EGA

Comparison of transcriptional response of induced pluripotent stem iPS cell derived and monocyte derived macrophages to bacterial lipopolysaccharide stimulation

Project description:In the first part of this project, we will differentiate IPS cells from 5 human donors into macrophages, and extract RNA from unstimulated and LPS stimulated macrophages to perform RNA sequencing. We will also extract RNA before and after stimulation in blood- derived macrophages from 5 additional, unrelated healthy samples. In the second part of the project, RNA-seq data will be analysed to compare LPS response of these two macrophage populations. In summary, we will perform 75bp PE RNA-seq on 20 samples (10 pre and post stimulus), on the HiSeq 2500 platform. Samples will be multiplexed at 5 samples / lane, so we will require 4 flow cells in total.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2016-05-17 | E-ERAD-192 | biostudies-arrayexpress