TUBE pulldown of K63 ubiquitylated proteins from phagosomes
Ontology highlight
ABSTRACT:
INSTRUMENT(S):
ORGANISM(S): Mus Musculus (mouse)
TISSUE(S): Cell Culture, Macrophage
SUBMITTER: 
Matthias Trost
LAB HEAD: Matthias Trost
PROVIDER: PXD010478 | Pride | 2019-03-22
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Manman_TAB2IP_MUT_1.raw | Raw | |||
| Manman_TAB2IP_MUT_2.raw | Raw | |||
| Manman_TAB2IP_MUT_3.raw | Raw | |||
| Manman_TAB2IP_WT_1.raw | Raw | |||
| Manman_TAB2IP_WT_2.raw | Raw |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Proteomics of carboxylated polystyrene bead (1.0 um) phagosomes from murine bone marrow-derived macrophages. cells were either resting or treated with 100 U/ml IFN-γ (PeproTech) and 100 ng/ml LPS (Sigma) for 24 h, 20 ng/ml Interleukin-4 (IL4) (BD Pharmingen) for 48 h, 20 ng/ml Interleukin-13 (IL13), 10 ng/ml Interleukin-10 (IL10)for 48 h or Reprogrammed (IL4 was incubated with BMDMs for 24 h, and the medium was replaced with fresh medium containing IFN-γ/LPS to incubate for another 24 h). Phagosomes were isolated after 30 min bead inoculation.
2019-03-22 | PXD004520 | Pride
Project description:We developed a new sequencing assay to track the de novo deposition of the histone H3 variants H3.1 and H3.3 during S phase. We use cells stably expressing H3.1-SNAP or H3.3-SNAP, and synchronize them in G1/S by double-thymidine block. The SNAP-tag enables to discriminate newly synthesized histones from preexisting ones, via a quench-chase-capture strategy. We applied this strategy to isolate new H3.1 and H3.3 after releasing cells into S phase, and probed their distribution by MNase digestion and sequencing. We could thus characterize H3.1 and H3.3 dynamics from early to mid S phase at genome-wide resolution. We further applied our method to investigate the consequences of perturbations upon deletion of the H3.3 chaperone HIRA. We used HIRA knockout and control cells, and compared H3.1 and H3.3 distribution to early replication patterns by EdU labeling and sequencing of nascent DNA.
2022-03-31 | E-MTAB-10619 | biostudies-arrayexpress
Project description:This dataset contains ChIP-seq data of H3K4me3 and Pol III in single cell-derived control and CRISPR/Cas9 induced tRNA gene deletion clones in human cancer cell lines HAP1 and HepG2. In this study, we looked into functional Cas9-induced on-target genomic alteration in our tRNA gene deletion clones, HAP1 t72 and HepG2 t15.
2022-09-16 | E-MTAB-10651 | biostudies-arrayexpress
Project description:This dataset contains ChIP-seq data profiling genomic binding of H3K27ac and H3K4me3 in single cell-derived control, as well as CRISPR/Cas9 induced tRNA gene deletion clones and intergenic region deletion clones in human cancer cell lines HAP1. In this study, we found a large genomic deletion of 10q23 in Cas9 modified clones and further investigate the effect of H3K27ac binding.
2023-10-24 | E-MTAB-11859 | biostudies-arrayexpress
Project description:In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems. Results We find radically different conformations for the two female mouse X chromosomes. The inactive X has two superdomains of frequent intrachromosomal contacts separated by a boundary/hinge region. Comparison with the recently reported bipartite 3D structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the hinge is conserved and located near the Dxz4/DXZ4 locus. In mouse, the hinge region also contains a minisatellite Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation, compared to the active alleles and to genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele. Conclusions By applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing. Examination of Nucleophosmin-binding profiles in male and female mouse livers
2015-08-11 | E-GEOD-71903 | biostudies-arrayexpress
Project description:Current human reproductive risk assessment methods rely on semen and serum hormone analyses, which are not easily comparable to the histopathological endpoints and mating studies used in animal testing. Because of these limitations, there is a need to develop universal evaluations that reliably reflect male reproductive function. We hypothesized that toxicant-induced testicular injury can be detected in sperm using mRNA transcripts as indicators of insult. To test this, we exposed adult male Fischer 344 rats to low doses of model testicular toxicants and classically characterized the testicular injury while simultaneously evaluating sperm mRNA transcripts from the same animals. Overall, this study aimed to: 1) identify sperm transcripts altered after exposure to the model testicular toxicant, 2,5-hexanedione (HD) using microarrays; 2) expand on the HD-induced transcript changes in a comprehensive time course experiment using qRT-PCR arrays; and 3) test these injury indicators after exposure to another model testicular toxicant, carbendazim (CBZ). Microarray analysis of HD-treated adult Fischer 344 rats identified 128 altered sperm mRNA transcripts when compared to control using linear models of microarray analysis (q < 0.05). All transcript alterations disappeared after 3 months of post-exposure recovery. In the time course experiment, time-dependent alterations were observed for 12 candidate transcripts selected from the microarray data based upon fold change and biological relevance, and 8 of these transcripts remained significantly altered after the 3-month recovery period (p < 0.05). In the last experiment, 8 candidate transcripts changed after exposure to CBZ (p < 0.05). The two testicular toxicants produced distinct molecular signatures with only 4 overlapping transcripts between them, each occurring in opposite directions. Overall, these results suggest that sperm mRNA transcripts are indicators of low dose toxicant-induced testicular injury in the rat. Rats were exposed to sub-chronic low doses of the Sertoli cell toxicant 2,5-hexanedione (HD) or water (control for HD) for 3 months. Some rats in each group underwent 3 months of post-exposure recovery.
2012-09-01 | E-GEOD-34641 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) is one of the most abundant modifications in eukaryotic RNA. Recent mapping of m6A methylomes in mammals, yeast, and plants as well as characterization of m6A methyltransferases, demethylases, and binding proteins have revealed regulatory functions of this dynamic RNA modification. In bacteria, although m6A is present in ribosomal RNA (rRNA), its occurrence in messenger RNA (mRNA) still remains elusive. Here, we used liquid chromatography-mass spectrometry (LC-MS) to calculate the m6A/A ratio in mRNA from a wide range of bacterial species, which demonstrates that m6A is an abundant mRNA modification in tested bacteria. Subsequent transcriptome-wide m6A profiling in Escherichia coli and Pseudomonas aeruginosa revealed a conserved distinct m6A pattern that is significantly different from that in eukaryotes. Most m6A peaks are located inside open reading frames (ORF), and carry a unique consensus motif (GCCAU). Functional enrichment analysis of bacterial m6A peaks indicates that the majority of m6A-modified transcripts are associated with respiration, amino acids metabolism, stress response, and small RNAs genes, suggesting potential regulatory roles of m6A in these pathways. m6A profiling in E.coli and P.aeruginosa mRNA
2015-07-08 | E-GEOD-65347 | biostudies-arrayexpress
Project description:H. volcanii Cdc48a, RecJ3/4 and RNase J associate with Ubl-coated beads. A) Strategy to isolate H. volcanii proteins that bind agarose beads charged with monomeric Ubl (vs. BSA) as bait. Cell lysate was from triplicate cultures of H. volcanii NH02-pJAM957. B) Left, Non-reducing SDS-PAGE of H. volcanii proteins that bound BSA- (control, lane 1) vs. Ubl- (lane 2) decorated beads in the presence of ATP. Gels were stained with SYPRO Ruby. Red bar, HMW(250kDa) and LMW(50kDa) (high and low molecular weight) regions of gel excised from lanes 1 and 2 for LC- MS/MS analysis. Right, Proteins identified at > 99.9% probability and < 0.1 % false discovery rate (FDR) in the Ubl (not BSA) samples. Similar trend was observed in independent experiment. ATP was required for this association. Theor. Mr, theoretical molecular mass based on genome sequence. Normalized total spectra of sample minus control is indicated.
2023-06-22 | PXD019897 | Pride
Project description:Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed M-bM-^@M-^XOhnoM-bM-^@M-^Ys hypothesisM-bM-^@M-^Y). To identify molecular mechanisms of X upregulation in mammals we established genome-wide profiles for the initiation and elongation forms of RNA polymerase II (PolII), PolII-S5p (phosphorylated at serine 5) and PolII-S2p (phosphorylated at serine 2), and for histone modifications in mouse cell lines and tissues. We found that in addition to being enriched in PolII-S5p but not in PolII-S2p, X-linked promoters were also enriched in two epigenetic marks, H4K16ac and H2AZ, dependent on expression levels. To address the function of the H4K16 acetyltransferase MOF occupancy profiles were established and knockdowns of MOF and MSL1 were done in mouse ES cells. Our results support a conserved role for the MSL complex to enhance transcription initiation of X-linked genes. Comparison of the profiles of RNA PolII, the H4K16ac acetyltransferase MOF and histone active marks on the X versus autosomes in mouse
2013-03-05 | E-GEOD-44835 | biostudies-arrayexpress
Project description:Myxococcus xanthus is a model organism to study the biosynthesis and secretion of polysaccharides. The exopolysaccharide (EPS) is synthesized and exported via the Wzx/Wzy-dependent EPS pathway. The phosphoglycosyl transferase EpsZ initiates EPS biosynthesis by transferring galactose-1-P to undecaprenyl phosphate. EPS biosynthesis is stimulated by the Dif chemosensory system through the single-domain response regulator EpsW, which is activated through phosphorylation by the DifE kinase. Importantly, the mechanism by which EpsW~P activates EPS biosynthesis is unknown. To investigate if EpsW regulates EPS biosynthesis at the transcriptional level, we extracted total RNA from vegetative cells of the wildtype and the ΔepsW mutant. Moreover, we extracted total RNA from vegetative cells of the ΔepsZ and ΔdifE mutants to investigate the effects of EpsZ and DifE on the transcriptome.
2025-02-01 | E-MTAB-14794 | biostudies-arrayexpress