Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

LinX - software for evaluation of CX-MS data

ABSTRACT: Chemical cross-linking mass spectrometry data from analysis of N14/N15 labeled proteins

INSTRUMENT(S): ultraflex

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

SUBMITTER: Zdenek Kukacka

LAB HEAD: Petr Novak

PROVIDER: PXD023522 | Pride | 2021-03-11

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	FOXO_DAF-16_tPt_Tg_EtMorf_agiTrap_10mM_AMBIC_FG_13072017_5115.mzXML	Mzxml
	FOXO_DAF-16_tPt_Tg_EtMorf_agiTrap_10mM_AMBIC_FG_13072017_5115_1_LCMSexport_search_woBal.sen	Other
	Foxo.fasta	Fasta
	LEDG.fasta	Fasta
	LEDG_Ctrl.mzXML	Mzxml

Items per page:

1 - 5 of 39

Publications

LinX: A Software Tool for Uncommon Cross-Linking Chemistry.

Kukačka Zdeněk Z Rosůlek Michal M Jelínek Jan J Slavata Lukáš L Kavan Daniel D Novák Petr P

Journal of proteome research 20210303 4

Chemical cross-linking mass spectrometry has become a popular tool in structural biology. Although several algorithms exist that efficiently analyze data-dependent mass spectrometric data, the algorithm to identify and quantify intermolecular cross-links located at the interaction interface of homodimer molecules was missing. The algorithm in LinX utilizes high mass accuracy for ion identification. In contrast with standard data-dependent analysis, LinX enables the elucidation of cross-linked pe ...[more]

PMID: 33657806

Similar Datasets

Identifying crossover locations in Arabidopsis thaliana asy1/+ Col × Ler F2 populations using genotyping-by-sequencing

Project description:Genomic DNA from 191 asy1/+ Col x Ler F2 individuals was extracted using CTAB and used to generate sequencing libraries as described (Lawrence et al, 2019 Current Biology). Sequencing data was analysed to identify crossovers using the TIGER pipeline as previously described (Rowan et al, 2015 G3 (Bethesda); Yelina et al, 2015 Genes & Dev; Lawrence et al, 2019 Current Biology).

2020-05-18 | E-MTAB-8725 | biostudies-arrayexpress

Autophagosome content profiling - STAR Protocol Data Set

Project description:The ascorbate peroxidase APEX2 is commonly used to study the neighborhood of a protein of interest by proximity-dependent biotinylation. Here, we describe a protocol for sample processing compatible with immunoblotting and mass spectrometry that is suitable to specifically map the content of autophagosomes and potentially other transient vesicles without the need of subcellular fractionation. By combining live-cell biotinylation with proteinase K digestion of cell homogenates, proteins enriched in membrane-protected compartments can be readily enriched and identified.

2021-04-06 | PXD024335 | Pride

Identification of SENP5 target proteins by endogenous SUMO2/3 IP-MS

Project description:Ribosome biogenesis is a complex and energy demanding process requiring tight coordination with cell growth and proliferation. Impairment of ribosome biogenesis activates a well-defined cell-cycle checkpoint that primarily relies on the activation of p53 signaling. However, there is mounting evidence that p53-independent signaling networks connect impaired ribosome biogenesis to cell cycle-checkpoints. So far, however, these pathways have remained largely enigmatic. By characterizing the nucleolar SUMO isopeptidase SENP3 and SENP5 we found that both isopeptidases control the SUMOylation state of specific ribosome biogenesis factors and regulate the 60S and 40S ribosome maturation pathways. Accordingly, inactivation of SENP3 and SENP5 induces a canonical p53-mediated G1/S arrest. Intriguingly, however, we discovered that inactivation of SENP3 or SENP5 drastically and specifically downregulates the expression of the key-cell cycle regulator CDK6 in a p53-independent process. Accordingly, depletion of SENP3 or SENP5 impairs G1/S transition and cell proliferation in both p53-proficient and p53-deficient cells. Strikingly, we further revealed that impaired ribosome maturation induced by depletion of a panel of ribosome biogenesis factors or by chemical inhibition of RNA polymerase I, generally triggers loss of CDK6 independent of the cellular p53 status. Altogether our data unveil a long-sought p53-independent checkpoint of impaired ribosome biogenesis. Since CDK6 represents a dependency in a subset of cancer entities, such as AML and lymphoma, we propose that this checkpoint can serve as an actionable drug target in tumor therapy.

2023-10-28 | PXD037796 | Pride

Secretome characterization of nucleus pulposus (NP) cells subjected to ER stress

Project description:Objective: Induction of ER stress has been shown to promote NP cell apoptosis and disc degeneration. However, little is known about its regulation by hypoxia and its contribution to extracellular matrix homeostasis. Methods: NP cells were culture under hypoxia (1% O2) and normoxia (21% O2) to assess ER stress status. Tunicamycin and thapsigargin were used to induce canonical ER stress pathways and effects on cell secretome were assessed by proteomic analysis using mass spectrometry. The relevance of these findings to aging and degeneration was investigated by analyzing microarray data of NP tissues from aged mice (GSE134955) and degenerated human discs (GSE70362). Results: NP cells exhibited lower ER stress levels under hypoxia. ER stress inducers tunicamycin and thapsigargin promoted a canonical unfolded protein response. UPR further induced HIF-1 activity under hypoxia. NP cell secretome under ER stress showed an increased secretory pathway with a concomitant decrease in collagens, HAPLN1, and cell adhesion related proteins. Similar to our cell culture studies, NP tissues from aged mice and degenerated human discs presented higher levels of UPR markers and decreased levels of matrix components.

2020-12-03 | PXD019151 | Pride

Role of Fft3 in nuclear organization [MNase-seq]

Project description:In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3M-NM-^T cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements at the borders of subtelomeres and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and components of the nuclear envelope by maintaining chromatin structure required for anchoring DNA insulators to nuclear pores. For MNase samples, duplicate mutant mononucleosome fractions were compared with duplicate WT mononucleosomes.

2015-03-02 | E-GEOD-58012 | biostudies-arrayexpress

Structural analysis of human cis-prenyltransferase

Project description:Isoprenoids are synthesized by the prenyltransferases superfamily, which is subdivided according to the product stereoisomerism and length. In short- and medium-chain isoprenoids, product length correlates with active site volume. However, enzymes synthesizing long-chain products and rubber synthases fail to conform to this paradigm, due to an unexpectedly small active site. Here, we focused on the human cis-prenyltransferase complex (hcis-PT), residing at the endoplasmic reticulum membrane and playing a crucial role in protein glycosylation. Crystallographic investigation of hcis-PT along the reaction cycle revealed an outlet for the elongating product. Hydrogen-deuterium exchange mass spectrometry analysis showed that the hydrophobic active site core is flanked by dynamic regions consistent with separate inlet and outlet orifices. Finally, using a fluorescence substrate analog, we show that product elongation and membrane association are closely correlated. Together, our results support direct membrane insertion of the elongating isoprenoid during catalysis, uncoupling active site volume from product length.

2022-06-09 | PXD031707 | Pride

N-terminal acetylation of yeast NAT-A mutants

Project description:Protein-protein interactions are fundamental to all cellular activities, with the ribosome increasingly recognized as a central platform steering the dynamics of nascent-chain interactions. In our focus on conserved N-terminal acetyltransferases (NATs), we identified distinct co-translational assembly pathways. This distinction persisted even among highly homologous subunits, with some playing contrasting roles. Notably, we found that only a few residues act as “hotspots”, initiating co-translational assembly interactions as they emerge from the ribosome exit tunnel. The significance of these hotspots was further validated in vivo through N-terminomics studies.

2024-06-22 | PXD048082 | Pride

RNAseq of epidermis reconstructed from TSG-6-/- and TSG-6+/+ immortalized N/TERT keratinocytes and stimulated or not with interleukins 4 and 13 for 48h

Project description:TNFα-stimulated gene 6 (TSG-6) is an anti-inflammatory protein. In human epidermis, TSG-6 is secreted in extracellular matrix where it interacts with hyaluronan (HA). However, their functions are not well understood. In this study, immortalized N/TERT keratinocytes were edited by CRISPR/Cas9, used to reconstruct in vitro epidermis (RHE) and stimulated or not with interleukins 4 and 13 for 48h to mimic atopic dermatitis (AD). Two TSG-6-/- clones (respectively TSG-6-/- (a) and TSG-6-/- (b)) harboring major deletions in both alleles were selected and compared to TSG-6+/+ cells. Epidermis reconstructed from TSG-6-/- (a) and TSG-6-/- (b) exhibit normal differentiation process and morphology but show an increased HA leakage in the underlying culture medium of both TSG-6-/- RHE compared to TSG-6+/+ tissues, especially in conditions that mimic AD. While IL-4/13 treatment of RHE induces regulation of genes associated with AD, the absence of TSG-6 don’t seem to show any major transcriptomic regulation.

2021-12-30 | E-MTAB-10095 | biostudies-arrayexpress

Mtf2 is a methylation-sensitive DNA-binding recruiter of Polycomb

Project description:Polycomb repression of gene expression is critical for development, with a pivotal role for trimethylation of lysine 27 of histone H3 (H3K27me3) deposited by Polycomb Repressive Complex 2 (PRC2). While the function and regulation of PRC2 have been extensively studied, the mechanism(s) by which it is recruited to specific genomic targets has remained largely elusive, in particular in vertebrates. Here we identify the PRC2-associated protein Mtf2 as a novel DNA methylation-sensitive PRC2 recruiter in mouse embryonic stem cells (mESCs). Mtf2 directly binds to DNA and is essential for recruitment of PRC2 both in vitro and in vivo. Genome-wide recruitment of the PRC2 catalytic subunit Ezh2 to genomic targets is drastically impaired in Mtf2 knock-out mESCs, resulting in largely reduced H3K27me3 deposition. Mtf2 selectively binds regions with high density of closely spaced unmethylated CpG-containing motifs with a locally unwound helical structure. This binding is dependent on one of the Mtf2 PHD domains, a protein domain shared among Pcl homologs, and an Mtf2-specific domain. The sequences bound by Mtf2 are enriched in PRC2-repressed CpG island-containing targets in zebrafish, Xenopus, mouse and human, suggesting that Mtf2-mediated PRC2 recruitment to unmethylated genomic regions is conserved among vertebrates.

2018-05-07 | PXD005821 | Pride

T cells of colorectal cancer patients’ stimulated by neoantigenic and cryptic peptides better recognize autologous tumor cells

Project description:Immunopeptidome analysis of patient-derived colorectal cancer cell lines HROC113 and HROC285 T0 M2 from the HROC collection [Mullins et al. Cancers (Basel). 2019;11(10):1520. doi: 10.3390/cancers11101520] was performed to characterize the natural HLA class I presented ligandome in native as well as IFNγ treated cells.

2023-03-11 | PXD037587 | Pride

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