Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DIA proteomics on mouse tissue to investigate the GAPDH redox switch

ABSTRACT: The glycolytic enzyme GAPDH is equipped with a redox switch that rapidly and reversibly inactivates the enzyme in the presence of hydrogen peroxide. The physiological implications of the redox switch were investigated in C57BL/6NTac wildtype and GAPDH(T175A) knock-in mice generated by CRISPR/Cas9 genome editing.

INSTRUMENT(S): timsTOF Pro 2

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Heart, Kidney

SUBMITTER: Justus L. Großmann

LAB HEAD: Markus Ralser

PROVIDER: PXD040620 | Pride | 2023-04-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20220518_Mouse-RefProteome_UP000000589_10090.fasta	Fasta
	20220804_PRO2_LS_02_60-0062_kidney_pool_A1_S1-C1_1_3592.d.Zip	Other
	20220804_PRO2_LS_03_60-0062_kidney_1_A2_S1-A2_1_3593.d.Zip	Other
	20220804_PRO2_LS_04_60-0062_kidney_2_B2_S1-B2_1_3594.d.Zip	Other
	20220804_PRO2_LS_05_60-0062_kidney_3_C2_S1-C2_1_3595.d.Zip	Other

Items per page:

1 - 5 of 63

Similar Datasets

RNA-seq analysis of fission yeast wild type and cbf11∆ mutant in standard and ammonium-supplemented complex media

Project description:Transcriptome analyses of the fission yeast Schizosaccharomyces pombe cells lacking the CSL transcription factor cbf11. Wild-type cells were used as a control. Both genotypes were analyzed when grown to exponential phase in the complex YES medium, or in YES supplemented with ammonium chloride. The aim was to identify Cbf11-regulated genes, and cbf11-associated phenotypes are affected by the presence of a good nitrogen source.

2024-04-05 | E-MTAB-13302 | biostudies-arrayexpress

ChIP-nexus analysis of fission yeast transcription factors Cbf11, Cbf11DBM, Cbf12, Cbf12DBM, Mga2 and Fkh2

Project description:Genome-wide identification of transcription factor (TF) binding sites in the genome of the fission yeast Schizosaccharomyces pombe. The ChIP-nexus method was used. TFs included were: Cbf11-TAP and Cbf12-TAP (and their DBM mutants with impaired DNA binding), TAP-Mga2, and Fkh2-TAP (as an irrelevant control TF). IPs from an untagged WT strain were also analyzed. Cbf11-related IPs were performed from exponential cultures, while Cbf12-related IPs were performed from stationary cultures. YES complex medium was used for all cultivations.

2024-04-05 | E-MTAB-13258 | biostudies-arrayexpress

Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics

Project description:Deciphering the intricate tumor-immune interactions within the microenvironment is crucial for advancing cancer immunotherapy. Here, we developed a novel approach integrating highly multiplexed imaging, laser microdissection, and deep visual proteomics to spatially profile the proteomes of 21 distinct cell populations in human colorectal and tonsil cancers with high sensitivity. In colorectal tumors, we uncovered an immunosuppressive macrophage barrier impeding T cell infiltration and regionally altering lymphocyte proteomes. Spatial proteomic analysis revealed distinct functional states of T cells in different tumor compartments. In tonsil cancer, we identified significant tumor cell proteomic heterogeneity influenced by proximity to specific T cell subtypes. Tumor-infiltrating T cells exhibited metabolic adaptations and enhanced stress resilience, enabling migration into hypoxic regions. Our spatially-resolved, highly multiplexed strategy provides a powerful tool to decipher the complex cellular interplay within the tumor microenvironment, with implications for identifying new immunotherapy targets and signatures.

2024-09-16 | PXD051891 | Pride

DNA-seq of an ELMSeq reporter cassette to study impact of C-terminal sequence variations on protein abundance

Project description:A ELMSeq reporter cassette was created to monitor Dam levels by methylation, and introduced in the genome. The regions of 6 nt upstream and 6 nt downstream the stop codon were randomized to study their effect on gene expression. The ELMSeq reporter cassette was composed of: promoter - dam - random N6 - stop codon TAA - random N6 - spacer - 4xGATC. The amplicon was spanning the C-terminal region. The cassette was introduced in Mycoplasma pneumoniae.

2020-05-04 | E-MTAB-8223 | biostudies-arrayexpress

Microarray for transcript expression comparison of normal and Sox18 dominant negative dermal spheres.

Project description:The experiment was designed to identify differential gene expression due to dominant negative mutation of the Sox18 gene in the ragged Opossum spontaneous mouse mutant. Gene expression was analysed after whole RNA isolation in dermal spheres as hair follicle inductive mesenchyme tissue, and was intended to identify gene expression patterns associated with alteration of hair induction post Sox18 mutation.

2017-05-16 | E-MTAB-5673 | biostudies-arrayexpress

A standardized and reproducible workflow for membrane glass slides in routine histology and spatial proteomics

Project description:Defining the molecular phenotype of single cells in-situ is essential for understanding tissue heterogeneity in health and disease. Powerful imaging technologies have recently been joined by spatial omics technologies, promising unparalleled insights into the molecular landscape of biological samples. One approach involves laser microdissection in combination with membrane glass slides for the isolation of single cells from specific anatomical regions for further analysis by spatial omics. However, so far this is not fully compatible with automated staining platforms and routine histology procedures such as heat-induced epitope retrieval, limiting reproducibility, throughput and integration of advanced staining procedures. This study describes a robust workflow for routine use of glass membrane slides, allowing precise extraction of tissue in combination with automated and multicolor immunofluorescence staining. The key advance is the addition of glycerol to standard heat-induced epitope retrieval protocol, preventing membrane distortion while preserving antigen retrieval properties. Importantly, we show that glycerol is fully compatible with mass-spectrometry based proteomics and does not affect proteome depth or quality. Further, we enable single focal plane imaging by removing remaining trapped air pockets with an incision. We demonstrate our workflow using the recently introduced Deep Visual Proteomics technology on the single-cell type analysis of adjacent suprabasal and basal keratinocytes of human skin. Our protocol extends the utility of membrane glass slides and enables much more robust integration with routine histology procedures, high-throughput multiplexed imaging and sophisticated downstream spatial omics technologies.

2023-10-24 | PXD040281 | Pride

Spatial Proteomics of a Human Brain Tumour at 40 Âµm resolution

Project description:The spatial organisation of Cellular protein expression profiles within tissues determines cellular function and are key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially resolved, quantitative proteomics of tissue that generates maps of protein expression across a tissue slice derived from a human atypical teratoid-rhabdoid tumour (AT/RT). We employ spatially-aware statistical methods that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with varying spatial abundance patterns. We identified PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response driven, spatially organized protein networks of the extracellular tumour matrix. Overall, this work informs on methods for spatially resolved deep proteo-phenotyping of tissue heterogeneity, which will push the boundaries of understanding tissue biology and pathology at the molecular level.

2023-10-10 | PXD044714 | Pride

Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to Interferon induction

Project description:Adenosine deaminase acting on RNA 1 (ADAR1), is an enzyme that catalyzes the conversion of adenosine to inosine in double-stranded RNA, a process critical for regulation of innate immune response and distinguishing between ‘self and non-self RNA’. It is expressed as two isoforms: nucleolar p110 and cytoplasmic, interferon (IFN)-inducible, p150. The interactome of the p110 under steady-state conditions is well-studied; however, less is known about the interactions of the p150 isoform, particularly during IFN response. To elucidate ADAR1's protein interactions during IFN stimulation, alongside steady-state conditions, three distinct methods of enrichment were used followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). These included: immunoprecipitation (IP) of endogenous ADAR1, IP of Strep II-tagged ADAR1, and proximity labeling using BioID. Individual ADAR1 isoforms (p110 and p150) and their respective dsRNA binding-deficient mutants were created to discern isoform-specific and dsRNA-dependent interactions. Altogether, our results reveal a comprehensive ADAR1 interaction map, identifying both known and novel partners, and highlighting the isoform-specific and dsRNA-binding-dependent nature of ADAR1 interactions. Under IFN stimulation, ADAR1's interaction spectrum encompasses viral replication inhibitors and LINE-1 regulators. Mimicking viral infection with HMW poly(I:C) changed the proximal network of proteins for both isoforms. Our findings provide new insights into ADAR1's roles and its dynamic during IFN response.

2024-12-08 | PXD049991 | Pride

An automated and fast sample preparation workflow for laser microdissection guided ultrasensitive proteomics

Project description:Spatial tissue proteomics integrating whole-slide imaging, laser microdissection and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONEÃ‚Â® robotic system, which has the capacity to process 192 samples in three hours. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows Ã¢â‚¬Ëœon-the-flyÃ¢â‚¬â„¢ sample clean-up, particularly pertinent for laser microdissected workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell and epithelial microregions of 4,000 Ã‚Âµm2 to a depth of ~2,000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility.

2024-03-22 | PXD047762 | Pride

Large-scale genetic screens identify BET-1 as a cytoskeleton regulator promoting actin health and lifespan

Project description:The actin cytoskeleton is a three-dimensional scaffold of proteins that is a regulatory, energy-consuming material with dynamic properties shaping the structure and function of the cell. The proper function of actin is required for many cellular pathways, including cell division, autophagy, chaperone function, endocytosis, and exocytosis (1–5). The breakdown of these cellular processes manifests during aging and exposure to stress, which is in part due to the breakdown of the actin cytoskeleton (5–9). However, the regulatory mechanisms involved in preservation of cytoskeletal form and function are not well understood. Here, we performed a multi-pronged, cross-organismal screen combining a whole-genome CRISPR-Cas9 screen in human fibroblasts with in vivo C. elegans synthetic lethality screening. We identified the bromodomain protein, BET-1, as a key regulator promoting actin health and longevity. Interestingly, overexpression of bet-1 preserves actin health at late age and promotes lifespan and healthspan in C. elegans. These beneficial effects are through preservation of actin, downstream of the function of BET-1 as a transcriptional regulator. Together, our discovery attributes assigns a key role of BET-1 in cytoskeletal health, highlighting regulatory cellular networks promoting cytoskeletal homeostasis.

2023-06-01 | E-MTAB-12289 | biostudies-arrayexpress