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Proteomics of tissue matrix scaffold derived from decellularized mice mammary tissues, LC-MS/MS

ABSTRACT: This project is intended to identify the compositions of the tissue matrix scaffold (TMS) generated from the extracellular matrix (ECM) of decellularized NON-SCID mice breast tissues (DBT). Since ECM is the physicochemical support for the cells living in the tissue microenvironment, it is important to know the protein contents within the ECM that are critical for extra- and intracellular signaling, cell growth, migration, cell-cell/ECM interactions. The LC-MS/MS data will serve as a foundation for the downstream applications of the TMS system, and be compared with those of the Matrigel mass spectrometry.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Mammary Gland

SUBMITTER: Weimin Li

LAB HEAD: Weimin Li

PROVIDER: PXD005697 | Pride | 2018-10-26

REPOSITORIES: Pride

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			Action	DRS
	ProteinReportforTMS-analysis_12-2016.xlsx	Xlsx
	SamplesViewReportforTMS-analysis_12-2016.xlsx	Xlsx
	TMS-analysis_12-2016.sf3	Other
	TMS-de-glycosylated_Li (F015557).mzid_TMS-de-glycosylated_Li_(F015557).pride.mgf.gz	Mzid
	TMS-de-glycosylated_Li (F015557).pride.mztab.gz	Mztab

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Publications

A versatile 3D tissue matrix scaffold system for tumor modeling and drug screening.

Rijal Girdhari G Li Weimin W

Science advances 20170913 9

Most of the anticancer drug candidates entering preclinical trials fail to be approved for clinical applications. The following are among the main causes of these failures: studying molecular mechanisms of cancer development, identifying therapeutic targets, and testing drug candidates using inappropriate tissue culture models, which do not recapitulate the native microenvironment where the cancer cells originate. It has become clear that three-dimensional (3D) cell cultures are more biologicall ...[more]

PMID: 28924608

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Proteomics of Matrigel, LC-MS/MS

Project description:ECM is the physicochemical support for the cells living in the tissue microenvironment. it is important to know the protein contents within the ECM that are critical for extra- and intracellular signaling, cell growth, migration, cell-cell/ECM interactions. The ECM gel derived from the Engelbreth-Holm-Swarm murine sarcoma (commonly known as Matrigel or lrECM) purchased from the Sigma Aldrich in the liquid concentration of 8-12 mg/ml (Lot # 064M4075V) was used for the LC-MS/MS analysis and to prepare the 3D scaffolds used for downstream experiments. The Matrigel mass spectrometry data will be used to compare with those of the decellularized mice mammary tissue ECM/DBT-TMS.

2018-10-26 | PXD005696 | Pride

Microarray based analysis of temperature and oxidative stress induced messenger RNA in Schistosoma mansoni

Project description:The body’s defense against schistosome infection can take many forms. For example, upon developing acute schistosomiasis, patients often have fever coinciding with larval maturation, migration and early oviposition. As the infection becomes established, the parasite comes under oxidative stress generated by the host immune system. The most common treatment for schistosomiasis is the anti-helmenthic drug praziquantel. Its effectiveness, however, is limited due to its inability to kill schistosomes 2 - 4 weeks post-infection. Clearly there is a need for new anti-schistosomal drugs. We hypothesize that gene products expressed as part of a protective response against heat and/or oxidative stress are potential therapeutic targets for future drug development. Using a 12,166 element oligonucleotide microarray to characterize Schistosoma mansoni genes induced by heat and oxidative stress we found that 1,878 Schistosoma mansoni elements were significantly induced by heat stress. These included previously reported heat-shock genes expressing homologs of HSP40, HSP70 and HSP86. One thousand and one elements were induced by oxidative stress including those expressing homologs of superoxide dismutase, glutathione peroxidase and aldehyde dehydrogenase. Seventy-two elements were common to both stressors that could potentially be exploited in the development of novel anti-schistosomal therapeutics. Keywords: Stress response, time course Eight samples performed in duplicate for each temperature and oxidative stresses at time points 0, 30, 60, and 240 min over a common reference sample for each stress

2008-08-25 | E-GEOD-11706 | biostudies-arrayexpress

Spatial transcriptomic analysis of the Arabidopsis thaliana - Botrytis cinerea interaction

Project description:A 10 ul drop of B. cinerea spores prepared in half-strength commercial grape juice was placed in the middle of detached Arabidopsis leaves. A cock-borer of 6 mm diameter was used to harvest leaf discs starting from the edge of the lesion (close, 0-6 mm) and the edge of the first disc (away, 6-12 mm) 48 hr after inoculation. Control plants were inoculated with a 10 ul drop of half-strength commercial grape juice with no spores. Three Biological replicates were done of which the third replicate was a dye-swap. In total 12 samples were analyzed. Each array constituted one replicate making six arrays for the whole experiment.

2011-03-01 | E-GEOD-24444 | biostudies-arrayexpress

HiC-sequencing in human monocyte differentiation (3D-MO)

Project description:This dataset consists of in situ HiC-seq data from human monocytes, monocyte-derived dendritic cells as well as monocyte-derived cells that were subjected to siRNA treatment targeting CTCF or RAD21. In total, the data set includes 42 samples.

2022-06-24 | E-MTAB-10848 | biostudies-arrayexpress

ECM-dependent gene expression in normal and tumor-derived mammary organoids

Project description:A critical step in metastasis is cancer cell dissemination. Dissemination and metastasis are associated with specific genetic changes and changes in extracellular matrix (ECM), but how these changes interact to enable dissemination remains unclear. Here we tested the importance of ECM to dissemination in both normal and malignant mammary epithelium. By time-lapse imaging, we observed collective invasion and dissemination directly in 3D culture. Our results reveal that the pattern of epithelial migration and local dissemination are constrained by the local ECM microenvironment. To identify RNA expression changes that could regulate these changes in cell behavior, we conducted whole genome RNA expression profiling from normal and malignant mammary epithelium in 3D culture. We collected RNA from normal and malignant epithelium during active growth at 4 days in culture in either Matrigel or collagen I. We hybridized the resulting RNA to Agilent single color microarrays with a minimum of three biologically independent microarray replicates per condition. We observed significant gene expression differences between normal and malignant epithelium, even when cultured in the same ECM. In contrast, the ECM microenvironment had a relatively small impact on RNA expression, despite its large effects on migratory strategy and local dissemination. Gene expression was measured in normal and malignant mammary epithelial fragments cultured in one of two 3D matrices (laminin-rich basement membrane gel or collagen I) and collected at day 4, which we observed to have peak invasion and dissemination. At least three independent experiments were performed at each time using different mice for each experiment.

2012-08-16 | E-GEOD-39173 | biostudies-arrayexpress

Interaction of Hsp70 Ssb1 and atypical Hsp70 Ssz1

Project description:Our goal was to better understand the interaction between the Hsp70 Ssb1 and the atypical Hsp70 Ssz1, which we had uncovered by in vivo site-specific Bpa crosslinking. Ssz1 having Bpa incorporated was purified and incubated with purified Ssb1 and the J-domain protein Zuo1 during activation of photo cross-linking. After protein gel electrophoresis and protease digestion of excised bands, the resulting cross-linked peptides were analyzed by mass spectrometry and identified by StavroX.

2021-08-26 | PXD024065 | Pride

Microorganisms with Novel Dissimilatory (Bi)Sulfite Reductase Genes are Widespread and Core Microbiota in Low-Sulfate Peatlands

Project description:Peatlands of the Lehstenbach catchment (Germany) house so far unidentified microorganisms with phylogenetically novel variants of the dissimilatory (bi)sulfite reductase genes dsrAB. These genes are characteristic for microorganisms that reduce sulfate, sulfite, or some organosulfonates for energy conservation, but can also be present in anaerobic syntrophs. However, nothing is currently known regarding the abundance, community dynamics, and biogeography of these dsrAB-carrying microorganisms in peatlands. To tackle these issues, soils from a Lehstenbach catchment site (Schlöppnerbrunnen II fen) from different depths were sampled at three time points over a six-year period to analyze the diversity and distribution of dsrAB-containing microorganisms by a newly developed functional gene microarray and quantitative PCR assays. Members of novel, uncultivated dsrAB lineages (approximately representing species-level groups) (i) dominated a temporally stable but spatially structured dsrAB community and (ii) represented ‘core’ members (up to 1-1.7% relative abundance) of the autochthonous microbial community in this fen. In addition, denaturing gradient gel electrophoresis (DGGE)- and clone library-based comparison of the dsrAB diversity in soils from a wet meadow, three bogs, and five fens of various geographic locations (distance ~1-400 km), identified one Syntrophobacter-related and nine novel dsrAB lineages to be widespread in low-sulfate peatlands. Signatures of biogeography in dsrB-DGGE data were not correlated with geographic distance but could largely be explained by soil pH and wetland type, implying that distribution of dsrAB-carrying microorganisms in wetlands on the scale of a few hundred kilometers is not limited by dispersal but determined by contemporary environmental conditions. 36 dsrAB clones for chip evaluation, 33 hybridizations of labeled dsrAB RNA from environmental peatsoil samples

2010-11-26 | E-GEOD-24582 | biostudies-arrayexpress

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2012-03-01 | E-GEOD-31882 | biostudies-arrayexpress

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