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The matrisome: in silico definition and in vivo characterization of tumor extracellular matrix

ABSTRACT: Naba A, Clauser KR, Hoersch S, Liu H, Carr SA, Hynes RO. Mol Cell Proteomics 2012, 11: M111.014647. doi:10.1074/mcp.M111.014647. PMCID:PMC3322572. Tranche_hash:onoKvMCC9umP0dW2GlZSGN/DVfz6tqoyRvsA16h351RjGJZiqjk0wWGYQB9+zPpRj+ASAgKsd779N0Td4250FCPJ6jUAAAAAAABFoQ==

PROVIDER: MSV000078494 | MassIVE | Wed Nov 20 11:06:00 GMT 2013

REPOSITORIES: MassIVE

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The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.

Naba Alexandra A Clauser Karl R KR Hoersch Sebastian S Liu Hui H Carr Steven A SA Hynes Richard O RO

Molecular & cellular proteomics : MCP 20111209 4

The extracellular matrix (ECM) is a complex meshwork of cross-linked proteins providing both biophysical and biochemical cues that are important regulators of cell proliferation, survival, differentiation, and migration. We present here a proteomic strategy developed to characterize the in vivo ECM composition of normal tissues and tumors using enrichment of protein extracts for ECM components and subsequent analysis by mass spectrometry. In parallel, we have developed a bioinformatic approach t ...[more]

PMID: 22159717

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Shotgun Protein Sequencing With Meta Contig Assembly

Project description:Guthals A, Clauser KR, Bandeira N. Mol Cell Proteomics 2012, 11, 1084-1096. doi:10.1074/mcp.M111.015768. Tranche_hash:s+8iy5TbHHydsOPmTf9yqotRGvkxeJPF8BXJxMxxZOnCRXqbje8wbn+Orpxr51YR3L0S2sZBTYljUdHUF35LjfTqeukAAAAAAv6xWQ==

2013-11-21 | MSV000078501 | MassIVE

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics

Project description:Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong, SE, Jaffe JD, Carr SA. Mol Cell Proteomics 2012, mcp.M111.014423. doi:10.1074/mcp.M111.014423. Tranche_hash:5cHw5Rj36vYNshNpy8k4nojtPyW27N/FHcImna3+zw4QV6KIlLOg3i6zesWBdWkEX608MEgdxWuVyKvvdOgB9BAanesAAAAAAACEzw==

2013-11-20 | MSV000078495 | MassIVE

HEK293 Quality Control example dataset - contamination test

Project description:A simple HEK293 lysate, with two files containing a putative mycoplasma contamination, and two negative control samples, taken from Geiger etc al. (Mol Cell Proteomics. 2012 Mar;11(3):M111.014050. doi: 10.1074/mcp.M111.014050. Epub 2012 Jan 25.) [PXD002395].

2015-11-04 | PXD003134 | Pride

11 human cell lines - Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins

Project description:Re-submission of raw data from Geiger T et. al., Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol Cell Proteomics. 2012 Mar;11(3):M111.014050. doi: 10.1074/mcp.M111.014050. Epub 2012 Jan 25.

2015-07-21 | PXD002395 | Pride

Extracellular Matrix Signatures of Human Mammary Carcinoma Identify Novel Metastasis Promoters

Project description:Naba A, Clauser K.R, Lamar J.M, Carr S.A and Hynes RO. eLife 2014

2014-01-27 | MSV000078535 | MassIVE

Extracellular Matrix Signatures of Human Primary Metastatic Colon Cancers and their Liver Metastases

Project description:Naba A, Clauser KR, Whittaker CA,Carr SA, Tanabe KK, Hynes RO. 2014

2014-02-20 | MSV000078555 | MassIVE

Impact of Cux2 overexpression on gene expression in male and female mouse liver (Mus musculus)

Project description:We identified genes expressed in mouse liver that are regulated by Cux2, a highly female-specific liver transcription factor whose expression is regulated by sex-dependent plasma GH patterns. Using adenovirus to overexpress Cux2 (Adeno-Cux2) in male liver, we show that Cux2 represses ~35% of male-biased genes and induces/de-represses ~35% of female-biased genes. Adeno-CMV was used as a control for adenoviral infection. (Published in: TL Conforto et al 2012, Mol Cell Biol. 2012, 32:4611-4627. PubMed PMID: 22966202; PMCID: PMC3486175)

2012-09-10 | GSE35897 | GEO

Impact of Cux2 knockdown on gene expression in female mouse liver (Mus musculus)

Project description:We identified genes expressed in mouse liver that are regulated by Cux2, a highly female-specific liver transcription factor whose expression is regulated by sex-dependent plasma GH patterns. Using siRNA to knockdown Cux2 expression in female liver, we show that female specific genes are predominantly repressed by Cux2 knockdown. In contrast, similar numbers of male-biased genes are repressed as are induced by Cux2 knockdown. A scrambled, non-specific siRNA was used as a control. (Published in: TL Conforto et al 2012, Mol Cell Biol. 2012, 32:4611-4627. PubMed PMID: 22966202; PMCID: PMC3486175)

2012-09-10 | GSE37078 | GEO

FOXK2 ChIP-seq

Project description:Chromatin immunoprecipitation of FOXK2 (tagged with Flag and His tags) in U2OS cells detected by SOLiD sequencing. ***Correction March 2014: The sample “FOXK2_Dox_treated” has been renamed, it was originally named “FOXK2_rep2”. A new sample “FOXK2_rep2” has been added, with new files. It has come to our attention that one of the FOXK2 ChIP-seq replicates 'FOXK2_rep2' that we used in our paper recent paper (Ji, Z., Donaldson, I.J., Liu, J., Hayes, A., Zeef, L.A.H. and Sharrocks, A.D. (2012) The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation. Mol. Cell. Biol. 32, 385-398. doi:10.1128/MCB.05504-11) was incorrect. The replicate was actually treated with doxorubicin prior to ChIP-seq analysis resulting in the loss of many FOXK2 binding events.***

2011-01-20 | E-MTAB-565 | biostudies-arrayexpress

Identification of Cux2 binding sites in female and male mouse liver

Project description:Growth hormone (GH)-regulated transcription factors, notably STAT5 and BCL6, play a major role in regulating genes showing sex differences in expression in mouse liver, primarily through their effects in male liver, where male-biased genes are up regulated and many female-biased genes are actively repressed. Here we investigate whether complementary mechanisms, involving up regulation of female-biased genes and down regulation of male-biased genes occur in female liver. To address this question, we identified genes regulated by Cux2, a highly female-specific transcription factor that is repressed in male liver and is induced by the female plasma GH pattern in female liver. ChIP-seq analysis identified Cux2 binding sites in female liver only, where they are enriched at sites of male-biased DNase hypersensitivity and at genomic regions showing male-enriched STAT5 binding. Cux2 binding sites were enriched at genes repressed by adenoviral-Cux2, but not at genes induced by adenoviral-Cux2 (see GSE35897), indicating a direct binding mechanism in Cux2 repression but not in Cux2-dependent gene induction. (Published in: TL Conforto et al 2012, Mol Cell Biol. 2012, 32:4611-4627. PubMed PMID: 22966202; PMCID: PMC3486175)

2012-09-10 | GSE35985 | GEO

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