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Rat cell supernatant and the separation of supernatant LC-MSMS

ABSTRACT: We find one organ of body is special useful for skeletal muscle recovery from indury. To identify the active substance in TCM(special organ cell culturing supernatant which can activate satellite cell proliferation), we prepared serum-free TCM and also separate several fractions, subjected them to LC-MS/MS analysis. To our surprise, most proteins extracted belong to metabolite interconversion enzymes, nucleic acid binding proteins, cytoskeletal proteins, protein modifying enzymes, membrane traffic proteins and so on, but no cytokine was detected.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Cell Culture

SUBMITTER: zhang xuena

LAB HEAD: Zhang Xuena

PROVIDER: PXD027407 | Pride | 2022-02-17

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	6.wiff	Wiff
	6.wiff.scan	Wiff
	6_PeptideSummary.txt	Txt
	6_ProteinSummary.txt	Txt
	total-1.wiff	Wiff

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1 - 5 of 10

Publications

The thymus regulates skeletal muscle regeneration by directly promoting satellite cell expansion.

Zheng Yan-Yan YY Wang Ye Y Chen Xin X Wei Li-Sha LS Wang Han H Tao Tao T Zhou Yu-Wei YW Jiang Zhi-Hui ZH Qiu Tian-Tian TT Sun Zhi-Yuan ZY Sun Jie J Wang Pei P Zhao Wei W Li Ye-Qiong YQ Chen Hua-Qun HQ Zhu Min-Sheng MS Zhang Xue-Na XN

The Journal of biological chemistry 20211220 1

The thymus is the central immune organ, but it is known to progressively degenerate with age. As thymus degeneration is paralleled by the wasting of aging skeletal muscle, we speculated that the thymus may play a role in muscle wasting. Here, using thymectomized mice, we show that the thymus is necessary for skeletal muscle regeneration, a process tightly associated with muscle aging. Compared to control mice, the thymectomized mice displayed comparable growth of muscle mass, but decreased muscl ...[more]

PMID: 34942145

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Proteome profiling of microvesicles, exosomes and supernatant from SKOV3

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2014-10-23 | PXD001402 | Pride

Quantitative Proteomics Analysis of COVID-19 Patients

Project description:Treatment of severe cases of Coronavirus disease 2019 (COVID-19) is extremely important to decrease death and end organ damages. Herein, we performed a proteomic analysis of plasma samples from mild, moderate and sever Covid-19 patients. Analysis revealed differentially expressed proteins and different therapeutic potential targets related to innate immune responses

2023-05-02 | PXD037400 | Pride

RNA-seq of Mus musculus: WT and MTCH2 KO Naïve & Primed mouse embryonic stem cells

Project description:The role of mitochondria dynamics and its molecular regulators remains largely unknown during naïve-to-primed pluripotent cell interconversion. Here we report that mitochondrial MTCH2 is a regulator of mitochondrial fusion, essential for the naïve-to-primed interconversion of murine embryonic stem cells (ESCs). During this interconversion, wild-type ESCs elongate their mitochondria and slightly alter their glutamine utilization. In contrast, MTCH2-/- ESCs fail to elongate their mitochondria and to alter their metabolism, maintaining high levels of histone acetylation and expression of naïve pluripotency markers. Importantly, enforced mitochondria elongation by the pro-fusion protein Mitofusin (MFN) 2 or by a dominant negative form of the pro-fission protein dynamin-related protein (DRP) 1 is sufficient to drive the exit from naïve pluripotency of both MTCH2-/- and wild-type ESCs. Taken together, our data indicate that mitochondria elongation, governed by MTCH2, plays a critical role and constitutes an early driving force in the naïve-to-primed pluripotency interconversion of murine ESCs.

2018-11-10 | GSE122067 | GEO

Method to identify novel proteoform peptides from salivary supernatant.

Project description:We describe the use Galaxy framework to facilitate complete proteogenomic analysis for a representative salivary dataset. We demonstrate how Galaxy’s many features make it a unique and ideal solution for proteogenomic analysis. We highlight Galaxy’s flexibility by creating a modular workflow incorporating both established and customized software and processing steps that improve depth and quality of proteogenomic results. We demonstrate Galaxy’s accessibility, via the easy sharing of complete, and even complex (approximately 140 steps), proteogenomic workflows, which can be used and customized by others via a public instance of the framework (usegalaxyp.org). Our results provide a blueprint for the establishment of the Galaxy framework as an ideal solution for the emerging field of proteogenomics.

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Thymic Epithelial Cells with Human T cell Leukemia Virus type 1 (HTLV-1) Infected T cell supernatant (with or without supernatant)

Project description:The human T-lymphotropic virus type-1 (HTLV-1) is the cause of adult T cell leukemia/lymphoma (ATL) and HTLV-1 associated myelopathy/tropical spatic paraparesis (HAM/TSP). Both diseases have a late onset, although ATL has a medium survivor of 7.7 months after the onset despise aggressive treatment. T CD4+ cells are the main target of HTLV-1, but other cells types are known to be infected as T CD8+, CD34+ progenitor, dendritic cells and immature lymphocytes. The thymus gland is a primary lymphoid organ, in which the lymphocytes undergo differentiation, where selected T cell ultimately being exported from the organ and going to peripheral lymphoid organs. This process occurs along with immature lymphocyte migration and interaction with thymic microenvironment. Thymic epithelial cells (TECs) are the main component of the thymic stroma and are responsible for the process of intrathymic T cell maturation. This process are dependent of T cell receptor (TCR)-mediated recognition of antigenic peptide fragments presented by major histocompatibility complex (MHC) molecules in TEC and culminate in TCR repertoire formation. In this study, we show that TECs have the receptors for HTLV-1 entry and can be infected by cell-cell contact and cell-free virus. These cells change gene expression of anti-apoptosis, chemokine and adhesion molecules genes; however, there is no difference in antigen presentation molecules. Furthermore, HTLV-1 infected TECs can transmit the virus to a CD4 T cell lineage and CD4 T cells derived from peripheral blood of healthy donors after in vitro co-cultivation. Conjointly, our data points to the possibility that the human thymic epithelial cells must favor the HTLV-1 infection as a reservoir, transmitting the virus to maturing lymphocytes that cause the disease in the periphery.

2015-11-30 | GSE73170 | GEO

Transcription profiling of all major organ systems of Medicago truncatula to create a gene expression atlas

Project description:Medicago truncatula, which has a relatively small diploid genome, has been adopted as a model species for legume genomics. To enhance its value as a model, we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, with special emphasis on nodule and seed development.

2008-03-15 | E-MEXP-1097 | biostudies-arrayexpress

Synergistic activation by p38MAPK and glucocorticoid signaling mediates induction of M2-like tumor-associated macrophages expressing the novel CD20 homolog MS4A8A.

Project description:Tumor-associated macrophages (TAMs) represent alternatively activated (M2) macrophages that support tumor growth. Previously, we have described a special LYVE-1(+) M2 TAM subset in vitro and in vivo; gene profiling of this TAM subset identified MS4A8A as a novel TAM molecule expressed in vivo by TAM in mammary carcinoma and malignant melanoma. In vitro, Ms4a8a mRNA and MS4A8A protein expression was strongly induced in bone marrow-derived macrophages (BMDMs) by combining M2 mediators (IL-4, glucocorticoids) and tumor-conditioned media (TCM). Admixture of MS4A8A(+) TCM/IL-4/GC-treated BMDM significantly enhanced the tumor growth rate of subcutaneously transplanted TS/A mammary carcinomas. Upon forced overexpression of MS4A8A, Raw 264.7 macrophage-like cells displayed a special gene signature. Admixture of these MS4A8A(+) Raw 264.7 cells also significantly enhanced the tumor growth rate of subcutaneously transplanted mammary carcinomas. To identify the signaling pathways involved in synergistic induction of MS4A8A, the major signaling cascades with known functions in TAM were analyzed. Although inhibitors of NF-κB activation and of the MAPK JNK and ERK did not show relevant effects, the p38α/β MAPK inhibitor SB203580 strongly and highly significantly (p > 0.001) inhibited MS4A8A expression on mRNA and protein level. In addition, MS4A8A expression was restricted in M2 BMDM from mice with defective GC receptor (GR) dimerization indicating that classical GR gene regulation is mandatory for MS4A8A induction. In conclusion, expression of MS4A8A within the complex signal integration during macrophage immune responses may act to fine tune gene regulation. Furthermore, MS4A8A(+) TAM may serve as a novel cellular target for selective cancer therapy.

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Proteomics informed by transcriptomics for a qualitative and quantitative analysis of the sialoproteome of Ornithodoros moubata adult ticks. SWATH Spectral Library building

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