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Systematic discovery of endogenous ribonucleoprotein complexes - RNA DIF-FRAC Human HEK293T Cells Replicate2

ABSTRACT: The associated files are mass spec data from size exclusion chromatographic separations of Human HEK293T with and without RNAse A treatment.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Kevin Drew

LAB HEAD: Edward Marcotte

PROVIDER: PXD014820 | Pride | 2019-10-25

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	HEK293_SEC_Ctrl_10_01a_04252019..comet.pep.xml	Pepxml
	HEK293_SEC_Ctrl_10_01a_04252019.MSGF.mzid.gz	Mzid
	HEK293_SEC_Ctrl_10_01a_04252019.mzXML	Mzxml
	HEK293_SEC_Ctrl_10_01a_04252019.prot_count_mFDRpsm001.group	Other
	HEK293_SEC_Ctrl_10_01a_04252019.raw	Raw

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Publications

Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes.

Mallam Anna L AL Sae-Lee Wisath W Schaub Jeffrey M JM Tu Fan F Battenhouse Anna A Jang Yu Jin YJ Kim Jonghwan J Wallingford John B JB Finkelstein Ilya J IJ Marcotte Edward M EM Drew Kevin K

Cell reports 20191001 5

RNA-binding proteins (RBPs) play essential roles in biology and are frequently associated with human disease. Although recent studies have systematically identified individual RNA-binding proteins, their higher-order assembly into ribonucleoprotein (RNP) complexes has not been systematically investigated. Here, we describe a proteomics method for systematic identification of RNP complexes in human cells. We identify 1,428 protein complexes that associate with RNA, indicating that more than 20% o ...[more]

PMID: 31665645

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Systematic discovery of endogenous ribonucleoprotein complexes - RNA DIF-FRAC Human HEK293T Cells Replicate1

Project description:The associated files are mass spec data from size exclusion chromatographic separations of Human HEK293T with and without RNAse A treatment.

2019-10-18 | PXD015406 | Pride

Systematic Identification of Protein Phosphorylation-Mediated Interactions

Project description:Protein phosphorylation is a key regulatory mechanism involved in nearly every eukaryotic cellular process. Increasingly sensitive mass spectrometry approaches have identified hundreds of thousands of phosphorylation sites but the functions of a vast majority of these sites remain unknown, with less than 5% of sites currently assigned a function. To increase our understanding of functional protein phosphorylation we developed an approach for identifying the phosphorylation dependence of protein assemblies in a systematic manner. A combination of non-specific protein phosphatase treatment, size-exclusion chromatography, and mass spectrometry allowed us to identify changes in protein interactions after the removal of phosphates. With this approach we were able to identify 316 proteins involved in phosphorylation-sensitive interactions. We recovered known phosphorylation-dependent interactors such as the FACT complex and spliceosome, as well as identified novel interactions such as the tripeptidyl peptidase TPP2 and the supraspliceosome component ZRANB2. More generally, we find phosphorylation-dependent interactors to be strongly enriched for RNA-binding proteins, providing new insight into the role of phosphorylation in RNA binding. By searching directly for phosphorylated amino acid residues, we identified the likely regulatory phosphosites on ZRANB2 and FACT complex subunit SSRP1. This study provides both a method and resource for obtaining a better understanding of the role of phosphorylation in native macromolecular assemblies.

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RNA-seq of human HEK-293T cells treated with a nutraceutical formula (solution-3), or vehicle-(saline solution)-treated controls

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2024-06-19 | E-MTAB-13918 | biostudies-arrayexpress

RNAseq analyses in HEK293T-ACE2 cells infected with SARS-CoV-2 (VOC Delta, 24hours) vs untreated cells

Project description:In this study a gene expression (i.e., RNAseq) analysis was performed in HEK293T-ACE2 cellular model upon infection with viral particle belonging to VOC Delta (MOI: 0.026) for 24 hours in order to have a global picture of the transcriptome landscape in response to early phase of infection of SARS-CoV-2 ( VOC Delta infection and to evaluate the role of Ca2+ in HEK293-ACE2 cellular model and transfer to homeostasis in SARS-COV-2 patients (by Pasqualino de Antonellis1-2* and Veronica Ferrucci 1-2* (first authors) et al. and Massimo Zollo1-2# (corresponding author). Manuscript in preparation 2022 July 15th 2022. Short title "ATP2B1 (PMCA1), regulated by FOXO3, influences susceptibility to severe COVID19".

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TCF/LEF dependent and independent regulation of Wnt/beta-catenin transcription

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Early response of human monocyte-derived macrophages (MDM) to HIV-1

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HEK 293T cells RNA-seq data treated with 5-aza-2-deoxycytidine

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