PXD002680

PXD002680 is an original dataset announced via ProteomeXchange.

Title	Comprehensive Proteomic Profiling of Nuclear Fractions from Native Renal Inner Medullary Collecting Duct Cells
Description	Regulation of renal water excretion is dependent on control of the molecular water channel aquaporin‐2 by the peptide hormone vasopressin in renal collecting duct cells. The control is in part due to the regulation of transcription of the Aqp2 gene and other genes by vasopressin. A systems biology‐based approach to understanding transcriptional control in renal collecting duct cells depends on knowledge of what transcription factors and other regulatory proteins are present in the cells' nucleus. The goal of this paper is to report comprehensive proteomic profiling of nuclear proteins in native inner medullary collecting duct (IMCD) cells of the rat. Multi‐dimensional separation procedures and state‐of‐the art protein mass spectrometry allowed the high stringency identification of a total of 5105 proteins in nuclear pellet (NP) and nuclear extract (NE) fractions of biochemically isolated rat IMCD cells (URL: https://helixweb.nih.gov/ESBL/Database/IMCD_Nucleus/)*. The analysis identified 369 transcription factor proteins out of the 1371 transcription factors coded by the rat genome. The analysis added 1898 proteins to the recognized proteome of rat IMCD cells, now amounting to 7003 unique proteins. Analysis of samples treated with the vasopressin analog dDAVP (1 nM for 30min) or its vehicle revealed 99 proteins in the NP fraction and 88 proteins in the NE fraction with significant changes in spectral counts (Fisher Exact Test, P<0.005). Among those altered by vasopressin were 7 distinct histone proteins all of which showed decreased abundance in the NP fraction, consistent with a possible effect of vasopressin to induce chromatin remodeling.
HostingRepository	PRIDE
AnnounceDate	2018-10-24
AnnouncementXML	Submission_2018-10-24_10:49:54.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chung-Lin Chou
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2015-08-07 00:58:22	ID requested
⏵ 1	2018-10-24 10:49:55	announced

Pickering CM, Grady C, Medvar B, Emamian M, Sandoval PC, Zhao Y, Yang CR, Jung HJ, Chou CL, Knepper MA, Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells. Physiol Genomics, 48(2):154-66(2016) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: LC‐MS/MS, kidney, transcription, transcription factor, chromatin, mRNA splicing

Mark Knepper
contact affiliation	Epithelial Systems Biology Laboratory National Heart Lung and Blood Institute National Institutes of Health
contact email	knepperm@nhlbi.nih.gov
lab head
Chung-Lin Chou
contact affiliation	National Institutes of Health
contact email	chouj@nhlbi.nih.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002680
     1. Label: PRIDE project
     2. Name: Comprehensive Proteomic Profiling of Nuclear Fractions from Native Renal Inner Medullary Collecting Duct Cells