PXD048367

PXD048367 is an original dataset announced via ProteomeXchange.

Title	High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus
Description	Genome-wide association studies implicate multiple loci in risk for systemic lupus erythematosus (SLE), but few contain exonic variants, rendering systematic identification of non-coding variants essential to decoding SLE genetics. We utilized SNP-seq and bioinformatic enrichment to interrogate 2180 single-nucleotide polymorphisms (SNPs) from 87 SLE risk loci for potential binding of transcription factors and related proteins from B cells. 52 SNPs that passed initial screening were tested by electrophoretic mobility shift (EMSA) and luciferase reporter assays. To identify binding of transcription factors and/or other nuclear proteins in an allele-determined manner, we employed pulldown using nuclear extract from Daudi cells and silver staining in SNPs that had exhibited allele-specific differential binding by EMSA. Each pulldown product for each allele of the five high-probability SNPs (rs2297550 C/G, rs13213604 C/G, rs276461 T/C, rs9907955 C/T, rs7302634 T/C) was evaluated by mass spectrometry (MS) to identify binding nuclear proteins, yielding a set of candidate proteins for each.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:52:17.662.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD048367
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Taehyeung Kim
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-09 16:26:31	ID requested
1	2024-08-02 11:11:26	announced
⏵ 2	2024-10-22 06:52:18	announced	2024-10-22: Updated project metadata.

10.6019/PXD048367;

submitter keyword: LC-MSMS, Human, B cell,SLE

Peter A. Nigrovic
contact affiliation	Peter A. Nigrovic, MD Chief, Division of Immunology, Boston Children’s Hospital Professor of Pediatrics and Medicine
contact email	peter.nigrovic@childrens.harvard.edu
lab head
Taehyeung Kim
contact affiliation	Boston Childerns Hospital, Division of Immunology
contact email	taehyeung.kim@childrens.harvard.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/08/PXD048367

PRIDE project URI

• PRIDE
  1. PXD048367
     1. Label: PRIDE project
     2. Name: High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus