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PXD048367

PXD048367 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleHigh-throughput identification of functional regulatory SNPs in systemic lupus erythematosus
DescriptionGenome-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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_06:52:17.662.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD048367
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterTaehyeung Kim
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentLTQ Orbitrap Elite
Dataset History
RevisionDatetimeStatusChangeLog Entry
02024-01-09 16:26:31ID requested
12024-08-02 11:11:26announced
22024-10-22 06:52:18announced2024-10-22: Updated project metadata.
Publication List
10.6019/PXD048367;
Keyword List
submitter keyword: LC-MSMS, Human, B cell,SLE
Contact List
Peter A. Nigrovic
contact affiliationPeter A. Nigrovic, MD Chief, Division of Immunology, Boston Children’s Hospital Professor of Pediatrics and Medicine
contact emailpeter.nigrovic@childrens.harvard.edu
lab head
Taehyeung Kim
contact affiliationBoston Childerns Hospital, Division of Immunology
contact emailtaehyeung.kim@childrens.harvard.edu
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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