PXD011952

PXD011952 is an original dataset announced via ProteomeXchange.

Title	Rapid Proteomic Screen of CRISPR Experiment Outcome by Data Independent Acquisition Mass Spectrometry: A Case Study for HMGN1
Description	CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, we performed gene knockout of HMGN1 by CRISPR in cancer cells and studied the following proteomic regulation events. In particular we utilized DIA mass spectrometry (DIA-MS) and reproducibly measured more than 6200 proteins (protein- FDR 1%) and more than 82,000 peptide precursors in the single MS shots of two hours. HMGN1 protein deletion was confidently verified in all of the clone- and dish- replicates following CRISPR by DIA-MS. Statistical analysis revealed 144 proteins changed their expressions significantly after HMGN1 knockout. Functional annotation and enrichment analysis indicate the deletion of HMGN1 induces the histone inactivation, various stress pathways, remodeling of extracellular proteomes, and immune regulation processes related to complement and coagulation cascade and interferon alpha/ gamma response in cancer cells. These results shed new lights on the cellular functions of HMGN1. We suggest that DIA-MS can be reliably used as a rapid, robust, and cost-effective proteomic-screening tool to assess the outcome of the CRISPR experiments.
HostingRepository	PRIDE
AnnounceDate	2019-03-26
AnnouncementXML	Submission_2019-03-26_10:41:44.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Wenxue Li
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion Lumos; TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-12-06 01:38:30	ID requested
⏵ 1	2019-03-26 10:41:45	announced

Mehnert M, Li W, Wu C, Salovska B, Liu Y, Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics, 19(13):e1800438(2019) [pubmed]

curator keyword: Biological

submitter keyword: CRISPR, DIA, Proteomics,HMGN1

Yansheng Liu
contact affiliation	Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
contact email	yansheng.liu@yale.edu
lab head
Wenxue Li
contact affiliation	Yale University
contact email	wenxue.li@yale.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/2019/03/PXD011952

PRIDE project URI

• PRIDE
  1. PXD011952
     1. Label: PRIDE project
     2. Name: Rapid Proteomic Screen of CRISPR Experiment Outcome by Data Independent Acquisition Mass Spectrometry: A Case Study for HMGN1