Proteomics

Dataset Information

0

Rapid Proteomic Screen of CRISPR Experiment Outcome by Data Independent Acquisition Mass Spectrometry: A Case Study for HMGN1

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion Lumos, TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Cervix Carcinoma

SUBMITTER: Wenxue Li  

LAB HEAD: Yansheng Liu

PROVIDER: PXD011952 | Pride | 2019-03-26

REPOSITORIES: Pride

Json Xml
altmetric image

Publications

Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1.

Mehnert Martin M   Li Wenxue W   Wu Chongde C   Salovska Barbora B   Liu Yansheng Y  

Proteomics 20190614 13

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, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the following proteomic regulation events are studied. In particular, DIA mass spectrometry (DIA-MS) is utilized, and more than 6200 proteins (protein- FDR 1%) and more than 82 000 pep  ...[more]

Similar Datasets

Proteomics Assessing the relationship between mass window width and retention time scheduling on protein coverage for data-independent acquisition
2019-07-01 | PXD013477 | Pride
Transcriptomics Transcriptome profiling of MED1 wild-type and knockout human pre-B ALL cell line 697 (RNA-seq)
2020-05-13 | E-MTAB-8178 | biostudies-arrayexpress
Proteomics Narrow precursor window for DIA-MS enhances protein identification and quantification
2021-10-01 | PXD026965 | Pride
Proteomics Shared and specific functions of Arfs 1-5 at the golgi revealed by systematic knockouts
2021-11-02 | PXD028846 | Pride
Transcriptomics RNA-Seq analysis of EZH2 mutants in isogenic cell lines
2023-07-17 | GSE235013 | GEO
Genomics H3K27me3 CUT&Tag analysis of EZH2 mutants in isogenic cell lines
2023-07-17 | GSE235011 | GEO
Genomics ATAC-Seq analysis of EZH2 mutants in isogenic cell lines
2023-07-17 | GSE235010 | GEO
Transcriptomics Microarray analysis of HCT116 cells with and without a 1.4kb deletion
2016-08-16 | E-MTAB-4839 | biostudies-arrayexpress
Proteomics Comparative analyses of data independent acquisition mass spectrometric approaches: DIA, WiSIM-DIA and directDIA
2017-11-20 | PXD006934 | Pride
Proteomics Data-independent Acquisition-based Proteome and Phosphoproteome Profiling across Six Melanoma Cell Lines
2021-03-15 | PXD022992 | Pride