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Deepening into intracellular signaling landscape through integrative spatial proteomics and transcriptomics in a lymphoma model
- Source :
- Biomolecules, Vol 11, Iss 1776, p 1776 (2021), Digital.CSIC. Repositorio Institucional del CSIC, instname, Biomolecules, Biomolecules; Volume 11; Issue 12; Pages: 1776
- Publication Year :
- 2021
- Publisher :
- Multidisciplinary Digital Publishing Institute, 2021.
-
Abstract
- © 2021 by the authors.<br />Human Proteome Project (HPP) presents a systematic characterization of the protein landscape under different conditions using several complementary-omic techniques (LC-MS/MS proteomics, affinity proteomics, transcriptomics, etc.). In the present study, using a B-cell lymphoma cell line as a model, comprehensive integration of RNA-Seq transcriptomics, MS/MS, and antibody-based affinity proteomics (combined with size-exclusion chromatography) (SEC-MAP) were performed to uncover correlations that could provide insights into protein dynamics at the intracellular level. Here, 5672 unique proteins were systematically identified by MS/MS analysis and subcellular protein extraction strategies (neXtProt release 2020-21, MS/MS data are available via ProteomeXchange with identifier PXD003939). Moreover, RNA deep sequencing analysis of this lymphoma B-cell line identified 19,518 expressed genes and 5707 protein coding genes (mapped to neXtProt). Among these data sets, 162 relevant proteins (targeted by 206 antibodies) were systematically analyzed by the SEC-MAP approach, providing information about PTMs, isoforms, protein complexes, and subcellular localization. Finally, a bioinformatic pipeline has been designed and developed for orthogonal integration of these high-content proteomics and transcriptomics datasets, which might be useful for comprehensive and global characterization of intracellular protein profiles.<br />We are financial support from the Spanish Health Institute Carlos III (ISCIII) for the grants: FIS PI14/01538, FIS PI17/01930 and CB16/12/00400.
- Subjects :
- Proteomics
Lymphoma, B-Cell
Protein Array Analysis
Affinity-based proteomics
Computational biology
Biology
Biochemistry
Microbiology
Article
Transcriptome
affinity-based proteomics
human proteome project
LC-MS/MS
transcriptomics
size-exclusion-chromatography (SEC)
Tandem Mass Spectrometry
Cell Line, Tumor
Databases, Genetic
medicine
Humans
Human proteome project
Transcriptomics
Molecular Biology
Sequence Analysis, RNA
Size-exclusion-chromatography (SEC)
Gene Expression Profiling
High-Throughput Nucleotide Sequencing
medicine.disease
QR1-502
Lymphoma
Gene Expression Regulation, Neoplastic
Chromatography, Gel
Intracellular
Chromatography, Liquid
Signal Transduction
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Biomolecules, Vol 11, Iss 1776, p 1776 (2021), Digital.CSIC. Repositorio Institucional del CSIC, instname, Biomolecules, Biomolecules; Volume 11; Issue 12; Pages: 1776
- Accession number :
- edsair.doi.dedup.....0bd7dd166d4d05dcbe6a2c2c88baef7a