Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

1 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SubCellBarcode: Scalable proteome-wide mapping of protein localization and relocalization

ABSTRACT: We have devised a simple and robust LC-MS/MS compatible protocol for subcellular protein localization studies. Here, we combine it with in depth proteome profiling and utilize the resulting dataset to predict the subcellular localization of more than 12000 proteins in 5 human cancer cell lines. The data allows for exploration of both cell line specific and perturbation related protein localization changes as well as domain and splice variant effects and protein complex formation. The data is made accessible through the online resource www.subcellbarcode.org.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Janne Lehti�

PROVIDER: MSV000086899 | MassIVE | Wed Feb 17 22:59:00 GMT 2021

SECONDARY ACCESSION(S): PXD006895

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Publications

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization.

Orre Lukas Minus LM Vesterlund Mattias M Pan Yanbo Y Arslan Taner T Zhu Yafeng Y Fernandez Woodbridge Alejandro A Frings Oliver O Fredlund Erik E Lehtiö Janne J

Molecular cell 20190101 1

Subcellular localization is a main determinant of protein function; however, a global view of cellular proteome organization remains relatively unexplored. We have developed a robust mass spectrometry-based analysis pipeline to generate a proteome-wide view of subcellular localization for proteins mapping to 12,418 individual genes across five cell lines. Based on more than 83,000 unique classifications and correlation profiling, we investigate the effect of alternative splicing and protein doma ...[more]

PMID: 30609389

Similar Datasets

SubCellBarcode: Scalable proteome-wide mapping of protein localization and relocalization

Project description:We have devised a simple and robust LC-MS/MS compatible protocol for subcellular protein localization studies. Here, we combine it with in depth proteome profiling and utilize the resulting dataset to predict the subcellular localization of more than 12000 proteins in 5 human cancer cell lines. The data allows for exploration of both cell line specific and perturbation related protein localization changes as well as domain and splice variant effects and protein complex formation. The data is made accessible through the online resource www.subcellbarcode.org.

2019-01-03 | PXD006895 | Pride

Atlas of subcellular RNA localization in human embryonic stem cells and its flow during differentiation

Project description:The distribution of RNA in human embryonic stem cells (hESC) and the function of RNA localization in maintaining hESC pluripotency and differentiation are currently unknown. Here, by isolating five subcellular components of hESCs and differentiated cells, we uncovered the global subcellular RNA localization in hESC. For protein-coding mRNA, different transcripts of the same gene exhibit an “isoform switch” between subcellular components, which is regulated by localization cis-elements in their variable regions. For noncoding RNA, multiple sequence features such as polyA tail, length, and GC content jointly regulate their subcellular localization. In addition, we found that some developmental genes can be transcribed in advance and confined to chromatin in undifferentiated hESCs. Finally, we revealed significant changes in overall RNA distribution, mapped RNA dynamic localization atlas, and characterized different dynamic RNA localization patterns during hESC differentiation into mesoderm. The multiple RNA localization patterns we revealed will provide some new enlightenment for hESC stemness maintenance and differentiation.

2023-12-22 | GSE206328 | GEO

Transcriptome-wide Regulation of Splicing and mRNA Localization by Muscleblind Proteins

Project description:The Muscleblind-like (Mbnl) family of RNA-binding proteins plays important roles in muscle and eye development and in Myotonic Dystrophy (DM), where expanded CUG or CCUG repeats functionally deplete Mbnl proteins. We identified transcriptome-wide functional and biophysical targets of Mbnl proteins in brain, heart, muscle, and myoblasts using RNA sequencing and crosslinking/immunoprecipitation-sequencing approaches. This analysis identified several hundred splicing events whose regulation depended on Mbnl function, in a pattern indicative of functional interchangeability between Mbnl1 and Mbnl2. A nucleotide resolution RNA map associated repression or activation of exon splicing with Mbnl binding near either 3' splice site or near the downstream 5' splice site, respectively. Transcriptomic analysis of sub-cellular compartments uncovered a global role for Mbnls in regulating localization of mRNAs encoding membrane, synaptic and other proteins in both mouse and Drosophila cells, and Mbnls also contribute to protein secretion. These findings hold several new implications for DM pathogenesis. To assess global functions of Muscleblind proteins, RNA-Seq was performed using WT and Mbnl1 KO brain, heart, and muscle (5 mice each). Additionally, C2C12 mouse myoblasts were depleted of Mbnl1, Mbnl2, or both. Subcellular fractionation experiments were performed to analyze mRNA localization following depletion of Mbnl1 and Mbnl2 in C2C12 mouse myoblasts, and following depletion of Mbnl in Drosophila S-2R+ cells. CLIP-Seq was also performed against Mbnl1 in mouse brain, heart, muscle, and C2C12 myoblasts. Finally, ribosome footprinting was performed with C2C12 mouse myoblasts that were depleted of Mbnl1, Mbnl2, or both.

2012-08-17 | E-GEOD-39911 | biostudies-arrayexpress

Homo sapiens

Project description:Alternative Splicing regulation protein subcellular localization

| PRJNA481540 | ENA

Regulation of RNA localization by FMR1

Project description:We use subcellular fractionation to probe the regulation of RNA localization by FMR1 in neuronal cells.

2020-05-28 | GSE137878 | GEO

GAR-Driven Subcellular Localization of the Growth Controlling RNA Binding Protein Nucleolin

Project description:GAR-Driven Subcellular Localization of the Growth Controlling RNA Binding Protein Nucleolin

| PRJNA597482 | ENA

RNA localization to protrusions of mouse melanoma YUMM1.7 cells.

Project description:Subcellular localization of messenger RNA (mRNA) is a widespread phenomenon that can impact the regulation and function of the encoded protein. In non-neuronal cells, a subset of mRNAs localize to cell protrusions and proper mRNA localization is required for cell migration. However, the mechanisms by which mRNA localization regulates protein function in this setting remain unclear. Here, we examined the functional consequences of localization of the mRNA encoding KIF1C. KIF1C is a kinesin motor protein required for cell migration and mRNA trafficking, including trafficking of its own mRNA. We show that Kif1c mRNA localization does not regulate KIF1C protein abundance, distribution, οr ability to traffic other mRNAs. Conversely, robust Kif1c mRNA localization is required for directed cell migration. We used mass spectrometry to identify binding partners of endogenous KIF1C, which revealed dramatic dysregulation of the number and identity of KIF1C interactors in response to Kif1c mRNA mis-localization. These results therefore uncovered a mechanistic connection between mRNA localization to cell protrusions and the specificity of protein-protein interactions. We anticipate that this mechanism is not limited to Kif1c and is likely to be a general principle used by protrusion-enriched mRNAs in non-neuronal cells.

2023-02-24 | GSE219089 | GEO

HNRNPU regulates lncRNAs nuclear localization

Project description:To elucidate the role of HNRNPU in regulation of lncRNAs nuclear localization, we knocked down HNRNPU in K562 cells using short interfering RNAs and performed subcellular RNA-seq using nuclear or cytosolic RNAs

2021-01-23 | GSE165310 | GEO

Atlas of Subcellular RNA Localization Revealed by APEX-seq

Project description:Atlas of Subcellular RNA Localization Revealed by APEX-seq

| PRJNA476786 | ENA

Subcellular RNA localization during Drosophila embryonic neurogenesis [fractionation-Seq]

Project description:Subcellular RNA localization during Drosophila embryonic neurogenesis [fractionation-Seq]

| PRJNA415601 | ENA