RNA Deep Sequencing as a Tool for Selection of Cell Lines for Systematic Subcellular Localization of All Human Proteins
2013 (English)In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 12, no 1, 231-239 p.Article in journal (Refereed) Published
One of the major challenges of a chromosome-centric proteome project is to explore in a systematic manner the potential proteins identified from the chromosomal genome sequence, but not yet characterized on a protein level. Here, we describe the use of RNA deep sequencing to screen human cell lines for RNA profiles and to use this information to select cell lines suitable for characterization of the corresponding gene product. In this manner, the subcellular localization of proteins can be analyzed systematically using antibody-based confocal microscopy. We demonstrate the usefulness of selecting cell lines with high expression levels of RNA transcripts to increase the likelihood of high quality immunofluorescence staining and subsequent successful subcellular localization of the corresponding protein. The results show a path to combine transcriptomics with affinity proteomics to characterize the proteins in a gene- or chromosome-centric manner.
Place, publisher, year, edition, pages
2013. Vol. 12, no 1, 231-239 p.
antibody, Human Protein Atlas, Human Proteome Project, RNA sequencing, subcellular localization
Biochemistry and Molecular Biology
IdentifiersURN: urn:nbn:se:kth:diva-119069DOI: 10.1021/pr3009308ISI: 000313156300026ScopusID: 2-s2.0-84874045044OAI: oai:DiVA.org:kth-119069DiVA: diva2:609382
FunderKnut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
QC 201303052013-03-052013-03-052013-03-05Bibliographically approved