title: RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.
abstract: 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.
authors.affiliation: Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden.
authors.forename: Frida
authors.initials: F
authors.lastname: Danielsson
authors.forename: Mikaela
authors.initials: M
authors.lastname: Wiking
authors.forename: Diana
authors.initials: D
authors.lastname: Mahdessian
authors.forename: Marie
authors.initials: M
authors.lastname: Skogs
authors.forename: Hammou
authors.initials: H
authors.lastname: Ait Blal
authors.forename: Martin
authors.initials: M
authors.lastname: Hjelmare
authors.forename: Charlotte
authors.initials: C
authors.lastname: Stadler
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlén
authors.forename: Emma
authors.initials: E
authors.lastname: Lundberg
mesh_terms: D001483:Base Sequence; D002460:Cell Line / Q000378:metabolism; D002877:Chromosomes, Human; D020869:Gene Expression Profiling; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D020543:Proteome; D012313:RNA / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D011506:Proteins; D020543:Proteome; D012313:RNA