title: Chromosome 18 transcriptoproteome of liver tissue and HepG2 cells and targeted proteome mapping in depleted plasma: update 2013.
abstract: We report the results obtained in 2012-2013 by the Russian Consortium for the Chromosome-centric Human Proteome Project (C-HPP). The main scope of this work was the transcriptome profiling of genes on human chromosome 18 (Chr 18), as well as their encoded proteome, from three types of biomaterials: liver tissue, the hepatocellular carcinoma-derived cell line HepG2, and blood plasma. The transcriptome profiling for liver tissue was independently performed using two RNaseq platforms (SOLiD and Illumina) and also by droplet digital PCR (ddPCR) and quantitative RT-PCR. The proteome profiling of Chr 18 was accomplished by quantitatively measuring protein copy numbers in the three types of biomaterial (the lowest protein concentration measured was 10(-13) M) using selected reaction monitoring (SRM). In total, protein copy numbers were estimated for 228 master proteins, including quantitative data on 164 proteins in plasma, 171 in the HepG2 cell line, and 186 in liver tissue. Most proteins were present in plasma at 10(8) copies/μL, while the median abundance was 10(4) and 10(5) protein copies per cell in HepG2 cells and liver tissue, respectively. In summary, for liver tissue and HepG2 cells a "transcriptoproteome" was produced that reflects the relationship between transcript and protein copy numbers of the genes on Chr 18. The quantitative data acquired by RNaseq, PCR, and SRM were uploaded into the "Update_2013" data set of our knowledgebase (www.kb18.ru) and investigated for linear correlations.
authors: Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences , 10 Pogodinskaya Street, Moscow 119121, Russia.
authors: Elena A
authors: EA
authors: Ponomarenko
authors: Arthur T
authors: AT
authors: Kopylov
authors: Andrey V
authors: AV
authors: Lisitsa
authors: Sergey P
authors: SP
authors: Radko
authors: Yana Yu
authors: YY
authors: Kiseleva
authors: Leonid K
authors: LK
authors: Kurbatov
authors: Konstantin G
authors: KG
authors: Ptitsyn
authors: Olga V
authors: OV
authors: Tikhonova
authors: Alexander A
authors: AA
authors: Moisa
authors: Svetlana E
authors: SE
authors: Novikova
authors: Ekaterina V
authors: EV
authors: Poverennaya
authors: Ekaterina V
authors: EV
authors: Ilgisonis
authors: Alexey D
authors: AD
authors: Filimonov
authors: Nadezhda A
authors: NA
authors: Bogolubova
authors: Valentina V
authors: VV
authors: Averchuk
authors: Pavel A
authors: PA
authors: Karalkin
authors: Igor V
authors: IV
authors: Vakhrushev
authors: Konstantin N
authors: KN
authors: Yarygin
authors: Sergei A
authors: SA
authors: Moshkovskii
authors: Victor G
authors: VG
authors: Zgoda
authors: Alexey S
authors: AS
authors: Sokolov
authors: Alexander M
authors: AM
authors: Mazur
authors: Egor B
authors: EB
authors: Prokhortchouck
authors: Konstantin G
authors: KG
authors: Skryabin
authors: Elena N
authors: EN
authors: Ilina
authors: Elena S
authors: ES
authors: Kostrjukova
authors: Dmitry G
authors: DG
authors: Alexeev
authors: Alexander V
authors: AV
authors: Tyakht
authors: Alexey Yu
authors: AY
authors: Gorbachev
authors: Vadim M
authors: VM
authors: Govorun
authors: Alexander I
authors: AI
authors: Archakov
mesh_terms: D002887:Chromosomes, Human, Pair 18; D056945:Hep G2 Cells; D006801:Humans; D008099:Liver / Q000378:metabolism*; D010949:Plasma; D016133:Polymerase Chain Reaction / Q000379:methods; D020543:Proteome; D059467:Transcriptome
chemical_list: D020543:Proteome