1 Chromosome 18 Transcriptoproteome of Liver Tissue and 2 HepG2 Cells and Targeted Proteome Mapping in Depleted Plasma: 3 Update 2013 4 Elena A. Ponomarenko, † Arthur T. Kopylov, † Andrey V. Lisitsa, † Sergey P. Radko, † Yana Yu. Kiseleva, † 5 Leonid K. Kurbatov, † Konstantin G. Ptitsyn, † Olga V. Tikhonova, † Alexander A. Moisa, † 6 Svetlana E. Novikova, † Ekaterina V. Poverennaya, † Ekaterina V. Ilgisonis, † Alexey D. Filimonov, † 7 Nadezhda A. Bogolubova, † Valentina V. Averchuk, † Pavel A. Karalkin, † Igor V. Vakhrushev, † 8 Konstantin N. Yarygin, † Sergei A. Moshkovskii, † Victor G. Zgoda, † Alexey S. Sokolov, ‡ 9 Alexander M. Mazur, § Egor B. Prokhortchouck, ‡,§ Konstantin G. Skryabin, ‡,§ Elena N. Ilina, ∥ 10 Elena S. Kostrjukova, ∥ Dmitry G. Alexeev, ∥ Alexander V. Tyakht, ∥ Alexey Yu. Gorbachev, ∥ 11 Vadim M. Govorun, ∥ and Alexander I. Archakov* ,† 12 † Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10 Pogodinskaya Street, 13 Moscow 119121, Russia 14 ‡ National Research Centre “Kurchatov Institute”, 1 Akademika Kurchatova pl., Moscow 123182, Russia 15 § Center Bioengineering, Russian Academy of Sciences, 7/1 Prospekt 60-Letiya Oktyabrya, Moscow 117312, Russia 16 ∥ Scientific-Research Institute of Physical Chemical Medicine of the Federal Medical-Biological Agency of the Russian Federation, 17 1a Malaya Pirogovskaya Street, Moscow 119828, Russia 18 * S Supporting Information 19 ABSTRACT: We report the results obtained in 2012−2013 20 by the Russian Consortium for the Chromosome-centric Human 21 Proteome Project (C-HPP). The main scope of this work was the 22 transcriptome profiling of genes on human chromosome 18 (Chr 23 18), as well as their encoded proteome, from three types of 24 biomaterials: liver tissue, the hepatocellular carcinoma-derived cell 25 line HepG2, and blood plasma. The transcriptome profiling for 26 liver tissue was independently performed using two RNaseq 27 platforms (SOLiD and Illumina) and also by droplet digital PCR 28 (ddPCR) and quantitative RT-PCR. The proteome profiling of 29 Chr 18 was accomplished by quantitatively measuring protein 30 copy numbers in the three types of biomaterial (at a sensitivity of 31 10 −13 M) using selected reaction monitoring (SRM). In total, 32 protein copy numbers were estimated for 228 master proteins, 33 including quantitative data on 164 proteins in plasma, 171 in the HepG2 cell line, and 186 in liver tissue. Most proteins were present in 34 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, 35 respectively. In summary, for liver tissue and HepG2 cells a “transcriptoproteome” was produced that reflects the relationship between 36 transcript and protein copy numbers of the genes on Chr 18. The quantitative data acquired by RNaseq, PCR, and SRM were 37 uploaded into the “Update_2013” data set of our knowledgebase (www.kb18.ru) and investigated for linear correlations. 38 KEYWORDS: mRNA sequencing, quantitative PCR, selected reaction monitoring, human proteome project, transcriptome, proteome, 39 transcriptoproteome, chromosome 18 40 ■ INTRODUCTION 41 The final goal of the Russian Consortium for the Chromosome- 42 centric Human Proteome Project (C-HPP) was the analysis of 43 proteins encoded by chromosome 18 (Chr 18) in plasma, liver 44 tissue, and HepG2 cells with a sensitivity of 10 −18 M, which 45 corresponds to one protein copy per 10 6 liver cells, 10 7 HepG2 46 cells, or 1 μL of plasma. 1 47 The size of the human proteome, which requires estimates of 48 the width (number of protein species in a biosample) and depth 49 (number of copies of the same protein molecule in a biosample), Special Issue: Chromosome-centric Human Proteome Project Received: August 28, 2013 Article pubs.acs.org/jpr © XXXX American Chemical Society A dx.doi.org/10.1021/pr400883x | J. Proteome Res. XXXX, XXX, XXX−XXX * UNKNOWN *| MPSJCA | JCA10.0.1465/W Unicode | pr-2013-00883x.3d (R3.6.i4:4180 | 2.0 alpha 39) 2013/10/21 02:46:00 | PROD-JCAVA | rq_2930999 | 11/12/2013 16:39:59 | 8 | JCA-DEFAULT