1 research outputs found
State of the Art of Chromosome 18-Centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells
A gene-centric approach
was applied for a large-scale study of
expression products of a single chromosome. Transcriptome profiling
of liver tissue and HepG2 cell line was independently performed using
two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital
PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed
using shotgun LC–MS/MS as well as selected reaction monitoring
with stable isotope-labeled standards (SRM/SIS) for liver tissue and
HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers
were estimated for the Chromosome 18 (Chr 18) encoded proteins in
the selected types of biological material. These values were compared
with expression levels of corresponding mRNA. As a result, we obtained
information about 158 and 142 transcripts for HepG2 cell line and
liver tissue, respectively. SRM/SIS measurements and shotgun LC–MS/MS
allowed us to detect 91 Chr 18-encoded proteins in total, while an
intersection between the HepG2 cell line and liver tissue proteomes
was ∼66%. In total, there were 16 proteins specifically observed
in HepG2 cell line, while 15 proteins were found solely in the liver
tissue. Comparison between proteome and transcriptome revealed a poor
correlation (<i>R</i><sup>2</sup> ≈ 0.1) between
corresponding mRNA and protein expression levels. The SRM and shotgun
data sets (obtained during 2015–2016) are available in PASSEL
(PASS00697) and ProteomeExchange/PRIDE (PXD004407). All measurements
were also uploaded into the in-house Chr 18 Knowledgebase at http://kb18.ru/protein/matrix/416126