12 research outputs found
Chromosome 18 Transcriptoproteome of Liver Tissue and HepG2 Cells and Targeted Proteome Mapping in Depleted Plasma: Update 2013
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<sup>–13</sup> 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<sup>8</sup> copies/ÎĽL, while the median abundance was 10<sup>4</sup> and
10<sup>5</sup> 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
Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells
The final goal of the Russian part of the Chromosome-centric
Human
Proteome Project (C-HPP) was established as the analysis of the chromosome
18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells
with the sensitivity of 10<sup>–18</sup> M. Using SRM, we have
recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2
cells. On the basis of the results of the survey, the SRM assays were
drafted for 250 proteins: 41 proteins were found only in the liver
tissue, 82 proteins were specifically detected in depleted plasma,
and 127 proteins were mapped in both samples. The targeted analysis
of HepG2 cells was carried out for 49 proteins; 41 of them were successfully
registered using ordinary SRM and 5 additional proteins were registered
using a combination of irreversible binding of proteins on CN-Br Sepharose
4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq
and RT-PCR has shown a significant correlation (<i>r</i> = 0.78) for 42 gene transcripts. A pilot affinity-based interactome
analysis was performed for cytochrome b5 using analytical and preparative
optical biosensor fishing followed by MS analysis of the fished proteins.
All of the data on the proteome complement of the Chr 18 have been
integrated into our gene-centric knowledgebase (www.kb18.ru)
Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells
The final goal of the Russian part of the Chromosome-centric
Human
Proteome Project (C-HPP) was established as the analysis of the chromosome
18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells
with the sensitivity of 10<sup>–18</sup> M. Using SRM, we have
recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2
cells. On the basis of the results of the survey, the SRM assays were
drafted for 250 proteins: 41 proteins were found only in the liver
tissue, 82 proteins were specifically detected in depleted plasma,
and 127 proteins were mapped in both samples. The targeted analysis
of HepG2 cells was carried out for 49 proteins; 41 of them were successfully
registered using ordinary SRM and 5 additional proteins were registered
using a combination of irreversible binding of proteins on CN-Br Sepharose
4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq
and RT-PCR has shown a significant correlation (<i>r</i> = 0.78) for 42 gene transcripts. A pilot affinity-based interactome
analysis was performed for cytochrome b5 using analytical and preparative
optical biosensor fishing followed by MS analysis of the fished proteins.
All of the data on the proteome complement of the Chr 18 have been
integrated into our gene-centric knowledgebase (www.kb18.ru)
Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells
The final goal of the Russian part of the Chromosome-centric
Human
Proteome Project (C-HPP) was established as the analysis of the chromosome
18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells
with the sensitivity of 10<sup>–18</sup> M. Using SRM, we have
recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2
cells. On the basis of the results of the survey, the SRM assays were
drafted for 250 proteins: 41 proteins were found only in the liver
tissue, 82 proteins were specifically detected in depleted plasma,
and 127 proteins were mapped in both samples. The targeted analysis
of HepG2 cells was carried out for 49 proteins; 41 of them were successfully
registered using ordinary SRM and 5 additional proteins were registered
using a combination of irreversible binding of proteins on CN-Br Sepharose
4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq
and RT-PCR has shown a significant correlation (<i>r</i> = 0.78) for 42 gene transcripts. A pilot affinity-based interactome
analysis was performed for cytochrome b5 using analytical and preparative
optical biosensor fishing followed by MS analysis of the fished proteins.
All of the data on the proteome complement of the Chr 18 have been
integrated into our gene-centric knowledgebase (www.kb18.ru)
Chromosome 18 Transcriptoproteome of Liver Tissue and HepG2 Cells and Targeted Proteome Mapping in Depleted Plasma: Update 2013
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<sup>–13</sup> 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<sup>8</sup> copies/ÎĽL, while the median abundance was 10<sup>4</sup> and
10<sup>5</sup> 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
Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells
The final goal of the Russian part of the Chromosome-centric
Human
Proteome Project (C-HPP) was established as the analysis of the chromosome
18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells
with the sensitivity of 10<sup>–18</sup> M. Using SRM, we have
recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2
cells. On the basis of the results of the survey, the SRM assays were
drafted for 250 proteins: 41 proteins were found only in the liver
tissue, 82 proteins were specifically detected in depleted plasma,
and 127 proteins were mapped in both samples. The targeted analysis
of HepG2 cells was carried out for 49 proteins; 41 of them were successfully
registered using ordinary SRM and 5 additional proteins were registered
using a combination of irreversible binding of proteins on CN-Br Sepharose
4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq
and RT-PCR has shown a significant correlation (<i>r</i> = 0.78) for 42 gene transcripts. A pilot affinity-based interactome
analysis was performed for cytochrome b5 using analytical and preparative
optical biosensor fishing followed by MS analysis of the fished proteins.
All of the data on the proteome complement of the Chr 18 have been
integrated into our gene-centric knowledgebase (www.kb18.ru)
Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells
The final goal of the Russian part of the Chromosome-centric
Human
Proteome Project (C-HPP) was established as the analysis of the chromosome
18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells
with the sensitivity of 10<sup>–18</sup> M. Using SRM, we have
recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2
cells. On the basis of the results of the survey, the SRM assays were
drafted for 250 proteins: 41 proteins were found only in the liver
tissue, 82 proteins were specifically detected in depleted plasma,
and 127 proteins were mapped in both samples. The targeted analysis
of HepG2 cells was carried out for 49 proteins; 41 of them were successfully
registered using ordinary SRM and 5 additional proteins were registered
using a combination of irreversible binding of proteins on CN-Br Sepharose
4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq
and RT-PCR has shown a significant correlation (<i>r</i> = 0.78) for 42 gene transcripts. A pilot affinity-based interactome
analysis was performed for cytochrome b5 using analytical and preparative
optical biosensor fishing followed by MS analysis of the fished proteins.
All of the data on the proteome complement of the Chr 18 have been
integrated into our gene-centric knowledgebase (www.kb18.ru)
Chromosome 18 Transcriptoproteome of Liver Tissue and HepG2 Cells and Targeted Proteome Mapping in Depleted Plasma: Update 2013
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<sup>–13</sup> 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<sup>8</sup> copies/ÎĽL, while the median abundance was 10<sup>4</sup> and
10<sup>5</sup> 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
Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells
The final goal of the Russian part of the Chromosome-centric
Human
Proteome Project (C-HPP) was established as the analysis of the chromosome
18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells
with the sensitivity of 10<sup>–18</sup> M. Using SRM, we have
recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2
cells. On the basis of the results of the survey, the SRM assays were
drafted for 250 proteins: 41 proteins were found only in the liver
tissue, 82 proteins were specifically detected in depleted plasma,
and 127 proteins were mapped in both samples. The targeted analysis
of HepG2 cells was carried out for 49 proteins; 41 of them were successfully
registered using ordinary SRM and 5 additional proteins were registered
using a combination of irreversible binding of proteins on CN-Br Sepharose
4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq
and RT-PCR has shown a significant correlation (<i>r</i> = 0.78) for 42 gene transcripts. A pilot affinity-based interactome
analysis was performed for cytochrome b5 using analytical and preparative
optical biosensor fishing followed by MS analysis of the fished proteins.
All of the data on the proteome complement of the Chr 18 have been
integrated into our gene-centric knowledgebase (www.kb18.ru)
Chromosome 18 Transcriptome Profiling and Targeted Proteome Mapping in Depleted Plasma, Liver Tissue and HepG2 Cells
The final goal of the Russian part of the Chromosome-centric
Human
Proteome Project (C-HPP) was established as the analysis of the chromosome
18 (Chr 18) protein complement in plasma, liver tissue and HepG2 cells
with the sensitivity of 10<sup>–18</sup> M. Using SRM, we have
recently targeted 277 Chr 18 proteins in plasma, liver, and HepG2
cells. On the basis of the results of the survey, the SRM assays were
drafted for 250 proteins: 41 proteins were found only in the liver
tissue, 82 proteins were specifically detected in depleted plasma,
and 127 proteins were mapped in both samples. The targeted analysis
of HepG2 cells was carried out for 49 proteins; 41 of them were successfully
registered using ordinary SRM and 5 additional proteins were registered
using a combination of irreversible binding of proteins on CN-Br Sepharose
4B with SRM. Transcriptome profiling of HepG2 cells performed by RNAseq
and RT-PCR has shown a significant correlation (<i>r</i> = 0.78) for 42 gene transcripts. A pilot affinity-based interactome
analysis was performed for cytochrome b5 using analytical and preparative
optical biosensor fishing followed by MS analysis of the fished proteins.
All of the data on the proteome complement of the Chr 18 have been
integrated into our gene-centric knowledgebase (www.kb18.ru)