Abstract
Protein and RNA profiles are highly informative when generating a comprehensive understanding of the dynamics of complex biological systems. Quantitative correlations between protein and RNA profiles are not always high, yet simultaneous acquisition of both profiles remains challenging, in part because of the limited availability of samples and the inconvenience of separately preparing protein and RNA fractions. In a previous study, protein, DNA, and RNA fractions were simultaneously prepared from the same sample using phenol-guanidinium isothiocyanate reagent (P/GTC), although the performance of P/GTC-extracts in proteogenomic analyses remains poorly understood. We therefore evaluated the performance of the P/GTC-extraction method in proteogenomic analyses using standard HEK293-F cells and human peripheral blood neutrophils. The latter cell type is renowned for its extreme vulnerability to protein/RNA degradation, reflecting high protease and RNase activities. Our data indicate that the P/GTC extraction method provides superior protein profiles from neutrophil and HEK293-F cell samples for simultaneous preparation of RNA and protein, as compared with those from conventional protein extraction methods. The P/GTC extraction method therefore provides a powerful and robust tool for a broad range of proteogenomic studies.
| Original language | English |
|---|---|
| Journal | Journal of Proteome Research |
| DOIs | |
| Publication status | Accepted/In press - 2018 Jan 1 |
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Keywords
- multiomics
- neutrophils
- P/GTC
- proteogenomics
- trans-omics
ASJC Scopus subject areas
- Biochemistry
- Chemistry(all)
Cite this
Proteogenomic Analyses of Cellular Lysates Using a Phenol-Guanidinium Thiocyanate Reagent. / Kawashima, Yusuke; Miyata, Jun; Watanabe, Takashi; Shioya, Juri; Arita, Makoto; Ohara, Osamu.
In: Journal of Proteome Research, 01.01.2018.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Proteogenomic Analyses of Cellular Lysates Using a Phenol-Guanidinium Thiocyanate Reagent
AU - Kawashima, Yusuke
AU - Miyata, Jun
AU - Watanabe, Takashi
AU - Shioya, Juri
AU - Arita, Makoto
AU - Ohara, Osamu
PY - 2018/1/1
Y1 - 2018/1/1
N2 - Protein and RNA profiles are highly informative when generating a comprehensive understanding of the dynamics of complex biological systems. Quantitative correlations between protein and RNA profiles are not always high, yet simultaneous acquisition of both profiles remains challenging, in part because of the limited availability of samples and the inconvenience of separately preparing protein and RNA fractions. In a previous study, protein, DNA, and RNA fractions were simultaneously prepared from the same sample using phenol-guanidinium isothiocyanate reagent (P/GTC), although the performance of P/GTC-extracts in proteogenomic analyses remains poorly understood. We therefore evaluated the performance of the P/GTC-extraction method in proteogenomic analyses using standard HEK293-F cells and human peripheral blood neutrophils. The latter cell type is renowned for its extreme vulnerability to protein/RNA degradation, reflecting high protease and RNase activities. Our data indicate that the P/GTC extraction method provides superior protein profiles from neutrophil and HEK293-F cell samples for simultaneous preparation of RNA and protein, as compared with those from conventional protein extraction methods. The P/GTC extraction method therefore provides a powerful and robust tool for a broad range of proteogenomic studies.
AB - Protein and RNA profiles are highly informative when generating a comprehensive understanding of the dynamics of complex biological systems. Quantitative correlations between protein and RNA profiles are not always high, yet simultaneous acquisition of both profiles remains challenging, in part because of the limited availability of samples and the inconvenience of separately preparing protein and RNA fractions. In a previous study, protein, DNA, and RNA fractions were simultaneously prepared from the same sample using phenol-guanidinium isothiocyanate reagent (P/GTC), although the performance of P/GTC-extracts in proteogenomic analyses remains poorly understood. We therefore evaluated the performance of the P/GTC-extraction method in proteogenomic analyses using standard HEK293-F cells and human peripheral blood neutrophils. The latter cell type is renowned for its extreme vulnerability to protein/RNA degradation, reflecting high protease and RNase activities. Our data indicate that the P/GTC extraction method provides superior protein profiles from neutrophil and HEK293-F cell samples for simultaneous preparation of RNA and protein, as compared with those from conventional protein extraction methods. The P/GTC extraction method therefore provides a powerful and robust tool for a broad range of proteogenomic studies.
KW - multiomics
KW - neutrophils
KW - P/GTC
KW - proteogenomics
KW - trans-omics
UR - http://www.scopus.com/inward/record.url?scp=85056902254&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85056902254&partnerID=8YFLogxK
U2 - 10.1021/acs.jproteome.8b00609
DO - 10.1021/acs.jproteome.8b00609
M3 - Article
C2 - 30394753
AN - SCOPUS:85056902254
JO - Journal of Proteome Research
JF - Journal of Proteome Research
SN - 1535-3893
ER -