A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors

Anand Venkataraman; Kun Yang; Jose Irizarry; Mark Mackiewicz; Paolo Mita; Zheng Kuang; Lin Xue; Devlina Ghosh; Shuang Liu; Pedro Ramos; Shaohui Hu; Diane Bayron Kain; Sarah Keegan; Richard Saul; Simona Colantonio; Hongyan Zhang; Florencia Pauli-Behn; Guang Song; Edisa Albino; Lillyann Asencio; Leonardo Ramos; Luvir Lugo; Gloriner Morell; Javier Rivera; Kimberly Ruiz; Ruth Almodovar; Luis Nazario; Keven Murphy; Ivan Vargas; Zully Ann Rivera-Pacheco; Christian Rosa; Moises Vargas; Jessica McDade; Brian S. Clark; Sooyeon Yoo; Seva G. Khambadkone; Jimmy De Melo; Milanka Stevanovic; Lizhi Jiang; Yana Li; Wendy Y. Yap; Brittany Jones; Atul Tandon; Elliot Campbell; Gaetano T. Montelione; Stephen Anderson; Richard M. Myers; Jef D. Boeke; David Fenyö; Gordon Whiteley; Joel S. Bader; Ignacio Pino; Daniel J. Eichinger; Heng Zhu; Seth Blackshaw

doi:10.1038/nmeth.4632

A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors

Anand Venkataraman, Kun Yang, Jose Irizarry, Mark Mackiewicz, Paolo Mita, Zheng Kuang, Lin Xue, Devlina Ghosh, Shuang Liu, Pedro Ramos, Shaohui Hu, Diane Bayron Kain, Sarah Keegan, Richard Saul, Simona Colantonio, Hongyan Zhang, Florencia Pauli-Behn, Guang Song, Edisa Albino, Lillyann AsencioLeonardo Ramos, Luvir Lugo, Gloriner Morell, Javier Rivera, Kimberly Ruiz, Ruth Almodovar, Luis Nazario, Keven Murphy, Ivan Vargas, Zully Ann Rivera-Pacheco, Christian Rosa, Moises Vargas, Jessica McDade, Brian S. Clark, Sooyeon Yoo, Seva G. Khambadkone, Jimmy De Melo, Milanka Stevanovic, Lizhi Jiang, Yana Li, Wendy Y. Yap, Brittany Jones, Atul Tandon, Elliot Campbell, Gaetano T. Montelione, Stephen Anderson, Richard M. Myers, Jef D. Boeke, David Fenyö, Gordon Whiteley, Joel S. Bader, Ignacio Pino, Daniel J. Eichinger, Heng Zhu, Seth Blackshaw

Research output: Contribution to journal › Article › peer-review

43 Scopus citations

Abstract

A key component of efforts to address the reproducibility crisis in biomedical research is the development of rigorously validated and renewable protein-affinity reagents. As part of the US National Institutes of Health (NIH) Protein Capture Reagents Program (PCRP), we have generated a collection of 1,406 highly validated immunoprecipitation- and/or immunoblotting-grade mouse monoclonal antibodies (mAbs) to 737 human transcription factors, using an integrated production and validation pipeline. We used HuProt human protein microarrays as a primary validation tool to identify mAbs with high specificity for their cognate targets. We further validated PCRP mAbs by means of multiple experimental applications, including immunoprecipitation, immunoblotting, chromatin immunoprecipitation followed by sequencing (ChIP-seq), and immunohistochemistry. We also conducted a meta-analysis that identified critical variables that contribute to the generation of high-quality mAbs. All validation data, protocols, and links to PCRP mAb suppliers are available at http://proteincapture.org.

Original language	English (US)
Pages (from-to)	330-338
Number of pages	9
Journal	Nature methods
Volume	15
Issue number	5
DOIs	https://doi.org/10.1038/nmeth.4632
State	Published - Apr 27 2018
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Venkataraman, A., Yang, K., Irizarry, J., Mackiewicz, M., Mita, P., Kuang, Z., Xue, L., Ghosh, D., Liu, S., Ramos, P., Hu, S., Kain, D. B., Keegan, S., Saul, R., Colantonio, S., Zhang, H., Pauli-Behn, F., Song, G., Albino, E., ... Blackshaw, S. (2018). A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nature methods, 15(5), 330-338. https://doi.org/10.1038/nmeth.4632

Venkataraman, A, Yang, K, Irizarry, J, Mackiewicz, M, Mita, P, Kuang, Z, Xue, L, Ghosh, D, Liu, S, Ramos, P, Hu, S, Kain, DB, Keegan, S, Saul, R, Colantonio, S, Zhang, H, Pauli-Behn, F, Song, G, Albino, E, Asencio, L, Ramos, L, Lugo, L, Morell, G, Rivera, J, Ruiz, K, Almodovar, R, Nazario, L, Murphy, K, Vargas, I, Rivera-Pacheco, ZA, Rosa, C, Vargas, M, McDade, J, Clark, BS, Yoo, S, Khambadkone, SG, De Melo, J, Stevanovic, M, Jiang, L, Li, Y, Yap, WY, Jones, B, Tandon, A, Campbell, E, Montelione, GT, Anderson, S, Myers, RM, Boeke, JD, Fenyö, D, Whiteley, G, Bader, JS, Pino, I, Eichinger, DJ, Zhu, H & Blackshaw, S 2018, 'A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors', Nature methods, vol. 15, no. 5, pp. 330-338. https://doi.org/10.1038/nmeth.4632

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title = "A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors",

abstract = "A key component of efforts to address the reproducibility crisis in biomedical research is the development of rigorously validated and renewable protein-affinity reagents. As part of the US National Institutes of Health (NIH) Protein Capture Reagents Program (PCRP), we have generated a collection of 1,406 highly validated immunoprecipitation- and/or immunoblotting-grade mouse monoclonal antibodies (mAbs) to 737 human transcription factors, using an integrated production and validation pipeline. We used HuProt human protein microarrays as a primary validation tool to identify mAbs with high specificity for their cognate targets. We further validated PCRP mAbs by means of multiple experimental applications, including immunoprecipitation, immunoblotting, chromatin immunoprecipitation followed by sequencing (ChIP-seq), and immunohistochemistry. We also conducted a meta-analysis that identified critical variables that contribute to the generation of high-quality mAbs. All validation data, protocols, and links to PCRP mAb suppliers are available at http://proteincapture.org.",

author = "Anand Venkataraman and Kun Yang and Jose Irizarry and Mark Mackiewicz and Paolo Mita and Zheng Kuang and Lin Xue and Devlina Ghosh and Shuang Liu and Pedro Ramos and Shaohui Hu and Kain, {Diane Bayron} and Sarah Keegan and Richard Saul and Simona Colantonio and Hongyan Zhang and Florencia Pauli-Behn and Guang Song and Edisa Albino and Lillyann Asencio and Leonardo Ramos and Luvir Lugo and Gloriner Morell and Javier Rivera and Kimberly Ruiz and Ruth Almodovar and Luis Nazario and Keven Murphy and Ivan Vargas and Rivera-Pacheco, {Zully Ann} and Christian Rosa and Moises Vargas and Jessica McDade and Clark, {Brian S.} and Sooyeon Yoo and Khambadkone, {Seva G.} and {De Melo}, Jimmy and Milanka Stevanovic and Lizhi Jiang and Yana Li and Yap, {Wendy Y.} and Brittany Jones and Atul Tandon and Elliot Campbell and Montelione, {Gaetano T.} and Stephen Anderson and Myers, {Richard M.} and Boeke, {Jef D.} and David Feny{\"o} and Gordon Whiteley and Bader, {Joel S.} and Ignacio Pino and Eichinger, {Daniel J.} and Heng Zhu and Seth Blackshaw",

note = "Funding Information: This work was supported by the NIH Common Fund (awards U54HG006434 (to J.D.B., S.B., and H.Z.) and U01DC011485 (to S.A. and G.T.M.)). Cy5-UTP-incorporated cRNA probes of Xist produced by T7-directed transcription were a kind gift from E. Lander's lab (MIT, Cambridge, Massachusetts, USA). Publisher Copyright: {\textcopyright} 2018 Nature America, Inc., part of of Springer Nature. All rights reserved.",

year = "2018",

month = apr,

day = "27",

doi = "10.1038/nmeth.4632",

language = "English (US)",

volume = "15",

pages = "330--338",

journal = "Nature methods",

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T1 - A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors

AU - Venkataraman, Anand

AU - Yang, Kun

AU - Irizarry, Jose

AU - Mackiewicz, Mark

AU - Mita, Paolo

AU - Kuang, Zheng

AU - Xue, Lin

AU - Ghosh, Devlina

AU - Liu, Shuang

AU - Ramos, Pedro

AU - Hu, Shaohui

AU - Kain, Diane Bayron

AU - Keegan, Sarah

AU - Saul, Richard

AU - Colantonio, Simona

AU - Zhang, Hongyan

AU - Pauli-Behn, Florencia

AU - Song, Guang

AU - Albino, Edisa

AU - Asencio, Lillyann

AU - Ramos, Leonardo

AU - Lugo, Luvir

AU - Morell, Gloriner

AU - Rivera, Javier

AU - Ruiz, Kimberly

AU - Almodovar, Ruth

AU - Nazario, Luis

AU - Murphy, Keven

AU - Vargas, Ivan

AU - Rivera-Pacheco, Zully Ann

AU - Rosa, Christian

AU - Vargas, Moises

AU - McDade, Jessica

AU - Clark, Brian S.

AU - Yoo, Sooyeon

AU - Khambadkone, Seva G.

AU - De Melo, Jimmy

AU - Stevanovic, Milanka

AU - Jiang, Lizhi

AU - Li, Yana

AU - Yap, Wendy Y.

AU - Jones, Brittany

AU - Tandon, Atul

AU - Campbell, Elliot

AU - Montelione, Gaetano T.

AU - Anderson, Stephen

AU - Myers, Richard M.

AU - Boeke, Jef D.

AU - Fenyö, David

AU - Whiteley, Gordon

AU - Bader, Joel S.

AU - Pino, Ignacio

AU - Eichinger, Daniel J.

AU - Zhu, Heng

AU - Blackshaw, Seth

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PY - 2018/4/27

Y1 - 2018/4/27

N2 - A key component of efforts to address the reproducibility crisis in biomedical research is the development of rigorously validated and renewable protein-affinity reagents. As part of the US National Institutes of Health (NIH) Protein Capture Reagents Program (PCRP), we have generated a collection of 1,406 highly validated immunoprecipitation- and/or immunoblotting-grade mouse monoclonal antibodies (mAbs) to 737 human transcription factors, using an integrated production and validation pipeline. We used HuProt human protein microarrays as a primary validation tool to identify mAbs with high specificity for their cognate targets. We further validated PCRP mAbs by means of multiple experimental applications, including immunoprecipitation, immunoblotting, chromatin immunoprecipitation followed by sequencing (ChIP-seq), and immunohistochemistry. We also conducted a meta-analysis that identified critical variables that contribute to the generation of high-quality mAbs. All validation data, protocols, and links to PCRP mAb suppliers are available at http://proteincapture.org.

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A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors

Abstract

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