Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

Eric W. Deutsch; Catherine A. Ball; Jules J. Berman; G. Steven Bova; Alvis Brazma; Roger E. Bumgarner; David Campbell; Helen C. Causton; Jeffrey H. Christiansen; Fabrice Daian; Delphine Dauga; Duncan R. Davidson; Gregory Gimenez; Young Ah Goo; Sean Grimmond; Thorsten Henrich; Bernhard G. Herrmann; Michael H. Johnson; Martin Korb; Jason C. Mills; Asa J. Oudes; Helen E. Parkinson; Laura E. Pascal; Nicolas Pollet; John Quackenbush; Mirana Ramialison; Martin Ringwald; David Salgado; Susanna Assunta Sansone; Gavin Sherlock; Christian J. Stoeckert; Jason Swedlow; Ronald C. Taylor; Laura Walashek; Anthony Warford; David G. Wilkinson; Yi Zhou; Leonard I. Zon; Alvin Y. Liu; Lawrence D. True

doi:10.1038/nbt1391

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

Eric W. Deutsch, Catherine A. Ball, Jules J. Berman, G. Steven Bova, Alvis Brazma, Roger E. Bumgarner, David Campbell, Helen C. Causton, Jeffrey H. Christiansen, Fabrice Daian, Delphine Dauga, Duncan R. Davidson, Gregory Gimenez, Young Ah Goo, Sean Grimmond, Thorsten Henrich, Bernhard G. Herrmann, Michael H. Johnson, Martin Korb, Jason C. MillsAsa J. Oudes, Helen E. Parkinson, Laura E. Pascal, Nicolas Pollet, John Quackenbush, Mirana Ramialison, Martin Ringwald, David Salgado, Susanna Assunta Sansone, Gavin Sherlock, Christian J. Stoeckert, Jason Swedlow, Ronald C. Taylor, Laura Walashek, Anthony Warford, David G. Wilkinson, Yi Zhou, Leonard I. Zon, Alvin Y. Liu, Lawrence D. True

PCE - Proteomics Center of Excellence

Research output: Contribution to journal › Review article › peer-review

90 Scopus citations

Abstract

One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.

Original language	English (US)
Pages (from-to)	305-312
Number of pages	8
Journal	Nature biotechnology
Volume	26
Issue number	3
DOIs	https://doi.org/10.1038/nbt1391
State	Published - Mar 2008

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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Deutsch, E. W., Ball, C. A., Berman, J. J., Bova, G. S., Brazma, A., Bumgarner, R. E., Campbell, D., Causton, H. C., Christiansen, J. H., Daian, F., Dauga, D., Davidson, D. R., Gimenez, G., Goo, Y. A., Grimmond, S., Henrich, T., Herrmann, B. G., Johnson, M. H., Korb, M., ... True, L. D. (2008). Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Nature biotechnology, 26(3), 305-312. https://doi.org/10.1038/nbt1391

Deutsch, Eric W. ; Ball, Catherine A. ; Berman, Jules J. ; Bova, G. Steven ; Brazma, Alvis ; Bumgarner, Roger E. ; Campbell, David ; Causton, Helen C. ; Christiansen, Jeffrey H. ; Daian, Fabrice ; Dauga, Delphine ; Davidson, Duncan R. ; Gimenez, Gregory ; Goo, Young Ah ; Grimmond, Sean ; Henrich, Thorsten ; Herrmann, Bernhard G. ; Johnson, Michael H. ; Korb, Martin ; Mills, Jason C. ; Oudes, Asa J. ; Parkinson, Helen E. ; Pascal, Laura E. ; Pollet, Nicolas ; Quackenbush, John ; Ramialison, Mirana ; Ringwald, Martin ; Salgado, David ; Sansone, Susanna Assunta ; Sherlock, Gavin ; Stoeckert, Christian J. ; Swedlow, Jason ; Taylor, Ronald C. ; Walashek, Laura ; Warford, Anthony ; Wilkinson, David G. ; Zhou, Yi ; Zon, Leonard I. ; Liu, Alvin Y. ; True, Lawrence D. / Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). In: Nature biotechnology. 2008 ; Vol. 26, No. 3. pp. 305-312.

@article{7184c479063b4f1ea92a569e3e329da2,

title = "Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)",

abstract = "One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.",

author = "Deutsch, {Eric W.} and Ball, {Catherine A.} and Berman, {Jules J.} and Bova, {G. Steven} and Alvis Brazma and Bumgarner, {Roger E.} and David Campbell and Causton, {Helen C.} and Christiansen, {Jeffrey H.} and Fabrice Daian and Delphine Dauga and Davidson, {Duncan R.} and Gregory Gimenez and Goo, {Young Ah} and Sean Grimmond and Thorsten Henrich and Herrmann, {Bernhard G.} and Johnson, {Michael H.} and Martin Korb and Mills, {Jason C.} and Oudes, {Asa J.} and Parkinson, {Helen E.} and Pascal, {Laura E.} and Nicolas Pollet and John Quackenbush and Mirana Ramialison and Martin Ringwald and David Salgado and Sansone, {Susanna Assunta} and Gavin Sherlock and Stoeckert, {Christian J.} and Jason Swedlow and Taylor, {Ronald C.} and Laura Walashek and Anthony Warford and Wilkinson, {David G.} and Yi Zhou and Zon, {Leonard I.} and Liu, {Alvin Y.} and True, {Lawrence D.}",

note = "Funding Information: We?thank?R.?Drysdale,?L.?Eichner,?M.?Heiskanen?and?M.? Westerfield?for?comments? and?discussions?during?the?preparation?of?the?MISFISHIE?specification?and? C.?Emswiler?for?assistance?with?the?figures.?This?work?was?funded?in?part?with? support?from?the?US?National?Institute?of?Diabetes?&?Digestive?&?Kidney?Diseases? to?members?of?the?Stem?Cell?Genome? Anatomy?Projects?Consortium,?including? DK63483?to?J.?Gordon,?DK63481?to?I.?Lemischka,?DK63400?to?M.?Little,?DK63630?to? A.?Liu?and?DK63328?to?L.?Zon?(Children{\textquoteright}s?Hospital?Boston).",

year = "2008",

month = mar,

doi = "10.1038/nbt1391",

language = "English (US)",

volume = "26",

pages = "305--312",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "3",

}

Deutsch, EW, Ball, CA, Berman, JJ, Bova, GS, Brazma, A, Bumgarner, RE, Campbell, D, Causton, HC, Christiansen, JH, Daian, F, Dauga, D, Davidson, DR, Gimenez, G, Goo, YA, Grimmond, S, Henrich, T, Herrmann, BG, Johnson, MH, Korb, M, Mills, JC, Oudes, AJ, Parkinson, HE, Pascal, LE, Pollet, N, Quackenbush, J, Ramialison, M, Ringwald, M, Salgado, D, Sansone, SA, Sherlock, G, Stoeckert, CJ, Swedlow, J, Taylor, RC, Walashek, L, Warford, A, Wilkinson, DG, Zhou, Y, Zon, LI, Liu, AY & True, LD 2008, 'Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)', Nature biotechnology, vol. 26, no. 3, pp. 305-312. https://doi.org/10.1038/nbt1391

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). / Deutsch, Eric W.; Ball, Catherine A.; Berman, Jules J.; Bova, G. Steven; Brazma, Alvis; Bumgarner, Roger E.; Campbell, David; Causton, Helen C.; Christiansen, Jeffrey H.; Daian, Fabrice; Dauga, Delphine; Davidson, Duncan R.; Gimenez, Gregory; Goo, Young Ah; Grimmond, Sean; Henrich, Thorsten; Herrmann, Bernhard G.; Johnson, Michael H.; Korb, Martin; Mills, Jason C.; Oudes, Asa J.; Parkinson, Helen E.; Pascal, Laura E.; Pollet, Nicolas; Quackenbush, John; Ramialison, Mirana; Ringwald, Martin; Salgado, David; Sansone, Susanna Assunta; Sherlock, Gavin; Stoeckert, Christian J.; Swedlow, Jason; Taylor, Ronald C.; Walashek, Laura; Warford, Anthony; Wilkinson, David G.; Zhou, Yi; Zon, Leonard I.; Liu, Alvin Y.; True, Lawrence D.

In: Nature biotechnology, Vol. 26, No. 3, 03.2008, p. 305-312.

Research output: Contribution to journal › Review article › peer-review

TY - JOUR

T1 - Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

AU - Deutsch, Eric W.

AU - Ball, Catherine A.

AU - Berman, Jules J.

AU - Bova, G. Steven

AU - Brazma, Alvis

AU - Bumgarner, Roger E.

AU - Campbell, David

AU - Causton, Helen C.

AU - Christiansen, Jeffrey H.

AU - Daian, Fabrice

AU - Dauga, Delphine

AU - Davidson, Duncan R.

AU - Gimenez, Gregory

AU - Goo, Young Ah

AU - Grimmond, Sean

AU - Henrich, Thorsten

AU - Herrmann, Bernhard G.

AU - Johnson, Michael H.

AU - Korb, Martin

AU - Mills, Jason C.

AU - Oudes, Asa J.

AU - Parkinson, Helen E.

AU - Pascal, Laura E.

AU - Pollet, Nicolas

AU - Quackenbush, John

AU - Ramialison, Mirana

AU - Ringwald, Martin

AU - Salgado, David

AU - Sansone, Susanna Assunta

AU - Sherlock, Gavin

AU - Stoeckert, Christian J.

AU - Swedlow, Jason

AU - Taylor, Ronald C.

AU - Walashek, Laura

AU - Warford, Anthony

AU - Wilkinson, David G.

AU - Zhou, Yi

AU - Zon, Leonard I.

AU - Liu, Alvin Y.

AU - True, Lawrence D.

N1 - Funding Information: We?thank?R.?Drysdale,?L.?Eichner,?M.?Heiskanen?and?M.? Westerfield?for?comments? and?discussions?during?the?preparation?of?the?MISFISHIE?specification?and? C.?Emswiler?for?assistance?with?the?figures.?This?work?was?funded?in?part?with? support?from?the?US?National?Institute?of?Diabetes?&?Digestive?&?Kidney?Diseases? to?members?of?the?Stem?Cell?Genome? Anatomy?Projects?Consortium,?including? DK63483?to?J.?Gordon,?DK63481?to?I.?Lemischka,?DK63400?to?M.?Little,?DK63630?to? A.?Liu?and?DK63328?to?L.?Zon?(Children’s?Hospital?Boston).

PY - 2008/3

Y1 - 2008/3

N2 - One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.

AB - One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present reporting guidelines for gene expression localization experiments: the minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). MISFISHIE is modeled after the Minimum Information About a Microarray Experiment (MIAME) specification for microarray experiments. Both guidelines define what information should be reported without dictating a format for encoding that information. MISFISHIE describes six types of information to be provided for each experiment: experimental design, biomaterials and treatments, reporters, staining, imaging data and image characterizations. This specification has benefited the consortium within which it was developed and is expected to benefit the wider research community. We welcome feedback from the scientific community to help improve our proposal.

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U2 - 10.1038/nbt1391

DO - 10.1038/nbt1391

M3 - Review article

C2 - 18327244

AN - SCOPUS:40449117669

VL - 26

SP - 305

EP - 312

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 3

ER -