Article

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities.
Müller, P. ORCID: https://orcid.org/0000-0003-3290-8251, de la Cuesta-Zuluaga, J. ORCID: https://orcid.org/0000-0002-7369-992X, Kuhn, M. ORCID: https://orcid.org/0000-0002-2841-872X, Baghai Arassi, M. ORCID: https://orcid.org/0000-0002-8957-7767, Treis, T. ORCID: https://orcid.org/0000-0002-9686-4799, Blasche, S. ORCID: https://orcid.org/0000-0001-9422-0474, Zimmermann, M., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Patil, K.R., Typas, A. ORCID: https://orcid.org/0000-0002-0797-9018, Garcia-Santamarina, S. and Maier, L. ORCID: https://orcid.org/0000-0002-6473-4762
Nature Protocols 19 (3): 668-699. March 2024

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility.
Lareau, C.A. ORCID: https://orcid.org/0000-0003-4179-4807, Liu, V. ORCID: https://orcid.org/0000-0002-6790-6603, Muus, C., Praktiknjo, S.D. ORCID: https://orcid.org/0000-0002-0186-5271, Nitsch, L. ORCID: https://orcid.org/0000-0003-0775-1969, Kautz, P. ORCID: https://orcid.org/0000-0002-9658-1676, Sandor, K. ORCID: https://orcid.org/0000-0003-2892-4865, Yin, Y. ORCID: https://orcid.org/0000-0002-2220-005X, Gutierrez, J.C., Pelka, K. ORCID: https://orcid.org/0000-0003-2856-8602, Satpathy, A.T. ORCID: https://orcid.org/0000-0002-5167-537X, Regev, A., Sankaran, V.G. ORCID: https://orcid.org/0000-0003-0044-443X and Ludwig, L.S. ORCID: https://orcid.org/0000-0002-2916-2164
Nature Protocols 18 (5): 1416-1440. May 2023

Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications.
Malinovska, L. ORCID: https://orcid.org/0000-0002-8514-4569, Cappelletti, V., Kohler, D., Piazza, I. ORCID: https://orcid.org/0000-0001-5895-6134, Tsai, T.H. ORCID: https://orcid.org/0000-0001-5211-2985, Pepelnjak, M., Stalder, P., Dörig, C. ORCID: https://orcid.org/0000-0002-4213-8855, Sesterhenn, F., Elsässer, F., Kralickova, L., Beaton, N., Reiter, L. ORCID: https://orcid.org/0000-0001-5751-3139, de Souza, N., Vitek, O. and Picotti, P.
Nature Protocols 18 : 659-682. 16 March 2023

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Moriel, N., Senel, E. ORCID: https://orcid.org/0000-0003-1966-1186, Friedman, N. ORCID: https://orcid.org/0000-0002-9678-3550, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947 and Nitzan, M. ORCID: https://orcid.org/0000-0003-0074-9196
Nature Protocols 16 (9): 4177-4200. September 2021

Determination of G-protein-coupled receptor oligomerization by molecular brightness analyses in single cells.
Işbilir, A. ORCID: https://orcid.org/0000-0002-9629-1150, Serfling, R., Möller, J. ORCID: https://orcid.org/0000-0001-8429-3784, Thomas, R. ORCID: https://orcid.org/0000-0001-8663-3682, De Faveri, C., Zabel, U., Scarselli, M., Beck-Sickinger, A.G., Bock, A. ORCID: https://orcid.org/0000-0002-6344-6494, Coin, I. ORCID: https://orcid.org/0000-0002-7722-004X, Lohse, M.J. ORCID: https://orcid.org/0000-0002-0599-3510 and Annibale, P. ORCID: https://orcid.org/0000-0003-3208-5347
Nature Protocols 16 (3): 1419-1451. March 2021

Visualizing the functional 3D shape and topography of long noncoding RNAs by single-particle atomic force microscopy and in-solution hydrodynamic techniques.
Uroda, T., Chillón, I. ORCID: https://orcid.org/0000-0002-3107-8738, Annibale, P. ORCID: https://orcid.org/0000-0003-3208-5347, Teulon, J.M., Pessey, O., Karuppasamy, M., Pellequer, J.L. ORCID: https://orcid.org/0000-0002-8944-2715 and Marcia, M. ORCID: https://orcid.org/0000-0003-2430-0713
Nature Protocols 15 (6): 2107-2139. June 2020

A computational framework to integrate high-throughput '-omics' datasets for the identification of potential mechanistic links.
Pedersen, H.K., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993, Gudmundsdottir, V., Petersen, A.Ø., Hildebrand, F., Hyötyläinen, T., Nielsen, T. ORCID: https://orcid.org/0000-0002-2066-7895, Hansen, T., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Ehrlich, S.D., Brunak, S., Oresic, M., Pedersen, O. and Nielsen, H.B.
Nature Protocols 13 (12): 2781-2800. December 2018

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry.
Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Tang, L.C. ORCID: https://orcid.org/0000-0001-8786-5418, Krug, K., Clark, D.J., Gritsenko, M.A., Chen, L., Clauser, K.R., Clauss, T.R., Shah, P., Gillette, M.A., Petyuk, V.A., Thomas, S.N. ORCID: https://orcid.org/0000-0003-1679-5453, Mani, D.R., Mundt, F., Moore, R.J., Hu, Y., Zhao, R., Schnaubelt, M., Keshishian, H., Monroe, M.E., Zhang, Z., Udeshi, N.D. ORCID: https://orcid.org/0000-0001-5312-1402, Mani, D., Davies, S.R., Townsend, R.R., Chan, D.W., Smith, R.D., Zhang, H., Liu, T. ORCID: https://orcid.org/0000-0001-9529-6550 and Carr, S.A. ORCID: https://orcid.org/0000-0002-7203-4299
Nature Protocols 13 (7): 1632-1661. July 2018

Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry.
Schopper, S., Kahraman, A., Leuenberger, P., Feng, Y., Piazza, I. ORCID: https://orcid.org/0000-0001-5895-6134, Müller, O., Boersema, P.J. and Picotti, P.
Nature Protocols 12 (11): 2391-2410. November 2017

Single-cell template strand sequencing by strand-seq enables the characterization of individual homologs.
Sanders, A.D. ORCID: https://orcid.org/0000-0003-3945-0677, Falconer, E., Hills, M., Spierings, D.C.J. and Lansdorp, P.M.
Nature Protocols 12 (6): 1151-1176. June 2017

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.
Sugimoto, Y. ORCID: https://orcid.org/0000-0003-1646-7679, Chakrabarti, A.M., Luscombe, N.M. and Ule, J.
Nature Protocols 12 (3): 611-637. March 2017

Self-organization of human embryonic stem cells on micropatterns.
Deglincerti, A., Etoc, F., Guerra, M.C., Martyn, I., Metzger, J. ORCID: https://orcid.org/0000-0001-6813-4425, Ruzo, A., Simunovic, M., Yoney, A., Brivanlou, A.H., Siggia, E. and Warmflash, A.
Nature Protocols 11 (11): 2223-2232. November 2016

Isolation and cultivation of naive-like human pluripotent stem cells based on HERVH expression.
Wang, J. ORCID: https://orcid.org/0000-0002-7027-0298, Singh, M., Sun, C., Besser, D. ORCID: https://orcid.org/0000-0002-4958-9624, Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952, Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658, Hurst, L.D. and Izsvák, Z. ORCID: https://orcid.org/0000-0002-2053-2384
Nature Protocols 11 (2): 327-346. February 2016

Quantitative assessment of angiogenesis, perfused blood vessels and endothelial tip cells in the postnatal mouse brain.
Wälchli, T., Mateos, J.M., Weinman, O., Babic, D., Regli, L., Hoerstrup, S.P., Gerhardt, H. ORCID: https://orcid.org/0000-0002-3030-0384, Schwab, M.E. and Vogel, J.
Nature Protocols 10 (1): 53-74. January 2015

In vivo shRNA screens in solid tumors.
Gargiulo, G. ORCID: https://orcid.org/0000-0001-5414-4251, Serresi, M. ORCID: https://orcid.org/0000-0001-6839-8658, Cesaroni, M., Hulsman, D. and van Lohuizen, M.
Nature Protocols 9 (12): 2880-2902. December 2014

Germline transgenesis in pigs by cytoplasmic microinjection of Sleeping Beauty transposons.
Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658, Garrels, W., Mátés, L., Yau, T.Y., Bashir, S. ORCID: https://orcid.org/0000-0002-1281-8710, Zidek, V., Landa, V., Geurts, A., Pravenec, M. ORCID: https://orcid.org/0000-0001-9197-5871, Rülicke, T., Kues, W.A. and Izsvák, Z. ORCID: https://orcid.org/0000-0002-2053-2384
Nature Protocols 9 (4): 810-827. April 2014

Germline transgenesis in rabbits by pronuclear microinjection of Sleeping Beauty transposons.
Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658, Hiripi, L., Hoffmann, O.I., Mátés, L., Yau, T.Y., Bashir, S. ORCID: https://orcid.org/0000-0002-1281-8710, Zidek, V., Landa, V., Geurts, A., Pravenec, M. ORCID: https://orcid.org/0000-0001-9197-5871, Rülicke, T., Bösze, Z. and Izsvák, Z. ORCID: https://orcid.org/0000-0002-2053-2384
Nature Protocols 9 (4): 794-809. April 2014

Germline transgenesis in rodents by pronuclear microinjection of Sleeping Beauty transposons.
Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658, Mátés, L., Yau, T.Y., Landa, V., Zidek, V., Bashir, S. ORCID: https://orcid.org/0000-0002-1281-8710, Hoffmann, O.I., Hiripi, L., Garrels, W., Kues, W.A., Boesze, Z., Geurts, A., Pravenec, M. ORCID: https://orcid.org/0000-0001-9197-5871, Rülicke, T. and Izsvák, Z. ORCID: https://orcid.org/0000-0002-2053-2384
Nature Protocols 9 (4): 773-793. April 2014

Generation of targeted mouse mutants by embryo microinjection of TALEN mRNA.
Wefers, B., Panda, S.K., Ortiz, O., Brandl, C., Hensler, S., Hansen, J., Wurst, W. and Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803
Nature Protocols 8 (12): 2355-2379. December 2013

Large-scale identification of ubiquitination sites by mass spectrometry.
Udeshi, N.D., Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Svinkina, T. and Carr, S.A.
Nature Protocols 8 (10): 1950-1960. October 2013

Single-molecule mRNA detection and counting in mammalian tissue.
Lyubimova, A., Itzkovitz, S., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Fan, Z.P., Wu, X. and van Oudenaarden, A.
Nature Protocols 8 (9): 1743-1758. September 2013

Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast-embryonic stem cell fusion.
Li, L. and Blankenstein, T.
Nature Protocols 8 (8): 1567-1582. August 2013

Elucidating membrane structure and protein behavior using giant plasma membrane vesicles.
Sezgin, E., Kaiser, H.J., Baumgart, T., Schwille, P., Simons, K. and Levental, I.
Nature Protocols 7 (6): 1042-1051. June 2012

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
Bonn, S., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, Perez-Gonzalez, A., Riddell, A., Gavin, A.C. and Furlong, E.E.
Nature Protocols 7 (5): 978-994. May 2012

Sleeping Beauty transposon mutagenesis in rat spermatogonial stem cells.
Ivics, Z. ORCID: https://orcid.org/0000-0002-7803-6658, Izsvak, Z. ORCID: https://orcid.org/0000-0002-2053-2384, Medrano, G., Chapman, K.M. and Hamra, F.K.
Nature Protocols 6 (10): 1521-1535. October 2011

A differential proteome screening system for post-translational modification-dependent transcription factor interactions.
Pless, O. ORCID: https://orcid.org/0000-0002-1468-316X, Kowenz-Leutz, E., Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623 and Leutz, A. ORCID: https://orcid.org/0000-0001-8259-927X
Nature Protocols 6 (3): 359-364. February 2011

Preparation of retinal explant cultures to study ex vivo tip endothelial cell responses.
Sawamiphak, S. ORCID: https://orcid.org/0000-0003-2298-3565, Ritter, M. and Acker-Palmer, A.
Nature Protocols 5 (10): 1659-1665. October 2010

Phylogenetic classification and identification of bacteria by mass spectrometry.
Freiwald, A. and Sauer, S. ORCID: https://orcid.org/0000-0002-4794-3693
Nature Protocols 4 (5): 732-742. 23 April 2009

A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics.
Cox, J., Matic, I., Hilger, M., Nagaraj, N., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Olsen, J.V. and Mann, M.
Nature Protocols 4 (5): 698-705. 2009

Single-nucleotide polymorphisms: analysis by mass spectrometry.
Sauer, S. ORCID: https://orcid.org/0000-0002-4794-3693, Reinhardt, R., Lehrach, H. and Gut, I.G.
Nature Protocols 1 (4): 1761-1771. 22 November 2006

Analysis of translation initiation using a translation control reporter system.
Wiesenthal, V., Leutz, A. ORCID: https://orcid.org/0000-0001-8259-927X and Calkhoven, C.F.
Nature Protocols 1 (3): 1531-1537. 9 November 2006

Cysteine engineering of polyproteins for single-molecule force spectroscopy.
Dietz, H., Bertz, M., Schlierf, M., Berkemeier, F., Bornschloegl, T., Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290 and Rief, M.
Nature Protocols 1 (1): 80-84. 2006

Review

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.
Müller, A. ORCID: https://orcid.org/0000-0002-3560-5769, Schmidt, D. ORCID: https://orcid.org/0000-0002-8621-9438, Albrecht, J.P. ORCID: https://orcid.org/0000-0002-3792-9695, Rieckert, L., Otto, M. ORCID: https://orcid.org/0009-0003-1919-5880, Galicia Garcia, L.E. ORCID: https://orcid.org/0009-0006-7891-7785, Fabig, G. ORCID: https://orcid.org/0000-0003-3017-0978, Solimena, M. and Weigert, M. ORCID: https://orcid.org/0000-0002-7780-9057
Nature Protocols 19 (5): 1436-1466. May 2024