Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Science

Volumn 353, Issue 6294, 2016, Pages 78-82

  Ståhl, Patrik L ^a,b   Salmén, Fredrik ^b   Vickovic, Sanja ^b   Lundmark, Anna ^a,b   Navarro, José Fernández ^a,b   Magnusson, Jens ^a   Giacomello, Stefania ^b   Asp, Michaela ^a   Westholm, Jakub O ^c   Huss, Mikael ^c   Mollbrink, Annelie ^b   Linnarsson, Sten ^a   Codeluppi, Simone ^a   Borg, Åke ^d   Pontén, Fredrik ^e   Costea, Paul Igor ^b   Sahlén, Pelin ^b   Mulder, Jan ^a   Bergmann, Olaf ^a   Lundeberg, Joakim ^b   Frisén, Jonas ^a   more..

^a KAROLINSKA INSTITUTE   (Sweden)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^c STOCKHOLM UNIVERSITY   (Sweden)

^d LUND UNIVERSITY   (Sweden)

^e UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; TRANSCRIPTOME; COMPLEMENTARY DNA;

BIOINFORMATICS; BRAIN; CANCER; CELLS AND CELL COMPONENTS; GENE EXPRESSION; GENETIC ANALYSIS; PROTEIN; RODENT; SPATIAL RESOLUTION; VISUALIZATION;

ANIMAL CELL; BIOINFORMATICS; BREAST CANCER; EPITHELIAL MESENCHYMAL TRANSITION; GENE EXPRESSION; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION; REVIEW; RNA SEQUENCE; SPATIAL TRANSCRIPTOMICS; TISSUE SECTION; TRANSCRIPTOMICS; ANIMAL; ANTIBODY SPECIFICITY; BIOSYNTHESIS; BRAIN; BREAST TUMOR; FEMALE; GENE EXPRESSION PROFILING; HUMAN; METABOLISM; MOUSE; PROCEDURES; SEQUENCE ANALYSIS;

ANIMALS; BRAIN; BREAST NEOPLASMS; DNA, COMPLEMENTARY; FEMALE; GENE EXPRESSION PROFILING; HUMANS; MICE; ORGAN SPECIFICITY; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84976875145     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.aaf2403     Document Type: Review

References (17)

1. Z. Wang, M. Gerstein, M. Snyder, Nat. Rev. Genet. 10, 57-63 (2009).
2. N. Crosetto, M. Bienko, A. van Oudenaarden, Nat. Rev. Genet. 16, 57-66 (2015).
3. R. Satija, J. A. Farrell, D. Gennert, A. F. Schier, A. Regev, Nat. Biotechnol. 33, 495-502 (2015).
4. P. A. Combs, M. B. Eisen, PLOS ONE 8, e71820 (2013).
5. K. Achim et al., Nat. Biotechnol. 33, 503-509 (2015).
6. Materials and methods are available as supplementary materials on Science Online.
7. T. Hashimshony, F. Wagner, N. Sher, I. Yanai, Cell Reports 2, 666-673 (2012).
8. R. N. Van Gelder et al., Proc. Natl. Acad. Sci. U.S.A. 87, 1663-1667 (1990).
9. R. Vassar et al., Cell 79, 981-991 (1994).
10. K. D. Pruitt et al., Nucleic Acids Res. 42 (D1), D756-D763 (2014).
11. S. Zechel, P. Zajac, P. Lönnerberg, C. F. Ibáñez, S. Linnarsson, Genome Biol. 15, 486 (2014).
12. D. Grün, A. van Oudenaarden, Cell 163, 799-810 (2015).
13. E. S. Lein et al., Nature 445, 168-176 (2007).
14. A. Mahfouz et al., Methods 73,79-89 (2015).
15. L. J. P. van der Maaten, G. E. Hinton, J. Mach. Learn. Res. 9, 2579-2605 (2008).
16. M. Kittaneh, A. J. Montero, S. Glück, Biomarkers Cancer 5, 61-70 (2013).
17. C. Gjerdrum et al., Proc. Natl. Acad. Sci. U.S.A. 107, 1124-1129 (2010).