Intelligent image-based in situ single-cell isolation

Nature Communications

Volumn 9, Issue 1, 2018, Pages

  Brasko, Csilla ^a   Smith, Kevin ^b,c   Molnar, Csaba ^d   Farago, Nora ^a,d,e   Hegedus, Lili ^d   Balind, Arpad ^d   Balassa, Tamas ^d   Szkalisity, Abel ^d   Sukosd, Farkas ^a   Kocsis, Katalin ^a   Balint, Balazs ^f   Paavolainen, Lassi ^g   Enyedi, Marton Z ^d   Nagy, Istvan ^d,f   Puskas, Laszlo G ^d,e   Haracska, Lajos ^d   Tamas, Gabor ^a   Horvath, Peter ^d,g  

^a UNIVERSITY OF SZEGED   (Hungary)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^c SCIENCE FOR LIFE LABORATORY   (Sweden)

^d INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^e AVIDIN LTD   (Hungary)

^f SEQOMICS BIOTECHNOLOGY LTD   (Hungary)

^g UNIVERSITY OF HELSINKI   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

SHORT HAIRPIN RNA; TRANSCRIPTOME;

BIOTECHNOLOGY; CELL; GENETIC ANALYSIS; HETEROGENEITY; IMAGE; IMAGE ANALYSIS; MACHINE LEARNING; MICROSCOPY;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; BRAIN CELL; CELL ISOLATION; CELL SELECTION; CELL STRUCTURE; DNA DAMAGE; GENE FUNCTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; HIGH RESOLUTION MICROSCOPY; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; IMAGE ANALYSIS; IMMUNOHISTOCHEMISTRY; LASER MICROCAPTURE MICROSCOPY; LIMIT OF QUANTITATION; MACHINE LEARNING; MALE; MICROSCOPY; MOLECULAR GENETIC ANALYSIS; NONHUMAN; PATTERN RECOGNITION; PHENOTYPE; PYRAMIDAL NERVE CELL; RAT; RNA INTERFERENCE; SINGLE CELL ANALYSIS; ANIMAL; CELL CULTURE; CELL SEPARATION; CONFOCAL MICROSCOPY; CYTOLOGY; GENE EXPRESSION PROFILING; IMAGE PROCESSING; METABOLISM; PROCEDURES; REPRODUCIBILITY;

ANIMALS; CELL SEPARATION; CELLS, CULTURED; GENE EXPRESSION PROFILING; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MACHINE LEARNING; MICROSCOPY, CONFOCAL; PYRAMIDAL CELLS; REPRODUCIBILITY OF RESULTS; SINGLE-CELL ANALYSIS;

EID: 85040796437     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-017-02628-4     Document Type: Article

References (22)

1. Altschuler, S. &Wu, L. Cellular heterogeneity: when do differences make a difference? Cell 141, 559-563 (2010).
2. Pelkmans, L. Using cell-to-cell variability-A new era in molecular biology. Science 336, 425-426 (2012).
3. Heppner, G. H. Tumor heterogeneity. Cancer Res. 44, 2259-2265 (1984).
4. Tay, S. et al. Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 466, 267-271 (2010).
5. Gawad, C., Koh, W. &Quake, S. R. Single-cell genome sequencing: current state of the science. Nat. Rev. Genet. 17, 175-188 (2016).
6. Anselmetti, D. Single Cell Analysis: Technologies and Applications. (Wiley, Hoboken, 2009).
7. Gross, A. et al. Technologies for single-cell isolation. Int. J. Mol. Sci. 16, 16897-16919 (2015).
8. Espina, V. et al. Laser-capture microdissection. Nat. Protoc. 1, 586-603 (2006).
9. Fujii, T. et al. Direct metabolomics for plant cells by live single-cell mass spectrometry. Nat. Protoc. 10, 1445-1456 (2015).
10. Molnar, C. et al. Accurate morphology preserving segmentation of overlapping cells based on active contours. Sci. Rep. 6, 32412 (2016).
11. Carpenter, A. E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006).
12. Piccinini, F. et al. Advanced cell classifier: user-friendly machine-learning-based software for discovering phenotypes in high-content imaging data. Cell Syst. 4, 651-655 (2017).
13. Farago, N. et al. Digital PCR to determine the number of transcripts from single neurons after patch-clamp recording. Biotechniques 54, 327-336 (2013).
14. Molnar, G. et al. GABAergic neurogliaform cells represent local sources of insulin in the cerebral cortex. J. Neurosci. 34, 1133-1137 (2014).
15. Friedberg, E. C. et al. DNA Repair and Mutagenesis. (ASM Press, Washington, DC, 2006).
16. Watanabe, K. et al. Rad18 guides polη to replication stalling sites through physical interaction and PCNA monoubiquitination. EMBO J. 23, 3886-3896 (2004).
17. Juhasz, S. et al. Characterization of human Spartan/C1orf124, an ubiquitin-PCNA interacting regulator of DNA damage tolerance. Nucleic Acids Res. 40, 10795-10808 (2012).
18. Buisson, R. et al. Breast cancer proteins PALB2 and BRCA2 stimulate polymerase η in recombination-associated DNA synthesis at blocked replication forks. Cell Rep. 6, 553-564 (2014).
19. Emmert-Buck, M. R. et al. Laser capture microdissection. Science 274, 998-1001 (1996).
20. Smith, K. et al. CIDRE: an illumination-correction method for optical microscopy. Nat. Methods 12, 404-406 (2015).
21. Olivo-Marin, J. C. Extraction of spots in biological images using multiscale products. Pattern Recognit. 35, 1989-1996 (2002).
22. Farago, N. et al. Human neuronal changes in brain edema and increased intracranial pressure. Acta Neuropathol. Commun. 4, 78 (2016).