Published August 2016
| Supplemental Material
Journal Article
Open
Dense transcript profiling in single cells by image correlation decoding
- Creators
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Coskun, Ahmet F.
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Cai, Long
Chicago
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Abstract
Sequential barcoded fluorescent in situ hybridization (seqFISH) allows large numbers of molecular species to be accurately detected in single cells, but multiplexing is limited by the density of barcoded objects. We present correlation FISH (corrFISH), a method to resolve dense temporal barcodes in sequential hybridization experiments. Using corrFISH, we quantified highly expressed ribosomal protein genes in single cultured cells and mouse thymus sections, revealing cell-type-specific gene expression.
Additional Information
© 2016 Macmillan Publishers Limited. Received 22 February 2016. Accepted 11 May 2016. Published online 06 June 2016. We thank J. Linton from the Elowitz laboratory (Caltech) for providing cell lines and M. Yui from the Rothenberg Laboratory (Caltech) for the intact thymus organ. We appreciate the help of the City of Hope Pathology Core to slice thymus into sections. This work is funded by US National Institute of Health single-cell analysis program award R01HD075605. A.F.C. is supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund. Code availability: Custom MATLAB source codes (Supplementary Software) with test images are available and updated at https://github.com/singlecelllab/correlationFISH. Author Contributions: A.F.C. and L.C. designed the project and wrote the manuscript. L.C. supervised the project. Competing financial interests: L.C. and A.F.C. declare conflict of interests and have filed a patent application.Attached Files
Supplemental Material - nmeth.3895-S1.pdf
Supplemental Material - nmeth.3895-S2.zip
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nmeth.3895-S2.zip
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Additional details
- PMCID
- PMC4965285
- Eprint ID
- 66792
- Resolver ID
- CaltechAUTHORS:20160509-170833016
- NIH
- R01HD075605
- Burroughs Wellcome Fund
- Created
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2016-06-06Created from EPrint's datestamp field
- Updated
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2021-11-11Created from EPrint's last_modified field