Profiling the transcriptome with RNA SPOTs
Abstract
Single-molecule FISH (smFISH) has been the gold standard for quantifying individual transcript abundances. Here, we scale up multiplexed smFISH to the transcriptome level and profile 10,212 different mRNAs from mouse fibroblast and embryonic stem cells. This method, called RNA sequential probing of targets (SPOTs), provides an accurate, flexible, and low-cost alternative to sequencing for profiling transcriptomes.
Additional Information
© 2017 Macmillan Publishers Limited, part of Springer Nature. Received: 05 July 2017; Accepted: 02 October 2017; Published online: 13 November 2017. We thank P. Sims, A. Raj, B. Wold, S. Linnarson, and R. Sandberg for discussions. We thank Y. Zhang for help with automated fluidics system, N. Koulena for helping in probe generation, and E. Lubeck for help at the early stage of the project. This work was supported by grants from US National Institutes of Health (NIHRNA-1-NIHP.HD075605 and RNASUPP-1-NIHP.HD075605). Author Contributions: C.-H.L.E. and L.C. conceived and designed experiments. C.-H.L.E. performed all the experiments. S.S. wrote the scripts for image analysis. C.-H.L.E. performed image analysis with the guidance of S.S. J.T. wrote the script for probe generations. C.-H.L.E. and L.C. performed data analysis. All authors contributed in writing the manuscripts. Competing interests: L.C., C.-H.L.E., and S.S have filed a patent on RNA SPOTs and its barcoding scheme.Attached Files
Accepted Version - nihms913215.pdf
Supplemental Material - nmeth.4500-S1.pdf
Supplemental Material - nmeth.4500-S2.pdf
Supplemental Material - nmeth.4500-S3.pdf
Supplemental Material - nmeth.4500-S4.xlsx
Supplemental Material - nmeth.4500-S5.xlsx
Supplemental Material - nmeth.4500-S6.xlsx
Supplemental Material - nmeth.4500-S7.xlsx
Supplemental Material - nmeth.4500-S8.csv
Supplemental Material - nmeth.4500-S9.zip
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Additional details
- Alternative title
- Profiling the transcriptome by RNA SPOTs
- PMCID
- PMC5819366
- Eprint ID
- 81948
- DOI
- 10.1038/nmeth.4500
- Resolver ID
- CaltechAUTHORS:20171002-110633228
- RNA-1-NIHP.HD075605
- NIH
- RNASUPP-1-NIHP.HD075605
- NIH
- Created
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2017-11-14Created from EPrint's datestamp field
- Updated
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2022-03-21Created from EPrint's last_modified field