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Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells - Nature

  • ️Regev, Aviv
  • ️Sun May 19 2013

Accession codes

Accessions

Gene Expression Omnibus

Data deposits

Data have been deposited in GEO under accession number GSE41265.

Change history

  • 12 June 2013

    Minor changes were made to the spelling of authors S.S. and J.J.T. Also, an accession number for GEO was added.

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Acknowledgements

We thank N. Chevrier, C. Villani, M. Jovanovic, M. Bray and J. Shuga for scientific discussions; N. Friedman and E. Lander for comments on the manuscript; B. Tilton, T. Rogers and M. Tam for assistance with cell sorting; J. Bochicchio, E. Shefler and C. Guiducci for project management; the Broad Genomics Platform for all sequencing work; K. Fitzgerald for the Irf7−/− bone marrow; and L. Gaffney for help with artwork. Work was supported by a National Institutes of Health (NIH) Postdoctoral Fellowship (1F32HD075541-01, to R.S.), a Charles H. Hood Foundation Postdoctoral Fellowship (to A. Goren), an NIH grant (U54 AI057159, to N.H.), an NIH New Innovator Award (DP2 OD002230, to N.H.), an NIH CEGS Award (1P50HG006193-01, to H.P., A.R. and N.H.), NIH Pioneer Awards (5DP1OD003893-03 to H.P., DP1OD003958-01 to A.R.), the Broad Institute (to H.P. and A.R.), HHMI (to A.R.), and the Klarman Cell Observatory at the Broad Institute (to A.R.).

Author information

Author notes

  1. Alex K. Shalek and Rahul Satija: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA,

    Alex K. Shalek, Rona S. Gertner, Jellert T. Gaublomme & Hongkun Park

  2. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, 02142, Massachuestts, USA

    Rahul Satija, Xian Adiconis, Raktima Raychowdhury, Schraga Schwartz, Nir Yosef, Christine Malboeuf, Diana Lu, John J. Trombetta, Dave Gennert, Andreas Gnirke, Alon Goren, Nir Hacohen, Joshua Z. Levin, Hongkun Park & Aviv Regev

  3. Department of Pathology & Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, 02129, Massachusetts, USA

    Alon Goren

  4. Center for Immunology and Inflammatory Diseases & Department of Medicine, Massachusetts General Hospital, Charlestown, 02129, Massachuestts, USA

    Nir Hacohen

  5. Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, 02140, Massachusetts, USA

    Aviv Regev

Authors

  1. Alex K. Shalek

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  2. Rahul Satija

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  3. Xian Adiconis

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  4. Rona S. Gertner

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  5. Jellert T. Gaublomme

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  6. Raktima Raychowdhury

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  7. Schraga Schwartz

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  8. Nir Yosef

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  9. Christine Malboeuf

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  10. Diana Lu

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  11. John J. Trombetta

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  12. Dave Gennert

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  13. Andreas Gnirke

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  14. Alon Goren

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  15. Nir Hacohen

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  16. Joshua Z. Levin

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  17. Hongkun Park

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  18. Aviv Regev

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Contributions

A.R., H.P., J.Z.L., N.H., A.K.S., R.S., A. Goren and A. Gnirke conceived and designed the study. A.K.S., X.A., R.S.G., J.T.G., R.R., C.M., D.L., J.J.T., D.G. and J.T.G. performed experiments. R.S., A.K.S., S.S. and N.Y. performed computational analyses. R.S., A.K.S., A. Goren, N.H., J.Z.L., H.P. and A.R. wrote the manuscript, with extensive input from all authors.

Corresponding authors

Correspondence to Hongkun Park or Aviv Regev.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion, Supplementary Methods, Supplementary Figures 1-20 and additional references. (PDF 5465 kb)

Supplementary Data

This zipped file contains Supplementary Tables 1-7. Supplementary Table 1 shows sequencing metrics for single cell, population, and molecularly barcoded RNA-seq libraries. Supplementary Table 2 shows transcript per million (TPM) levels for all UCSC genes (rows) for 18 single cells and 3 population replicates (columns), along with annotation of which genes are 'Housekeeping' and which are 'LPS Response'. Supplementary Table 3 shows single cell variability measures for 523 highly expressed (population average) genes, along with annotation of which genes are 'Housekeeping' and which are 'LPS Response'. Supplementary Table 4 shows percent spliced in (PSI) estimates for all genes that are very highly expressed (TPM>250) in at least one single cell, only PSI estimates for the highly expressing cells were used to generate Figure 3b (see Supplementary Information file). Supplementary Table 5 shows clustering assignments and principal component scores for 633 genes induced in response to LPS stimulation. Supplementary Table 6 contains gene list and PCR primer pairs used for the Fluidigm single cell qPCR codeset. Supplementary Table 7 contains TPM estimates and unique molecular identifier counts for each gene in the 3 libraries prepared using the modified SMARTer protocol. (ZIP 4525 kb)

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Shalek, A., Satija, R., Adiconis, X. et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498, 236–240 (2013). https://doi.org/10.1038/nature12172

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  • Received: 02 November 2012

  • Accepted: 05 April 2013

  • Published: 19 May 2013

  • Issue Date: 13 June 2013

  • DOI: https://doi.org/10.1038/nature12172