Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms

Abstract

Acknowledgement

We thank the E.V.R. laboratory members for helpful discussions, R. Diamond and members of the Caltech Flow Cytometry and Cell Sorting facility for sorting, I. Antoshechkin and V. Kumar of the Caltech Jacobs Genomics Facility for sequencing, H. Amrhein and D. Trout for computer support, J. Park and S. Chen from the Caltech Single Cell Profiling and Engineering Center for support for processing 10x Chromium samples, J. Vielmetter and the Caltech Protein Expression Center for purifying protein A-MNase, I. Soto for mouse care, M. Quiloan and M. Chau for mouse genotyping and supervision, and J. Longmate (formerly City of Hope) and M. Yui (formerly Caltech) for statistics advice. Support for this project came from USPHS grants (R01AI135200, R01HL119102 and R01HD100039) to E.V.R., and from a Cancer Research Institute Irvington Postdoctoral Fellowship CRI.SHIN and Caltech Baxter Fellowship (to B.S.). F.G. was supported in part by the National Institutes of Health award 1RF1NS122060-01. Support also came from The Beckman Institute at Caltech for all the Caltech facilities and from the Biology and Biological Engineering Division Bowes Leadership Chair Fund, the Louis A. Garfinkle Memorial Laboratory Fund and the Al Sherman Foundation to the E.V.R. laboratory. E.V.R. gratefully acknowledges support from the Edward B. Lewis Professorship and past support from the Albert Billings Ruddock Professorship.

Contributions

B.S. and E.V.R. conceptualized the project, wrote the paper and edited the paper. B.S. performed the experiments, and analyzed data with W.Z. and J.W. F.G. wrote the in-house bioinformatic pipeline for hashtag alignment and provided further analysis. E.V.R. supervised research, acquired funding and provided additional data analysis. All authors edited the paper and provided helpful comments.

Data Availability

All new genomic sequencing data have been deposited in Gene Expression Omnibus under accession numbers GSE218147 (C&R, ChIP–seq and ATAC-seq) and GSE218149 (scRNA-seq). The publicly available data utilized for analysis are presented in Supplementary Table 7. Publicly available data were utilized by downloading raw sequence read files using the Sequence Read Archive toolkit Fastq-dump (v.2.10.9). Source data are provided with this paper. All other data needed to evaluate the conclusions in the paper are present in the paper, the Extended Data or the Supplementary Information, or are available upon request.

Code Availability

All code used for data analysis in this work is publicly available and listed in the Methods and Reporting Summary.

Errata

27 November 2023: A Correction to this paper has been published: https://doi.org/10.1038/s41590-023-01716-6

Copyright and License

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