Transcript-indexed ATAC-seq for precision immune profiling
Open accessAbstract
T cells create vast amounts of diversity in the genes that encode their T cell receptors (TCRs), which enables individual clones to recognize specific peptide-major histocompatibility complex (MHC) ligands. Here we combined sequencing of the TCR-encoding genes with assay for transposase-accessible chromatin with sequencing (ATAC-seq) analysis at the single-cell level to provide information on the TCR specificity and epigenomic state of individual T cells. By using this approach, termed transcript-indexed ATAC-seq (T-ATAC-seq), we identified epigenomic signatures in immortalized leukemic T cells, primary human T cells from healthy volunteers and primary leukemic T cells from patient samples. In peripheral blood CD4+ T cells from healthy individuals, we identified cis and trans regulators of naive and memory T cell states and found substantial heterogeneity in surface-marker-defined T cell populations. In patients with a leukemic form of cutaneous T cell lymphoma, T-ATAC-seq enabled identification of leukemic and nonleukemic regulatory pathways in T cells from the same individual by allowing separation of the signals that arose from the malignant clone from the background T cell noise. Thus, T-ATAC-seq is a new tool that enables analysis of epigenomic landscapes in clonal T cells and should be valuable for studies of T cell malignancy, immunity and immunotherapy.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
ATAC-seq can be performed in single cells, revealing cell-to-cell variability and rare epigenomic phenotypes.
“Importantly, ATAC-seq can be performed in single cells (scATAC-seq), uncovering cell-to-cell variability and rare epigenomic phenotypes (Cusanovich et al., 2018; Satpathy et al., 2018; Buenrostro et al., 2018).”
From Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks (2019) · cites this paper as Satpathy et al., 2018
Single-cell ATAC-seq profiles can be paired with orthogonal measurements of RNA or protein expression in the same cell.
“Additionally, scATAC-seq profiles can be paired with orthogonal measurements of RNA or protein expression in the same cell (Satpathy et al., 2018; Chen et al., 2018a).”
From Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks (2019) · cites this paper as Satpathy et al., 2018
Prior work has shown that pooling five or more cells accurately reproduces chromatin accessibility profiles.
“previous reports have shown that aggregation of five or more cells is sufficient toaccurately reproduce chromatin accessibility profiles (Satpathy et al., 2018; Schep et al., 2017).”
From Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks (2019) · cites this paper as Satpathy et al., 2018
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
(2008) · Journal of Machine Learning Research · Cited by 33,051 · see citing works
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422 · see citing works
Self-citationIvanov, I. I., McKenzie, B. S., Zhou, L., Tadokoro, C. E., Lepelley, A., Lafaille, J. J., Cua, D. J., & Littman, D. R. (2006) · Cell · doi:10.1016/j.cell.2006.07.035 · Cited by 5,145 · see citing works
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016) · Science · doi:10.1126/science.aad0501 · Cited by 4,944 · see citing works
T-cell antigen receptor genes and T-cell recognition
Davis, M. M., & Bjorkman, P. J. (1988) · Nature · doi:10.1038/334395a0 · Cited by 3,202 · see citing works
Self-citationAnticancer activities of histone deacetylase inhibitors
Bolden, J. E., Peart, M. J., & Johnstone, R. W. (2006) · Nature Reviews Drug Discovery · doi:10.1038/nrd2133 · Cited by 2,919 · see citing works
Zheng, W.-P., & Flavell, R. A. (1997) · Cell · doi:10.1016/s0092-8674(00)80240-8 · Cited by 2,384 · see citing works
Single-cell chromatin accessibility reveals principles of regulatory variation
Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308 · see citing works
Self-citationRegev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C., Birney, E., Bodenmiller, B., Campbell, P., Carninci, P., Clatworthy, M., et al. (2017) · eLife · doi:10.7554/elife.27041 · Cited by 2,232 · see citing works
A human memory T cell subset with stem cell–like properties
Gattinoni, L., Lugli, E., Ji, Y., Pos, Z., Paulos, C. M., Quigley, M. F., Almeida, J. R., Gostick, E., Yu, Z., Carpenito, C., et al. (2011) · Nature Medicine · doi:10.1038/nm.2446 · Cited by 1,974 · see citing works
A function for interleukin 2 in Foxp3-expressing regulatory T cells
Fontenot, J. D., Rasmussen, J. P., Gavin, M. A., & Rudensky, A. Y. (2005) · Nature Immunology · doi:10.1038/ni1263 · Cited by 1,819 · see citing works
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
Weirauch, M. T., Yang, A. W. H., Albu, M., Coté, A. G., Montenegro‐Montero, A., Drewe, P., Najafabadi, H. S., Lambert, S. A., Mann, I. K., Cook, K. B., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.009 · Cited by 1,705 · see citing works
The Biological Functions of T Helper 17 Cell Effector Cytokines in Inflammation
Ouyang, W., Kolls, J. K., & Zheng, Y. (2008) · Immunity · doi:10.1016/j.immuni.2008.03.004 · Cited by 1,698 · see citing works
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods · doi:10.1038/nmeth.4401 · Cited by 1,680 · see citing works
Self-citationT Helper 17 Lineage Differentiation Is Programmed by Orphan Nuclear Receptors RORα and RORγ
Yang, X. O., Pappu, B. P., Nurieva, R., Akimzhanov, A., Kang, H. S., Chung, Y., Ma, L., Shah, B., Panopoulos, A. D., Schluns, K. S., et al. (2008) · Immunity · doi:10.1016/j.immuni.2007.11.016 · Cited by 1,605 · see citing works
Morita, R., Schmitt, N., Bentebibel, S.-E., Ranganathan, R., Bourdery, L., Zurawski, G., Foucat, E., Dullaers, M., Oh, S., Sabzghabaei, N., et al. (2011) · Immunity · doi:10.1016/j.immuni.2010.12.012 · Cited by 1,563 · see citing works
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., & al, E. (2017) · Zurich Open Repository and Archive (University of Zurich) · doi:10.5167/uzh-162597 · Cited by 1,457 · see citing works
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
Cusanovich, D. A., Daza, R., Adey, A., Pliner, H. A., Christiansen, L., Gunderson, K. L., Steemers, F. J., Trapnell, C., & Shendure, J. (2015) · Science · doi:10.1126/science.aab1601 · Cited by 1,248 · see citing works
DNA-Binding Specificities of Human Transcription Factors
Jolma, A., Yan, J., Whitington, T., Toivonen, J., Nitta, K. R., Rastas, P. M. A., Morgunova, E. Y., Enge, M., Taipale, M., Wei, G., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.009 · Cited by 1,228 · see citing works
A Validated Regulatory Network for Th17 Cell Specification
Ciofani, M., Madar, A., Galan, C., Sellars, M., Mace, K., Pauli, F., Agarwal, A., Huang, W., Parkurst, C. N., Muratet, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.016 · Cited by 1,160 · see citing works
Corces, M. R., Buenrostro, J. D., Wu, B., Greenside, P. G., Chan, S. M., Koenig, J. L., Snyder, M. P., Pritchard, J. K., Kundaje, A., Greenleaf, W. J., et al. (2016) · Nature Genetics · doi:10.1038/ng.3646 · Cited by 1,151 · see citing works
Self-citationTranscriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors
Paul, F., Arkin, Y., Giladi, A., Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Winter, D., Lara-Astiaso, D., Gury, M., Weiner, A., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.013 · Cited by 1,082 · see citing works
Identifying specificity groups in the T cell receptor repertoire
Glanville, J., Huang, H., Nau, A., Hatton, O., Wagar, L. E., Rubelt, F., Ji, X., Han, A., Krams, S. M., Pettus, C., et al. (2017) · Nature · doi:10.1038/nature22976 · Cited by 1,026 · see citing works
Self-citationSingle-cell RNA-seq reveals dynamic paracrine control of cellular variation
Shalek, A. K., Satija, R., Shuga, J., Trombetta, J. J., Gennert, D., Lu, D., Chen, P., Gertner, R. S., Gaublomme, J. T., Yosef, N., et al. (2014) · Nature · doi:10.1038/nature13437 · Cited by 1,000 · see citing works
Self-citationMathelier, A., Fornes, O., Arenillas, D. J., Chen, C.-Y., Denay, G., Lee, J., Shi, W., Shyr, C., Tan, G., Worsley-Hunt, R., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1176 · Cited by 937 · see citing works
Bauquet, A. T., Jin, H., Paterson, A. M., Mitsdoerffer, M., Ho, I.-C., Sharpe, A. H., & Kuchroo, V. K. (2009) · Nature Immunology · doi:10.1038/ni.1690 · Cited by 713 · see citing works
Buenrostro, J. D., Corces, M. R., Lareau, C. A., Wu, B., Schep, A. N., Aryee, M. J., Majeti, R., Chang, H. Y., & Greenleaf, W. J. (2018) · Cell · doi:10.1016/j.cell.2018.03.074 · Cited by 670 · see citing works
Self-citationThe AP-1 transcription factor Batf controls TH17 differentiation
Schraml, B. U., Hildner, K., Ise, W., Lee, W.-L., Smith, W. A.-E., Solomon, B. D., Sahota, G., Sim, J. E., Mukasa, R., Čemerski, S., et al. (2009) · Nature · doi:10.1038/nature08114 · Cited by 622 · see citing works
Single-cell genomics unveils critical regulators of Th17 cell pathogenicity
Gaublomme, J. T., Yosef, N., Lee, Y., Gertner, R. S., Yang, L. V., Wu, C., Pandolfi, P. P., Mak, T., Satija, R., Shalek, A. K., et al. (2015) · Cell · doi:10.1016/j.cell.2015.11.009 · Cited by 575 · see citing works
Deconstructing the Peptide-MHC Specificity of T Cell Recognition
Birnbaum, M. E., Mendoza, J. L., Sethi, D. K., Dong, S., Glanville, J., Dobbins, J., Özkan, E., Davis, M. M., Wucherpfennig, K. W., & García, K. C. (2014) · Cell · doi:10.1016/j.cell.2014.03.047 · Cited by 558 · see citing works
Self-citationLinking T-cell receptor sequence to functional phenotype at the single-cell level
Han, A. S., Glanville, J., Hansmann, L., & Davis, M. M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2938 · Cited by 534 · see citing works
Self-citationMumbach, M. R., Satpathy, A. T., Boyle, E. A., Dai, C., Gowen, B. G., Cho, S. W., Nguyen, M. L., Rubin, A. J., Granja, J. M., Kazane, K. R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3963 · Cited by 490 · see citing works
Self-citationKimmig, S., Przybylski, G. K., Schmidt, C. A., Laurisch, K., Möwes, B., Radbruch, A., & Thiel, A. (2002) · The Journal of Experimental Medicine · doi:10.1084/jem.20011756 · Cited by 439 · see citing works
T cell fate and clonality inference from single-cell transcriptomes
(2016) · doi:10.1038/nmeth.3800 · Cited by 434 · see citing works
Genomic landscape of cutaneous T cell lymphoma
Choi, J., Goh, G., Walradt, T. J., Hong, B. S., Bunick, C. G., Chen, K., Bjornson, R. D., Maman, Y., Wang, T. L., Tordoff, J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3356 · Cited by 429 · see citing works
A critical role for TCF-1 in T-lineage specification and differentiation
Weber, B., Chi, A. W. S., Chavez, A., Yashiro–Ohtani, Y., Yang, Q., Shestova, O. E., & Bhandoola, A. (2011) · Nature · doi:10.1038/nature10279 · Cited by 420 · see citing works
Developmental gene networks: a triathlon on the course to T cell identity
Yui, M. A., & Rothenberg, E. V. (2014) · Nature Reviews Immunology · doi:10.1038/nri3702 · Cited by 342 · see citing works
Continued maturation of thymic emigrants in the periphery
Boursalian, T. E., Golob, J. L., Soper, D. M., Cooper, C. J., & Fink, P. J. (2004) · Nature Immunology · doi:10.1038/ni1049 · Cited by 303 · see citing works
Weiskopf, D., Bangs, D. J., Sidney, J., Kolla, R. V., Silva, A. D. D., de Silva, A. M., Crotty, S., Peters, B., & Sette, A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1505956112 · Cited by 303 · see citing works
Genomic views of STAT function in CD4+ T helper cell differentiation
O'Shea, J. J., Lahesmaa, R., Vahedi, G., Laurence, A., & Kanno, Y. (2011) · Nature Reviews Immunology · doi:10.1038/nri2958 · Cited by 295 · see citing works
Genomic analysis of mycosis fungoides and Sézary syndrome identifies recurrent alterations in TNFR2
Ungewickell, A., Bhaduri, A., Rios, E. J., Reuter, J., Lee, C. S., Mah, A., Zehnder, A. M., Ohgami, R. S., Kulkarni, S., Armstrong, R. J., et al. (2015) · Nature Genetics · doi:10.1038/ng.3370 · Cited by 273 · see citing works
Self-citationTh2 Cytokine mRNA Expression in Skin in Cutaneous T-Cell Lymphoma
Vowels, B. R., Lessin, S. R., Cassin, M., Jaworsky, C., Benoit, B. M., Wolfe, J. T., & Rook, A. H. (1994) · Journal of Investigative Dermatology · doi:10.1111/1523-1747.ep12398454 · Cited by 263 · see citing works
Spatial and Temporal Dynamics of T Cell Receptor Signaling with a Photoactivatable Agonist
Huse, M., Klein, L. O., Girvin, A. T., Faraj, J. M., Li, Q.-J., Kuhns, M. S., & Davis, M. M. (2007) · Immunity · doi:10.1016/j.immuni.2007.05.017 · Cited by 236 · see citing works
Self-citationTH17 cells promote microbial killing and innate immune sensing of DNA via interleukin 26
Meller, S., Domizio, J. D., Voo, K. S., Hawerkamp, H. C., Chamilos, G., Ganguly, D., Conrad, C., Gregorio, J. D., Roy, D. L., Roger, T., et al. (2015) · Nature Immunology · doi:10.1038/ni.3211 · Cited by 231 · see citing works
RUNX proteins in transcription factor networks that regulate T-cell lineage choice
Collins, A., Littman, D. R., & Taniuchi, I. (2009) · Nature reviews. Immunology · doi:10.1038/nri2489 · Cited by 219 · see citing works
Roles of interferon-regulatory factors in T-helper-cell differentiation
Lohoff, M. D., & Mak, T. W. (2005) · Nature reviews. Immunology · doi:10.1038/nri1552 · Cited by 214 · see citing works
TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL
Kirsch, I. R., Watanabe, R., O’Malley, J. T., Williamson, D. W., Scott, L.-L., Elco, C. P., Teague, J. E., Gehad, A. E., Lowry, E. L., LeBoeuf, N. R., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aaa9122 · Cited by 213 · see citing works
Rutz, S., Noubade, R., Eidenschenk, C., Ota, N., Zeng, W., Zheng, Y., Hackney, J. A., Ding, J., Singh, H., & Ouyang, W. (2011) · Nature Immunology · doi:10.1038/ni.2134 · Cited by 193 · see citing works
Letourneur, F., & MALISSEN, B. (1989) · European Journal of Immunology · doi:10.1002/eji.1830191214 · Cited by 191 · see citing works
Harari, A., Vallelian, F., & Pantaleo, G. (2004) · European Journal of Immunology · doi:10.1002/eji.200425324 · Cited by 184 · see citing works
Qu, K., Zaba, L. C., Satpathy, A. T., Giresi, P. G., Li, R., Jin, Y., Armstrong, R. J., Chen, J., Schmitt, N., Rahbar, Z., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.05.008 · Cited by 178 · see citing works
Self-citationBeyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells
Newell, E. W., & Davis, M. M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2783 · Cited by 129 · see citing works
Self-citationBernengo, M. G., Quaglino, P., Novelli, M., Cappello, N., Doveil, G. C., Lisa, F., Matteis, A. D., Fierro, M. T., & Appino, A. (1998) · Annals of Oncology · doi:10.1023/a:1008397323199 · Cited by 116 · see citing works
Regulatory T cells and immunodeficiency in mycosis fungoides and Sézary syndrome
Krejsgaard, T., Ødum, N., Geisler, C., Wasik, M. A., & Woetmann, A. (2011) · Leukemia · doi:10.1038/leu.2011.237 · Cited by 113 · see citing works
Sufficool, K. E., Lockwood, C. M., Abel, H., Hagemann, I. S., Schumacher, J. A., Kelley, T. W., & Duncavage, E. J. (2015) · Journal of the American Academy of Dermatology · doi:10.1016/j.jaad.2015.04.030 · Cited by 105 · see citing works
Weng, W., Armstrong, R. J., Arai, S., Desmarais, C., Hoppe, R. T., & Kim, Y. H. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3007420 · Cited by 99 · see citing works
Self-citationThe Immunopathogenesis of Cutaneous T-Cell Lymphoma
Rook, A. H. (1993) · Archives of Dermatology · doi:10.1001/archderm.1993.01680250098016 · Cited by 98 · see citing works
Song, K., Rabin, R. L., Hill, B. J., Rosa, S. C. D., Perfetto, S. P., Zhang, H. H., Foley, J. F., Reiner, J. S., Liu, J., Mattapallil, J. J., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409720102 · Cited by 87 · see citing works
Afik, S., Yates, K. B., Bi, K., Darko, S. W., Godec, J., Gerdemann, U., Swadling, L., Douek, D. C., Klenerman, P., Barnes, E. J., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx615 · Cited by 79 · see citing works
The Human Cell AtlasPreprint
Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., Benoist, C. O., Birney, E., Bodenmiller, B., Campbell, P. J., Carninci, P., Clatworthy, M. R., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/121202 · Cited by 76 · see citing works
The Usefulness of CD26 in Flow Cytometric Analysis of Peripheral Blood in Sézary Syndrome
Kelemen, K., Guitart, J., Kuzel, T. M., Goolsby, C. L., & Peterson, L. C. (2007) · American Journal of Clinical Pathology · doi:10.1309/05gfg3ly3vycdmey · Cited by 65 · see citing works
A peripheral CD4+ T cell precursor for naive, memory, and regulatory T cells
Zhao, C., & Davies, J. D. (2010) · The Journal of Experimental Medicine · doi:10.1084/jem.20100598 · Cited by 28 · see citing works
Bigler, R. D., Boselli, C. M., Foley, B., & Vonderheid, E. C. (1996) · Europe PMC (PubMed Central) · Cited by 19 · see citing works
Buenrostro, J. D., Corces, M. R., Wu, B., Schep, A. N., Lareau, C. A., Majeti, R., Chang, H. Y., & Greenleaf, W. J. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/109843 · Cited by 14 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Chromatin accessibility and the regulatory epigenome
Klemm, S. L., Shipony, Z., & Greenleaf, W. J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-018-0089-8 · Cited by 1,793 · see citing works
Self-citationArchR is a scalable software package for integrative single-cell chromatin accessibility analysis
Granja, J. M., Corces, M. R., Pierce, S. E., Bagdatli, S. T., Choudhry, H., Chang, H. Y., & Greenleaf, W. J. (2021) · Nature Genetics · doi:10.1038/s41588-021-00790-6 · Cited by 1,392 · see citing works
Self-citationThe technological landscape and applications of single-cell multi-omics
Baysoy, A., Bai, Z., Satija, R., & Fan, R. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00615-w · Cited by 1,037 · see citing works
Satpathy, A. T., Granja, J. M., Yost, K. E., Qi, Y., Meschi, F., McDermott, G. P., Olsen, B. N., Mumbach, M. R., Pierce, S. E., Corces, M. R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0206-z · Cited by 980 · see citing works
Self-citationApplications of single-cell sequencing in cancer research: progress and perspectives
Lei, Y., Tang, R., Xu, J., Wang, W., Zhang, B., Liu, J., Yu, X., & Shi, S. (2021) · Journal of Hematology & Oncology · doi:10.1186/s13045-021-01105-2 · Cited by 597 · see citing works
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia
Granja, J. M., Klemm, S., McGinnis, L. M., Kathiria, A. S., Mezger, A., Corces, M. R., Parks, B., Gars, E., Liedtke, M., Zheng, G. X. Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0332-7 · Cited by 498 · see citing works
Self-citationSingle-cell multimodal omics: the power of many
Zhu, C., Preissl, S., & Ren, B. (2020) · Nature Methods · doi:10.1038/s41592-019-0691-5 · Cited by 386 · see citing works
Rubin, A. J., Parker, K. R., Satpathy, A. T., Qi, Y., Wu, B., Ong, A. J., Mumbach, M. R., Ji, A. L., Kim, D. S., Cho, S. W., et al. (2019) · Cell · doi:10.1016/j.cell.2018.11.022 · Cited by 314 · see citing works
Self-citationThe epigenetic basis of cellular heterogeneity
Carter, B. C., & Zhao, K. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-00300-0 · Cited by 314 · see citing works
Single-cell RNA sequencing in cardiovascular development, disease and medicine
Paik, D. T., Cho, S., Tian, L., Chang, H. Y., & Wu, J. C. (2020) · Nature Reviews Cardiology · doi:10.1038/s41569-020-0359-y · Cited by 306 · see citing works
Self-citationHigh-throughput and single-cell T cell receptor sequencing technologies
Pai, J. A., & Satpathy, A. T. (2021) · Nature Methods · doi:10.1038/s41592-021-01201-8 · Cited by 296 · see citing works
Self-citationNew paradigms on hematopoietic stem cell differentiation
Cheng, H., Zheng, Z., & Cheng, T. (2019) · Protein & Cell · doi:10.1007/s13238-019-0633-0 · Cited by 275 · see citing works
Single-cell sequencing techniques from individual to multiomics analyses
Kashima, Y., Sakamoto, Y., Kaneko, K., Seki, M., Suzuki, Y., & Suzuki, A. (2020) · Experimental & Molecular Medicine · doi:10.1038/s12276-020-00499-2 · Cited by 270 · see citing works
Understanding tumor ecosystems by single-cell sequencing: promises and limitations
Ren, X., Kang, B., & Zhang, Z. (2018) · Genome biology · doi:10.1186/s13059-018-1593-z · Cited by 214 · see citing works
Computational methods for single-cell omics across modalities
Efremova, M., & Teichmann, S. A. (2020) · Nature Methods · doi:10.1038/s41592-019-0692-4 · Cited by 201 · see citing works
Chromatin accessibility profiling methods
Minnoye, L., Marinov, G. K., Krausgruber, T., Pan, L., Marand, A. P., Secchia, S., Greenleaf, W. J., Furlong, E. E. M., Zhao, K., Schmitz, R. J., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00008-9 · Cited by 206 · see citing works
Self-citationSingle-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification
Ku, W. L., Nakamura, K., Gao, W., Cui, K., Hu, G., Tang, Q., Ni, B., & Zhao, K. (2019) · Nature Methods · doi:10.1038/s41592-019-0361-7 · Cited by 181 · see citing works
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation
Baek, S., & Lee, I. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.06.012 · Cited by 151 · see citing works
Xu, J., Nuno, K. A., Litzenburger, U. M., Qi, Y., Corces, M. R., Majeti, R., & Chang, H. Y. (2019) · eLife · doi:10.7554/elife.45105 · Cited by 150 · see citing works
Self-citationBorcherding, N. C., Voigt, A. P., Liu, V., Link, B. K., Zhang, W., & Jabbari, A. (2019) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-3309 · Cited by 128 · see citing works
Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen
Li, Z., Kuppe, C., Ziegler, S. M., Cheng, M., Kabgani, N., Menzel, S., Zenke, M., Kramann, R., & Costa, I. G. (2021) · Nature Communications · doi:10.1038/s41467-021-26530-2 · Cited by 120 · see citing works
Hamamoto, R., Komatsu, M., Takasawa, K., Asada, K., & Kaneko, S. (2019) · Biomolecules · doi:10.3390/biom10010062 · Cited by 126 · see citing works
You, M., Chen, L., Zhang, D., Zhao, P., Chen, Z., Qin, E., Gao, Y., Davis, M. M., & Yang, P. (2021) · Nature Cell Biology · doi:10.1038/s41556-021-00690-1 · Cited by 116 · see citing works
Self-citationSingle cell cancer epigenetics
Casado-Peláez, M., Bueno-Costa, A., & Esteller, M. (2022) · Trends in cancer · doi:10.1016/j.trecan.2022.06.005 · Cited by 113 · see citing works
Advanced model systems and tools for basic and translational human immunology
Wagar, L. E., DiFazio, R. M., & Davis, M. M. (2018) · Genome Medicine · doi:10.1186/s13073-018-0584-8 · Cited by 102 · see citing works
Self-citationAdvances in bulk and single-cell multi-omics approaches for systems biology and precision medicine
Li, Y., Ma, L., Wu, D., & Chen, G. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab024 · Cited by 101 · see citing works
Annotation of cell types (ACT): a convenient web server for cell type annotation
Quan, F., Liang, X., Cheng, M., Yang, H., Liu, K., He, S., Sun, S., Deng, M., He, Y., Liu, W., et al. (2023) · Genome Medicine · doi:10.1186/s13073-023-01249-5 · Cited by 91 · see citing works
High-throughput and high-dimensional single-cell analysis of antigen-specific CD8+ T cells
Ma, K.-Y., Schonnesen, A. A., He, C., Xia, A. Y., Sun, E., Chen, E., Sebastian, K., Guo, Y., BALDERAS, R. S., Kulkarni-Date, M. N., et al. (2021) · Nature Immunology · doi:10.1038/s41590-021-01073-2 · Cited by 84 · see citing works
Immunology in the Era of Single-Cell Technologies
Efremova, M., Vento‐Tormo, R., Park, J.-E., Teichmann, S. A., & James, K. R. (2020) · Annual Review of Immunology · doi:10.1146/annurev-immunol-090419-020340 · Cited by 77 · see citing works
Recharacterizing Tumor-Infiltrating Lymphocytes by Single-Cell RNA Sequencing
Zhang, L., & Zhang, Z. (2019) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-18-0658 · Cited by 77 · see citing works
Single-Cell Genomics and Epigenomics: Technologies and Applications in Plants
Luo, C. Y., Fernie, A. R., & Yan, J. (2020) · Trends in Plant Science · doi:10.1016/j.tplants.2020.04.016 · Cited by 74 · see citing works
Advances and applications of single‐cell omics technologies in plant research
Mo, Y., & Jiao, Y. (2022) · The Plant Journal · doi:10.1111/tpj.15772 · Cited by 74 · see citing works
Genetic and epigenetic insights into cutaneous T-cell lymphoma
Tensen, C. P., Quint, K. D., & Vermeer, M. H. (2021) · Blood · doi:10.1182/blood.2019004256 · Cited by 72 · see citing works
scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
Yu, W., Uzun, Y., Zhu, Q., Chen, C., & Tan, K. (2020) · Genome biology · doi:10.1186/s13059-020-02008-0 · Cited by 60 · see citing works
Epigenetic remodeling of the immune landscape in cancer: therapeutic hurdles and opportunities
Tien, F., Lu, H., Lin, S., & Tsai, H.-C. (2023) · Journal of Biomedical Science · doi:10.1186/s12929-022-00893-0 · Cited by 50 · see citing works
Profiling Chromatin Accessibility at Single-Cell Resolution
Sinha, S., Satpathy, A. T., Zhou, W., Ji, H., Stratton, J. A., Jaffer, A., Bahlis, N. J., Morrissy, A. S., & Biernaskie, J. A. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.06.010 · Cited by 47 · see citing works
Self-citationSingle-cell technologies — studying rheumatic diseases one cell at a time
Cheung, P., Khatri, P., Utz, P. J., & Kuo, A. J. (2019) · Nature Reviews Rheumatology · doi:10.1038/s41584-019-0220-z · Cited by 38 · see citing works
Xu, X., Hua, X., Han, M., Hu, S., & Song, J. (2023) · Basic Research in Cardiology · doi:10.1007/s00395-022-00972-1 · Cited by 37 · see citing works
Wimmers, F., & Pulendran, B. (2020) · Current Opinion in Immunology · doi:10.1016/j.coi.2020.05.001 · Cited by 36 · see citing works
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery
Hu‐Lieskovan, S., Bhaumik, S., Dhodapkar, K. M., Grivel, J., Gupta, S. V., Hanks, B. A., Janetzki, S., Kleen, T. O., Koguchi, Y., Lund, A. W., et al. (2020) · Journal for ImmunoTherapy of Cancer · doi:10.1136/jitc-2020-000705 · Cited by 35 · see citing works
Schoonhoven, A. O.-V., de Bruijn, M. J. W., Stikker, B., Brouwer, R. W. W., Braunstahl, G., van IJcken, W. F. J., Graf, T., Huylebroeck, D., Hendriks, R. W., Stik, G., et al. (2023) · Science Immunology · doi:10.1126/sciimmunol.adg3917 · Cited by 34 · see citing works
Seumois, G., & Vijayanand, P. (2019) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2019.09.014 · Cited by 30 · see citing works
Tagmentation-based single-cell genomicsPreprint
Adey, A. (2021) · Genome Research · doi:10.1101/gr.275223.121 · Cited by 32 · see citing works
Functional crosstalk between T cells and monocytes in cancer and atherosclerosis
Padgett, L. E., Araujo, D. J., Hedrick, C. C., & Olingy, C. E. (2020) · Journal of Leukocyte Biology · doi:10.1002/jlb.1mir0420-076r · Cited by 32 · see citing works
Applications of Single-Cell Omics to Dissect Tumor Microenvironment
Guo, T., Li, W., & Cai, X. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.548719 · Cited by 33 · see citing works
Borcherding, N. C., Severson, K. J., Henderson, N., Ortolan, L. D. S., Rosenthal, A. C., Bellizzi, A. M., Liu, V., Link, B. K., Mangold, A. R., & Jabbari, A. (2022) · Blood Advances · doi:10.1182/bloodadvances.2021005991 · Cited by 30 · see citing works
Update on Biology of Cutaneous T-Cell Lymphoma
Phyo, Z. H., Shanbhag, S., & Rozati, S. (2020) · Frontiers in Oncology · doi:10.3389/fonc.2020.00765 · Cited by 30 · see citing works
Omenn, G. S. (2021) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2021.100062 · Cited by 30 · see citing works
A Genetic Bottleneck of Mitochondrial DNA During Human Lymphocyte Development
Tang, Z., Lu, Z., Chen, B., Zhang, W., Chang, H. Y., Hu, Z., & Xu, J. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac090 · Cited by 29 · see citing works
Self-citationLi, R., & Quon, G. (2019) · Genome biology · doi:10.1186/s13059-019-1806-0 · Cited by 28 · see citing works
Self-citationEpigenetics of T cell fate decision
Pace, L., & Amigorena, S. (2020) · Current Opinion in Immunology · doi:10.1016/j.coi.2020.01.002 · Cited by 29 · see citing works
Personal regulome navigation of cancer
Chang, H. Y. (2021) · Nature reviews. Cancer · doi:10.1038/s41568-021-00381-x · Cited by 28 · see citing works
Self-citationPatient-Specific Multi-Omics Models and the Application in Personalized Combination Therapy
John, A. J., Qin, B., Kalari, K. R., Wang, L., & Yu, J. (2020) · Future Oncology · doi:10.2217/fon-2020-0119 · Cited by 27 · see citing works
Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection
Zhao, Y., Zhang, X., Song, Z., Wei, D., Wang, H., Chen, W., Sun, G., Ma, W., & Chen, K. (2020) · Frontiers in Medicine · doi:10.3389/fmed.2020.584728 · Cited by 28 · see citing works
Ren, L., Huang, D., Liu, H., Lin, N., Cai, P., Yu, X., Zhang, Y., Luo, N., Lin, H., Su, J., et al. (2024) · Oncology Letters · doi:10.3892/ol.2024.14285 · Cited by 27 · see citing works
Epigenetic Regulations in Mammalian Cells: Roles and Profiling Techniques
Kim, U., & Lee, D.-S. (2023) · Molecules and Cells · doi:10.14348/molcells.2023.0013 · Cited by 26 · see citing works
Maqbool, M. A., Pioger, L., Aabidine, A. Z. E., Karasu, N., Molitor, A. M., Dao, L. T. M., Charbonnier, G., Laethem, F. V., Fenouil, R., Koch, F., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108048 · Cited by 25 · see citing works
Applications of single-cell technologies in drug discovery for tumor treatment
Liu, B., Hu, S., & Wang, X. (2024) · iScience · doi:10.1016/j.isci.2024.110486 · Cited by 24 · see citing works
Recent advances in microfluidic single-cell analysis and its applications in drug development
Jiao, Y., Gao, L., Ji, Y., & Liu, W. (2022) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2022.116796 · Cited by 25 · see citing works
B4GALT1 Is a New Candidate to Maintain the Stemness of Lung Cancer Stem Cells
Vitis, C. D., Corleone, G., Salvati, V., Ascenzi, F., Pallocca, M., Nicola, F. D., Fanciulli, M., Martino, S. D., Bruschini, S., Napoli, C., et al. (2019) · Journal of Clinical Medicine · doi:10.3390/jcm8111928 · Cited by 24 · see citing works
Frontiers in single cell analysis: multimodal technologies and their clinical perspectives
Källberg, J., Xiao, W., Assche, D. V., Baret, J., & Taly, V. (2022) · Lab on a Chip · doi:10.1039/d2lc00220e · Cited by 23 · see citing works
Liu, J., Liu, L., He, J. H., Xu, Y., & Wang, Y. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103172 · Cited by 23 · see citing works
Development of circulating CD4+ T‐cell memory
Soon, M. S. F., Engel, J. A., Lee, H. J., & Haque, A. (2019) · Immunology and Cell Biology · doi:10.1111/imcb.12272 · Cited by 22 · see citing works
Reticker-Flynn, N. E., & Engleman, E. G. (2020) · eLife · doi:10.7554/elife.53839 · Cited by 22 · see citing works
Ferraro, A. R., Ameri, A. J., Lu, Z., Kamei, M., Schmitz, R. J., & Lewis, Z. (2021) · BMC Genomics · doi:10.1186/s12864-021-07774-0 · Cited by 21 · see citing works
Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells
Gao, W., Ku, W. L., Pan, L., Perrie, J., Zhao, T., Hu, G., Wu, Y., Zhu, J., Ni, B., & Zhao, K. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab102 · Cited by 21 · see citing works
Gong, Y., Fei, P., Zhang, Y., Xu, Y., & Wei, J. (2025) · Advanced Science · doi:10.1002/advs.202501095 · Cited by 22 · see citing works
Haematopoiesis in Zebrafish (Danio Rerio)
Stosik, M. P., Tokarz–Deptuła, B., & Deptuła, W. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.902941 · Cited by 18 · see citing works
Incorporating cell hierarchy to decipher the functional diversity of single cells
Chen, L., & Li, S. C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1044 · Cited by 18 · see citing works
Chen, M., Jiang, J., & Hou, J. (2023) · Biomarker Research · doi:10.1186/s40364-023-00502-8 · Cited by 19 · see citing works
Advances in Microfluidic Single-Cell RNA Sequencing and Spatial Transcriptomics
Sun, Y., Yu, N., Zhang, J., & Yang, B. (2025) · Micromachines · doi:10.3390/mi16040426 · Cited by 18 · see citing works
Pace, L. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a037754 · Cited by 18 · see citing works
Advances and challenges in epigenomic single-cell sequencing applications
Philpott, M., Cribbs, A. P., Brown, T. P., Brown, T. P., & Oppermann, U. C. T. (2020) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2020.01.013 · Cited by 17 · see citing works
Best practices for differential accessibility analysis in single-cell epigenomics
Teo, A. Y. Y., Squair, J. W., Courtine, G., & Skinnider, M. A. (2024) · Nature Communications · doi:10.1038/s41467-024-53089-5 · Cited by 17 · see citing works
New approaches to the study of immune responses in humans
Brodin, P. (2020) · Human Genetics · doi:10.1007/s00439-020-02129-3 · Cited by 17 · see citing works
APEC: an accesson-based method for single-cell chromatin accessibility analysis
Li, B., Li, Y., Li, K., Zhu, L., Yu, Q., Cai, P., Fang, J., Zhang, W., Du, P., Jiang, C., et al. (2020) · Genome biology · doi:10.1186/s13059-020-02034-y · Cited by 15 · see citing works
Multi-Omics Profiling of the Tumor Microenvironment
Oekelen, O. V., & Laganà, A. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-91836-1_16 · Cited by 13 · see citing works
Single-cell technologies and analyses in hematopoiesis and hematological malignancies
Campillo‐Marcos, I., Álvarez‐Errico, D., Alandes, R. A., Mereu, E., & Esteller, M. (2021) · Experimental Hematology · doi:10.1016/j.exphem.2021.05.001 · Cited by 14 · see citing works
Clinical implications of chromatin accessibility in human cancers
Liu, Y. (2020) · Oncotarget · doi:10.18632/oncotarget.27584 · Cited by 15 · see citing works
A roadmap for translational cancer glycoimmunology at single cell resolution
Peixoto, A., Miranda, A., Santos, L. L., & Ferreira, J. A. (2022) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-022-02335-z · Cited by 14 · see citing works
Wong, M., Wei, Y., & Ho, Y. (2023) · Current Opinion in HIV and AIDS · doi:10.1097/coh.0000000000000809 · Cited by 14 · see citing works
Self-citationSingle-cell sequencing: expansion, integration and translation
Dai, X., Cai, L., & He, F. (2022) · Briefings in Functional Genomics · doi:10.1093/bfgp/elac011 · Cited by 13 · see citing works
Single-Cell High-Throughput Technologies in Cerebrospinal Fluid Research and Diagnostics
Lanz, T. V., Pröbstel, A., Mildenberger, I. C., Platten, M., & Schirmer, L. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01302 · Cited by 13 · see citing works
Epigenomic technologies for precision oncology
Weichenhan, D., Lipka, D. B., Lutsik, P., Goyal, A., & Plass, C. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.08.004 · Cited by 13 · see citing works
Marshall, A. S., & Jones, N. S. (2021) · Biology · doi:10.3390/biology10060503 · Cited by 13 · see citing works
The future of vaccine development
Koff, W. C., & Schenkelberg, T. (2019) · Vaccine · doi:10.1016/j.vaccine.2019.07.101 · Cited by 12 · see citing works
Osteoimmunology research in rheumatoid arthritis: From single-cell omics approach
Hu, N., Wang, J., Ju, B., Li, Y., Fan, P., Jin, X., Kang, X., & Wu, S. (2023) · Chinese Medical Journal · doi:10.1097/cm9.0000000000002678 · Cited by 11 · see citing works
Sharma, S. M., Gioia, L., Abe, B. T., Holt, M., Costanzo, A. E., Kain, L., Su, A. I., & Teyton, L. (2018) · Molecular Immunology · doi:10.1016/j.molimm.2018.09.020 · Cited by 11 · see citing works
Sen, R., & Barnes, C. (2021) · Journal of Developmental Biology · doi:10.3390/jdb9020020 · Cited by 11 · see citing works
Chromatin-accessibility estimation from single-cell ATAC data with scOpenPreprint
Li, Z., Kuppe, C., Ziegler, S., Cheng, M., Kabgani, N., Menzel, S., Zenke, M., Kramann, R., & Costa, I. G. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/865931 · Cited by 10 · see citing works
Recent advances in single‐cell multimodal analysis to study immune cells
Louie, R. H. Y., & Luciani, F. (2020) · Immunology and Cell Biology · doi:10.1111/imcb.12432 · Cited by 10 · see citing works
Yao, Z., Li, M., & Lv, G. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1058296 · Cited by 9 · see citing works
Patterns of T‐Cell Phenotypes in Rheumatic Diseases From Single‐Cell Studies of Tissue
Gao, Y., Dunlap, G. S., Elahee, M., & Rao, D. A. (2021) · ACR Open Rheumatology · doi:10.1002/acr2.11296 · Cited by 9 · see citing works
Single-cell multi-omics in the study of digestive system cancers
Zhou, S., Lin, N., Yu, L., Su, X., Liu, Z., Yu, X., Gao, H., Lin, S., & Zeng, Y. (2023) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2023.12.007 · Cited by 9 · see citing works
ATAC‐seq exposes differences in chromatin accessibility leading to distinct leaf shapes in mulberry
Wang, L., Feng, Y., Wang, J., Jin, X., Zhang, Q., Ackah, M., Wang, Y., Xu, D., & Zhao, W. (2022) · Plant Direct · doi:10.1002/pld3.464 · Cited by 8 · see citing works
Beyond single cells: microfluidics empowering multiomics analysis
Tian, T., Lin, S., & Yang, C. J. (2023) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-023-05028-4 · Cited by 8 · see citing works
Akhtyamov, P., Shaheen, L., Raevskiy, M., Stupnikov, A., & Medvedeva, Y. A. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad447 · Cited by 8 · see citing works
Tracking the immune response with single-cell genomics
Yost, K. E., Chang, H. Y., & Satpathy, A. T. (2019) · Vaccine · doi:10.1016/j.vaccine.2019.11.035 · Cited by 8 · see citing works
Self-citationAn Informative Approach to Single-Cell Sequencing Analysis
Kashima, Y., Suzuki, A., & Suzuki, Y. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-981-13-6037-4_6 · Cited by 7 · see citing works
Pierce, S. E., Kim, S. H., & Greenleaf, W. J. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.11.008 · Cited by 7 · see citing works
Self-citation
- Authors
- Satpathy, A. T., Saligrama, N., Buenrostro, J. D., Wei, Y., Wu, B., Rubin, A. J., Granja, J. M., Lareau, C. A., Li, R., Qi, Y., Parker, K. R., Mumbach, M. R., Serratelli, W. S., Gennert, D. G., Schep, A. N., Corces, M. R., Khodadoust, M. S., Kim, Y. H., Khavari, P. A., Greenleaf, W. J., Davis, M. M., & Chang, H. Y.
- Affiliations
- Stanford Medicine (US)
- Broad Institute (US)
- Chan Zuckerberg Biohub San Francisco (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Davis, Mark M.
- Chang, Howard Y.
- ORCID
- Satpathy, Ansuman T.
- Saligrama, Naresha
- Buenrostro, Jason D.
- Rubin, Adam J.
- Granja, Jeffrey M.
- Lareau, Caleb A.
- Li, Rui
- Qi, Yanyan
- Parker, Kevin R.
- Mumbach, Maxwell R.
- Serratelli, William S.
- Gennert, David G.
- Schep, Alicia N.
- Corces, M. Ryan
- Khodadoust, Michael S.
- Kim, Youn H.
- Khavari, Paul A.
- Greenleaf, William J.
- Davis, Mark M.
- Chang, Howard Y.
- Venue
- Nature Medicine
- Published
- 2018-04-23
- Volume
- 24
- Issue
- 5
- Pages
- 580-590
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- PMC
- PMC5948148
- OpenAlex
- W2801515322
- Cited by
- 152
- References
- 64
- Citations by year
- 2026: 7 · 2025: 6 · 2024: 8 · 2023: 18 · 2022: 15 · 2021: 35 · 2020: 36 · 2019: 21 · 2018: 5
- FWCI
- 8.89
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Medicine (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health (1s10od018220-01)
- National Human Genome Research Institute (P50HG007735, T32HG000044)
- National Institute of General Medical Sciences (T32GM008294)
- National Institute of Allergy and Infectious Diseases (U19AI057229)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Keywords
- T cell receptor, single-cell epigenomics, T cell receptor diversity, T cell heterogeneity, naive and memory T cells, CD4+ T cells, cutaneous T-cell lymphoma, leukemic T cells, chromatin accessibility, T-cell malignancies, T cell clones, immunotherapy
- MeSH terms
- Cell Line, Transformed, Chromatin, Clone Cells, Humans, Immunity, Leukemia, Receptors, Antigen, T-Cell, RNA, Messenger, CD4-Positive T-Lymphocytes, Jurkat Cells, Transposases, Epigenomics, Single-Cell Analysis, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
