The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
The cis-Regulatory Atlas of the Mouse Immune System
Open accessAbstract
Summary A complete chart of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of differentiation and function of an organ system. We generated matched epigenome and transcriptome measurements in 86 primary cell-types that span the mouse immune system and its differentiation cascades. This breadth of data enables variance components analysis which suggests that genes fall into two distinct classes, controlled by either enhancer- or promoter-driven logic, and multiple regression that connects genes to the enhancers that regulate them. Relating transcription factor (TF) expression to the genome-wide accessibility of their binding motifs classifies them as predominantly openers or closers of local chromatin accessibility, pinpointing specific cis-regulatory elements where binding of given TFs is likely functionally relevant, validated by ChIP-seq. Overall, this cis-regulatory atlas provides a trove of information on transcriptional regulation through immune differentiation, and a foundational scaffold to define key regulatory events throughout the immunological genome.
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BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
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
Self-citationIntegrative analysis of 111 reference human epigenomes
Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · cited 2×
“Cell 176, 897–912, February 7, 2019 911 Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015).”
Full-length RNA-seq from single cells using Smart-seq2
Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137
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
Self-citationTissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment
Lavin, Y., Winter, D., Blecher-Gonen, R., David, E., Keren-Shaul, H., Merad, M., Jung, S., & Amit, I. (2014) · Cell · doi:10.1016/j.cell.2014.11.018 · Cited by 2,167
Batf3 Deficiency Reveals a Critical Role for CD8α + Dendritic Cells in Cytotoxic T Cell Immunity
Hildner, K., Edelson, B. T., Purtha, W. E., Diamond, M., Matsushita, H., Kohyama, M., Calderon, B., Schraml, B. U., Unanue, E. R., Diamond, M. S., et al. (2008) · Science · doi:10.1126/science.1164206 · Cited by 2,081
Dendritic cells, monocytes and macrophages: a unified nomenclature based on ontogeny
Guilliams, M., Ginhoux, F., Jakubzick, C., Naik, S. H., Onai, N., Schraml, B. U., Segura, E., Tussiwand, R., & Yona, S. (2014) · Nature Reviews Immunology · doi:10.1038/nri3712 · Cited by 1,819
Expression of a β-globin gene is enhanced by remote SV40 DNA sequences
Banerji, J., Rusconi, S., & Schaffner, W. (1981) · Cell · doi:10.1016/0092-8674(81)90413-x · Cited by 1,724
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Chen, H., Lareau, C., Andreani, T., Vinyard, M. E., Garcia, S. P., Clement, K., Andrade-Navarro, M. A., Buenrostro, J. D., & Pinello, L. (2019) · Genome Biology · doi:10.1186/s13059-019-1854-5 · Cited by 332
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Gal-Oz, S. T., Maier, B., Yoshida, H., Seddu, K., Elbaz, N., Czysz, C., Zuk, O., Stranger, B. E., Ner-Gaon, H., & Shay, T. (2019) · Nature Communications · doi:10.1038/s41467-019-12348-6 · Cited by 274
Self-citationDanaher, P., Kim, Y., Nelson, B., Griswold, M., Yang, Z., Piazza, E., & Beechem, J. M. (2022) · Nature Communications · doi:10.1038/s41467-022-28020-5 · Cited by 292
Metadata
- Authors
- Yoshida, H., Lareau, C. A., Ramirez, R. N., Rose, S. A., Maier, B., Wroblewska, A., Desland, F., Chudnovskiy, A., Mortha, A., Dominguez, C., Tellier, J., Kim, E., Dwyer, D., Shinton, S., Nabekura, T., Qi, Y., Yu, B., Robinette, M., Kim, K.-W., Wagers, A., Rhoads, A., Nutt, S. L., Brown, B. D., Mostafavi, S., Buenrostro, J. D., & Benoist, C.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2019-02
- Volume
- 176
- Issue
- 4
- Pages
- 897-912.e20
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W2911510951
- Cited by
- 395
- References
- 64
- FWCI
- 14.97
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Yoshida, H., Lareau, C. A., Ramirez, R. N., Rose, S. A., Maier, B., Wroblewska, A., Desland, F., Chudnovskiy, A., Mortha, A., Dominguez, C., Tellier, J., Kim, E., Dwyer, D., Shinton, S., Nabekura, T., Qi, Y., Yu, B., Robinette, M., Kim, K.-W., . . . Benoist, C. (2019). The cis-Regulatory Atlas of the Mouse Immune System. Cell. https://doi.org/10.1016/j.cell.2018.12.036
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