[ { "id": "https://authors.library.caltech.edu/records/ehp9v-cf510", "eprint_id": 108866, "eprint_status": "archive", "datestamp": "2023-08-20 05:31:55", "lastmod": "2023-12-22 23:28:42", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rebboah-Elisabeth", "name": { "family": "Rebboah", "given": "Elisabeth" }, "orcid": "0000-0003-2273-0189" }, { "id": "Reese-Fairlie", "name": { "family": "Reese", "given": "Fairlie" }, "orcid": "0000-0002-9240-0102" }, { "id": "Williams-Katherine", "name": { "family": "Williams", "given": "Katherine" }, "orcid": "0000-0001-8061-0105" }, { "id": "Balderrama-Gutierrez-Gabriela", "name": { "family": "Balderrama-Gutierrez", "given": "Gabriela" }, "orcid": "0000-0002-5794-4518" }, { "id": "McGill-Cassandra", "name": { "family": "McGill", "given": "Cassandra" } }, { "id": "Trout-Diane", "name": { "family": "Trout", "given": "Diane" }, "orcid": "0000-0002-4928-5532" }, { "id": "Rodriguez-Isaryhia", "name": { "family": "Rodriguez", "given": "Isaryhia" } }, { "id": "Liang-Heidi", "name": { "family": "Liang", "given": "Heidi" } }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara J." }, "orcid": "0000-0003-3235-8130" }, { "id": "Mortazavi-Ali", "name": { "family": "Mortazavi", "given": "Ali" }, "orcid": "0000-0002-4259-6362" } ] }, "title": "Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. \n\nReceived 28 April 2021; Accepted 20 September 2021; Published 07 October 2021. \n\nWe would like to thank Melanie Oakes at UC Irvine Genomics High-Throughput Facility (GHTF) for her help with PacBio sequencing. \n\nThis work was supported by the National Institutes of Health (UM1 HG009443) to A.M. and B.J.W. \n\nElisabeth Rebboah and Fairlie Reese contributed equally to this work. \n\nAuthor Contributions: E.R., G.B., I.R., C.M., and H.L. performed the experiments. F.R. and E.R. analyzed the data and wrote the manuscript with significant input from K.W., B.W., and A.M. F.R. supplied custom LR-Split-seq demultiplexing code and D.T. provided TSS-calling code. All authors read and approved the final manuscript. \n\nEthical approval and consent to participate: Ethics approval is not applicable. \n\nThe authors declare no competing financial interests. \n\nReview history: The review history is available as Additional file 3. \n\nPeer review information: Barbara Cheifet was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.\n\n
Published - Rebboah2021_Article_MappingAndModelingTheGenomicBa.pdf
Submitted - 2021.04.26.441522v1.full.pdf
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", "abstract": "The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.", "date": "2021-10-07", "date_type": "published", "publication": "Genome Biology", "volume": "22", "publisher": "BioMed Central", "pagerange": "Art. No. 286", "id_number": "CaltechAUTHORS:20210429-100236539", "issn": "1474-7596", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210429-100236539", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "UM1 HG009443" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1186/s13059-021-02505-w", "pmcid": "PMC8495978", "primary_object": { "basename": "13059_2021_2505_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/ehp9v-cf510/files/13059_2021_2505_MOESM1_ESM.pdf" }, "related_objects": [ { "basename": "13059_2021_2505_MOESM2_ESM.gz", "url": "https://authors.library.caltech.edu/records/ehp9v-cf510/files/13059_2021_2505_MOESM2_ESM.gz" }, { "basename": "13059_2021_2505_MOESM3_ESM.docx", "url": "https://authors.library.caltech.edu/records/ehp9v-cf510/files/13059_2021_2505_MOESM3_ESM.docx" }, { "basename": "2021.04.26.441522v1.full.pdf", "url": "https://authors.library.caltech.edu/records/ehp9v-cf510/files/2021.04.26.441522v1.full.pdf" }, { "basename": "Rebboah2021_Article_MappingAndModelingTheGenomicBa.pdf", "url": "https://authors.library.caltech.edu/records/ehp9v-cf510/files/Rebboah2021_Article_MappingAndModelingTheGenomicBa.pdf" } ], "resource_type": "article", "pub_year": "2021", "author_list": "Rebboah, Elisabeth; Reese, Fairlie; et el." }, { "id": "https://authors.library.caltech.edu/records/bbq8c-fbs42", "eprint_id": 90544, "eprint_status": "archive", "datestamp": "2023-08-22 05:44:22", "lastmod": "2023-10-23 16:15:38", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Gorkin-D-U", "name": { "family": "Gorkin", "given": "David U." }, "orcid": "0000-0003-4944-4107" }, { "id": "Williams-B-A", "name": { "family": "Williams", "given": "Brian A." } }, { "id": "Trout-Diane", "name": { "family": "Trout", "given": "Diane" }, "orcid": "0000-0002-4928-5532" }, { "id": "Amrhein-H", "name": { "family": "Amrhein", "given": "Henry" }, "orcid": "0000-0002-4264-140X" } ] }, "title": "An atlas of dynamic chromatin landscapes in mouse fetal development", "ispublished": "pub", "full_text_status": "public", "keywords": "Differentiation; Epigenomics", "note": "\u00a9 2020 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. \n\nReceived 08 August 2017; Accepted 11 June 2019; Published 29 July 2020. \n\nThis study was funded by the National Human Genome Research Institute as part of the Encyclopedia of DNA Elements (ENCODE) project (U54HG006997), and was performed in compliance with all relevant ethical regulations. D.U.G. was supported by the NIH Institutional Research and Academic Career Development Awards (IRACDA) program, and an A. P. Giannini Foundation fellowship. D.E.D, A.V., and L.A.P. were also supported by UM1HG009421, and research conducted at the E. O. Lawrence Berkeley National Laboratory was performed under Department of Energy Contract DE-AC02-05CH11231, University of California. I.B. is funded through an Imperial College Research Fellowship. Y.H. is supported by the H.A. and Mary K. Chapman Charitable Trust. J.R.E. is an Investigator of the Howard Hughes Medical Institute. The embryo image second from the right in Fig. 1a was adapted from ref. 89, an Open Access article distributed under the terms of the Creative Commons Attribution License. \n\nData availability: All raw and processed data can be accessed via the ENCODE Data Collection and Coordination (DCC) website: https://www.encodedcc.org via the experiment IDs listed in Supplementary Table 13. \n\nCode availability: The ENCODE histone ChIP\u2013seq pipeline is among the collection of ENCODE Uniform Processing Pipelines that can be found here: https://github.com/ENCODE-DCC/ChIP-seq-pipeline. \n\nAuthor Contributions: These authors contributed equally: David U. Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang. \n\nStudy conceived and overseen by B.R., D.U.G., L.A.P., A.V., D.E.D., Y.S., K.G., H.Y., J.R.E., W.W., and J.M.C. Tissue collections performed by V.A., J.A.A., I.P.-F., C.S.N., and M.K. ChIP\u2013seq experiments performed by A.Y.L. and S.C. ATAC\u2013seq experiments performed by H.H. and J.Y.H. Data curation and processing by J.S.S., J.M.D., B.L., B.A.W., D.T., H.A., and D.U.G. Analysis performed by I.B., D.U.G., Y. Zhao., Y. Zhang, Y.F.-Y., J.C., A.W., B.D., B.Z., M.W., Y.Q., Y.H., and S.P. Transgenic assays performed by V.A., J.A.A., I.P.-F., C.S.N, M.K., T.H.G., Q.T.P., A.N.H., B.J.M., and E.A.L. Manuscript written by D.U.G., I.B., Y. Zhao., Y. Zhang, D.E.D., and B.R. with input from all authors. \n\nCompeting interests: B.R. is co-founder and share holder of Arima Genomics. The other authors declare no competing interests.\n\nGorkin, D.U., Barozzi, I., Zhao, Y. et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature (2020). https://doi.org/10.1038/s41586-020-2841-4\n\nPublished - s41586-020-2093-3.pdf
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Erratum - s41586-020-2841-4.pdf
", "abstract": "The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP\u2013seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC\u2013seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.", "date": "2020-07-30", "date_type": "published", "publication": "Nature", "volume": "583", "number": "7818", "publisher": "Nature Publishing Group", "pagerange": "744-751", "id_number": "CaltechAUTHORS:20181031-110727092", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181031-110727092", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54HG006997" }, { "agency": "A. P. Giannini Foundation" }, { "agency": "NIH", "grant_number": "UM1HG009421" }, { "agency": "Department of Energy (DOE)", "grant_number": "DE-AC02-05CH11231" }, { "agency": "Imperial College London" }, { "agency": "H. A. and Mary K. Chapman Charitable Trust" }, { "agency": "Howard Hughes Medical Institute (HHMI)" } ] }, "doi": "10.1038/s41586-020-2093-3", "pmcid": "PMC7398618", "primary_object": { "basename": "41586_2020_2093_Fig22_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig22_ESM.webp" }, "related_objects": [ { "basename": "41586_2020_2093_MOESM1_ESM.pdf", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_MOESM1_ESM.pdf" }, { "basename": "41586_2020_2093_Fig19_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig19_ESM.webp" }, { "basename": "41586_2020_2093_MOESM5_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_MOESM5_ESM.xlsx" }, { "basename": "166652.full.pdf", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/166652.full.pdf" }, { "basename": "41586_2020_2093_Fig18_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig18_ESM.webp" }, { "basename": "41586_2020_2093_MOESM4_ESM.gz", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_MOESM4_ESM.gz" }, { "basename": "41586_2020_2093_MOESM8_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_MOESM8_ESM.xlsx" }, { "basename": "s41586-020-2841-4.pdf", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/s41586-020-2841-4.pdf" }, { "basename": "41586_2020_2093_Fig16_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig16_ESM.webp" }, { "basename": "41586_2020_2093_Fig23_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig23_ESM.webp" }, { "basename": "41586_2020_2093_MOESM6_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_MOESM6_ESM.xlsx" }, { "basename": "41586_2020_2093_Fig13_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig13_ESM.webp" }, { "basename": "41586_2020_2093_Fig14_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig14_ESM.webp" }, { "basename": "41586_2020_2093_Fig20_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig20_ESM.webp" }, { "basename": "41586_2020_2093_MOESM7_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_MOESM7_ESM.xlsx" }, { "basename": "41586_2020_2093_Fig9_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig9_ESM.webp" }, { "basename": "41586_2020_2093_MOESM2_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_MOESM2_ESM.xlsx" }, { "basename": "41586_2020_2093_MOESM3_ESM.xlsx", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_MOESM3_ESM.xlsx" }, { "basename": "s41586-020-2093-3.pdf", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/s41586-020-2093-3.pdf" }, { "basename": "41586_2020_2093_Fig12_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig12_ESM.webp" }, { "basename": "41586_2020_2093_Fig21_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig21_ESM.webp" }, { "basename": "41586_2020_2093_Fig7_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig7_ESM.webp" }, { "basename": "41586_2020_2093_Fig8_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig8_ESM.webp" }, { "basename": "41586_2020_2093_Fig10_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig10_ESM.webp" }, { "basename": "41586_2020_2093_Fig11_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig11_ESM.webp" }, { "basename": "41586_2020_2093_Fig15_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig15_ESM.webp" }, { "basename": "41586_2020_2093_Fig17_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig17_ESM.webp" }, { "basename": "41586_2020_2093_Fig6_ESM.webp", "url": "https://authors.library.caltech.edu/records/bbq8c-fbs42/files/41586_2020_2093_Fig6_ESM.webp" } ], "resource_type": "article", "pub_year": "2020", "author_list": "Gorkin, David U.; Williams, Brian A.; et el." }, { "id": "https://authors.library.caltech.edu/records/tj9gn-5gr81", "eprint_id": 91702, "eprint_status": "archive", "datestamp": "2023-08-19 18:25:12", "lastmod": "2023-10-20 22:12:21", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rahmanian-Sorena", "name": { "family": "Rahmanian", "given": "Sorena" } }, { "id": "Murad-Rabi", "name": { "family": "Murad", "given": "Rabi" } }, { "id": "Breschi-Alessandra", "name": { "family": "Breschi", "given": "Alessandra" } }, { "id": "Zeng-Weihua", "name": { "family": "Zeng", "given": "Weihua" } }, { "id": "Mackiewicz-Mark", "name": { "family": "Mackiewicz", "given": "Mark" } }, { "id": "Williams-Brian-A", "name": { "family": "Williams", "given": "Brian" } }, { "id": "Davis-Carrie-A", "name": { "family": "Davis", "given": "Carrie A." } }, { "id": "Roberts-Brian", "name": { "family": "Roberts", "given": "Brian" } }, { "id": "Meadows-Sarah-K", "name": { "family": "Meadows", "given": "Sarah" } }, { "id": "Moore-Dianne", "name": { "family": "Moore", "given": "Dianne" } }, { "id": "Trout-Diane", "name": { "family": "Trout", "given": "Diane" }, "orcid": "0000-0002-4928-5532" }, { "id": "Zaleski-Chris", "name": { "family": "Zaleski", "given": "Chris" } }, { "id": "Dobin-Alex", "name": { "family": "Dobin", "given": "Alex" } }, { "id": "Sei-Lei-Hoon", "name": { "family": "Sei", "given": "Lei-Hoon" } }, { "id": "Drenkow-Jorg", "name": { "family": "Drenkow", "given": "Jorg" } }, { "id": "Scavelli-Alex", "name": { "family": "Scavelli", "given": "Alex" } }, { "id": "Gingeras-Thomas-R", "name": { "family": "Gingeras", "given": "Thomas R." } }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara J." }, "orcid": "0000-0003-3235-8130" }, { "id": "Myers-Richard-M", "name": { "family": "Myers", "given": "Richard M." } }, { "id": "Guig\u00f3-Roderic", "name": { "family": "Guig\u00f3", "given": "Roderic" } }, { "id": "Mortazavi-Ali", "name": { "family": "Mortazavi", "given": "Ali" }, "orcid": "0000-0002-4259-6362" } ] }, "title": "Dynamics of microRNA expression during mouse prenatal development", "ispublished": "pub", "full_text_status": "public", "note": "\u00a9 2019 Rahmanian et al. Freely available online through the Genome Research Open Access option. This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International),\nas described at http://creativecommons.org/licenses/by-nc/4.0/. \n\nReceived January 30, 2019; Accepted August 29, 2019; published in Advance October 23, 2019. \n\nData access: All the miRNA-seq, short RNA-seq, and NanoString data from this study can be accessed through the ENCODE data portal (https://www.encodeproject.org) under the accession numbers listed in Supplemental Table S1. \n\nThis work was supported by the NIH, National Human Genome Research Institute under grants U54 HG006998 and UM1 HG009443.\n\nPublished - Genome_Res.-2019-Rahmanian-1900-9.pdf
Submitted - 492918.full.pdf
Supplemental Material - Supplemental_Material_v42.pdf
Supplemental Material - Supplemental_Tables.zip
", "abstract": "MicroRNAs (miRNAs) play a critical role as posttranscriptional regulators of gene expression. The ENCODE Project profiled the expression of miRNAs in an extensive set of organs during a time-course of mouse embryonic development and captured the expression dynamics of 785 miRNAs. We found distinct organ-specific and developmental stage\u2013specific miRNA expression clusters, with an overall pattern of increasing organ-specific expression as embryonic development proceeds. Comparative analysis of conserved miRNAs in mouse and human revealed stronger clustering of expression patterns by organ type rather than by species. An analysis of messenger RNA expression clusters compared with miRNA expression clusters identifies the potential role of specific miRNA expression clusters in suppressing the expression of mRNAs specific to other developmental programs in the organ in which these miRNAs are expressed during embryonic development. Our results provide the most comprehensive time-course of miRNA expression as part of an integrated ENCODE reference data set for mouse embryonic development.", "date": "2019-11", "date_type": "published", "publication": "Genome Research", "volume": "29", "number": "11", "publisher": "Cold Spring Harbor Laboratory Press", "pagerange": "1900-1909", "id_number": "CaltechAUTHORS:20181212-091659236", "issn": "1088-9051", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181212-091659236", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54 HG006998" }, { "agency": "NIH", "grant_number": "UM1 HG009443" }, { "agency": "National Human Genome Research Institute" } ] }, "doi": "10.1101/gr.248997.119", "pmcid": "PMC6836743", "primary_object": { "basename": "492918.full.pdf", "url": "https://authors.library.caltech.edu/records/tj9gn-5gr81/files/492918.full.pdf" }, "related_objects": [ { "basename": "Genome_Res.-2019-Rahmanian-1900-9.pdf", "url": "https://authors.library.caltech.edu/records/tj9gn-5gr81/files/Genome_Res.-2019-Rahmanian-1900-9.pdf" }, { "basename": "Supplemental_Material_v42.pdf", "url": "https://authors.library.caltech.edu/records/tj9gn-5gr81/files/Supplemental_Material_v42.pdf" }, { "basename": "Supplemental_Tables.zip", "url": "https://authors.library.caltech.edu/records/tj9gn-5gr81/files/Supplemental_Tables.zip" } ], "resource_type": "article", "pub_year": "2019", "author_list": "Rahmanian, Sorena; Murad, Rabi; et el." }, { "id": "https://authors.library.caltech.edu/records/46y1r-jap62", "eprint_id": 38472, "eprint_status": "archive", "datestamp": "2023-08-22 06:50:33", "lastmod": "2023-10-23 20:11:46", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Marinov-Georgi-K", "name": { "family": "Marinov", "given": "Georgi K." }, "orcid": "0000-0003-1822-7273" }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara" }, "orcid": "0000-0003-3235-8130" }, { "id": "Williams-Brian-A", "name": { "family": "Williams", "given": "Brian A." } }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Fejes-T\u00f3th-K", "name": { "family": "Fejes Toth", "given": "Kata" }, "orcid": "0000-0001-6558-2636" }, { "id": "King-Brandon-W", "name": { "family": "King", "given": "Brandon" } }, { "id": "Schaeffer-Lorain", "name": { "family": "Schaeffer", "given": "Lorain" } }, { "id": "Trout-Diane", "name": { "family": "Trout", "given": "Diane" }, "orcid": "0000-0002-4928-5532" }, { "id": "Vielmetter-Jost", "name": { "family": "Vielmetter", "given": "Jost" }, "orcid": "0000-0002-4314-7163" }, { "id": "Gasper-Clarke", "name": { "family": "Gasper", "given": "Clarke" } }, { "id": "Pepke-Shirley", "name": { "family": "Pepke", "given": "Shirley" } }, { "id": "Amrhein-Henry", "name": { "family": "Amrhein", "given": "Henry" }, "orcid": "0000-0002-4264-140X" }, { "id": "Anaya-Michael-A", "name": { "family": "Anaya", "given": "Michael" }, "orcid": "0000-0002-6944-3614" }, { "id": "McCue-Kenneth-F", "name": { "family": "McCue", "given": "Kenneth" } }, { "id": "Fisher-Aylor-Katherine-I", "name": { "family": "Fisher-Aylor", "given": "Katherine I." } }, { "id": "DeSalvo-Gilberto", "name": { "family": "DeSalvo", "given": "Gilberto" } }, { "id": "Balasubramanian-Sreeram", "name": { "family": "Balasubramanian", "given": "Sreeram" } } ] }, "title": "An integrated encyclopedia of DNA elements in the human genome", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics; Genomics; Molecular biology", "note": "\u00a9 2012 Macmillan Publishers Limited.\n\nThis\npaper is distributed under the terms of the Creative Commons\nAttribution-Non-Commercial-Share Alike licence, and the online version of the paper is\nfreely available to all readers. The authors declare no competing financial interests.\n\nReceived 24 November 2011; accepted 29 May 2012.\n\nWe thank additional members of our laboratories and institutions who have contributed to the experimental and analytical components of this project. We thank D. Leja for assistance with production of the figures. The Consortium is\nfunded by grants from the NHGRI as follows: production grants: U54HG004570 (B. E. Bernstein); U01HG004695 (E. Birney); U54HG004563 (G. E. Crawford); U54HG004557 (T. R. Gingeras); U54HG004555 (T. J. Hubbard); U41HG004568\n(W. J. Kent); U54HG004576 (R. M. Myers); U54HG004558 (M. Snyder); U54HG004592 (J. A. Stamatoyannopoulos). Pilot grants: R01HG003143 (J. Dekker); RC2HG005591 and R01HG003700 (M. C. Giddings); R01HG004456-03 (Y. Ruan);\nU01HG004571 (S. A. Tenenbaum); U01HG004561 (Z. Weng); RC2HG005679 (K. P. White). This project was supported in part by American Recovery and Reinvestment Act (ARRA) funds from the NHGRI through grants U54HG004570, U54HG004563, U41HG004568, U54HG004592, R01HG003143, RC2HG005591,\nR01HG003541, U01HG004561,RC2HG005679 and R01HG003988 (L. Pennacchio). In addition, work from NHGRI Groups was supported by the Intramural Research Program of the NHGRI (L. Elnitski, ZIAHG200323; E. H. Margulies, ZIAHG200341).\nResearch in the Pennachio laboratory was performed at Lawrence Berkeley National Laboratory and at the United States Department of Energy Joint Genome Institute,\nDepartment of Energy Contract DE-AC02-05CH11231, University of California.\n\nPublished - nature11247-s5.txt
Published - nature11247.pdf
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Supplemental Material - nature11247-s6.txt
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Supplemental Material - nature11247-s9.xls
", "abstract": "The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research.", "date": "2012-09-06", "date_type": "published", "publication": "Nature", "volume": "489", "number": "7414", "publisher": "Nature Publishing Group", "pagerange": "57-74", "id_number": "CaltechAUTHORS:20130513-153517455", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130513-153517455", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54HG004570" }, { "agency": "NIH", "grant_number": "U01HG004695" }, { "agency": "NIH", "grant_number": "U54HG004563" }, { "agency": "NIH", "grant_number": "U54HG004557" }, { "agency": "NIH", "grant_number": "U41HG004568" }, { "agency": "NIH", "grant_number": "U54HG004576" }, { "agency": "NIH", "grant_number": "U54HG004558" }, { "agency": "NIH", "grant_number": "U54HG004592" }, { "agency": "NIH", "grant_number": "R01HG003143" }, { "agency": "NIH", "grant_number": "RC2HG005591" }, { "agency": "NIH", "grant_number": "R01HG003700" }, { "agency": "NIH", "grant_number": "R01HG004456-03" }, { "agency": "NIH", "grant_number": "U01HG004571" }, { "agency": "NIH", "grant_number": "U01HG004561" }, { "agency": "NIH", "grant_number": "RC2HG005679" }, { "agency": "NIH", "grant_number": "U54HG004570" }, { "agency": "NIH", "grant_number": "U54HG004563" }, { "agency": "NIH", "grant_number": "U41HG004568" }, { "agency": "NIH", "grant_number": "U54HG004592" }, { "agency": "NIH", "grant_number": "R01HG003143" }, { "agency": "NIH", "grant_number": "RC2HG005591" }, { "agency": "NIH", "grant_number": "R01HG003541" }, { "agency": "NIH", "grant_number": "U01HG004561" }, { "agency": "NIH", "grant_number": "RC2HG005679" }, { "agency": "NIH", "grant_number": "R01HG003988" }, { "agency": "NIH", "grant_number": "ZIAHG200323" }, { "agency": "NIH", "grant_number": "ZIAHG200341" }, { "agency": "National Human Genome Research Institute" }, { "agency": "American Recovery and Reinvestment Act (ARRA)" } ] }, "corp_creators": { "items": [ "ENCODE Project Consortium" ] }, "doi": "10.1038/nature11247", "pmcid": "PMC4243026", "primary_object": { "basename": "nature11247-s2.pdf", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s2.pdf" }, "related_objects": [ { "basename": "nature11247-s3.xls", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s3.xls" }, { "basename": "nature11247-s8.xls", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s8.xls" }, { "basename": "nature11247-s10.xls", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s10.xls" }, { "basename": "nature11247.pdf", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247.pdf" }, { "basename": "nature11247-s5.txt", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s5.txt" }, { "basename": "nature11247-s6.txt", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s6.txt" }, { "basename": "nature11247-s7.xls", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s7.xls" }, { "basename": "nature11247-s9.xls", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s9.xls" }, { "basename": "nature11247-s4.xlsx", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s4.xlsx" }, { "basename": "nature11247-s11.mov", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s11.mov" }, { "basename": "nature11247-s12.mov", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s12.mov" }, { "basename": "nature11247-s1.pdf", "url": "https://authors.library.caltech.edu/records/46y1r-jap62/files/nature11247-s1.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Marinov, Georgi K.; Wold, Barbara; et el." }, { "id": "https://authors.library.caltech.edu/records/stqtp-40c75", "eprint_id": 35106, "eprint_status": "archive", "datestamp": "2023-08-22 06:50:06", "lastmod": "2023-10-20 15:21:24", "type": "article", "metadata_visibility": "show", "creators": { "items": [ { "id": "Djebali-Sarah", "name": { "family": "Djebali", "given": "Sarah" } }, { "id": "Mortazavi-Ali", "name": { "family": "Mortazavi", "given": "Ali" }, "orcid": "0000-0002-4259-6362" }, { "id": "Marinov-Georgi-K", "name": { "family": "Marinov", "given": "Georgi K." }, "orcid": "0000-0003-1822-7273" }, { "id": "Williams-Brian-A", "name": { "family": "Williams", "given": "Brian A." } }, { "id": "Antoshechkin-Igor-A", "name": { "family": "Antoshechkin", "given": "Igor" }, "orcid": "0000-0002-9934-3040" }, { "id": "Fejes-T\u00f3th-K", "name": { "family": "Fejes Toth", "given": "Kata" }, "orcid": "0000-0001-6558-2636" }, { "id": "King-Brandon-W", "name": { "family": "King", "given": "Brandon" } }, { "id": "Schaffer-Lorian", "name": { "family": "Schaffer", "given": "Lorian" } }, { "id": "Trout-Diane", "name": { "family": "Trout", "given": "Diane" }, "orcid": "0000-0002-4928-5532" }, { "id": "Wold-B-J", "name": { "family": "Wold", "given": "Barbara" }, "orcid": "0000-0003-3235-8130" } ] }, "title": "Landscape of transcription in human cells", "ispublished": "pub", "full_text_status": "public", "keywords": "Genetics; Genomics; Molecular biology", "note": "\u00a9 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike licence (http://creativecommons.org/licenses/by-nc-sa/3.0/).\n\nReceived 10 December 2011; accepted 15 May 2012.\n\nThis work was supported by the National Human Genome\nResearch Institute (NHGRI) production grants U54HG004557, U54HG004555, U54HG004576 and U54HG004558, and by the NHGRI pilot grant R01HG003700. It was also supported by the NHGRI ARRA stimulus grant 1RC2HG005591, the National Science Foundation (SNF) grant 127375, the European Research Council (ERC) grant 249968, a research grant for the RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology, and grants BIO2011-26205, CSD2007-00050 and INB GNV-1 from the Spanish Ministry of Science. We would also like to thank C. Gunter and W. Spitzer for editorial assistance with the manuscript.\nT.R.G., R.G., P.C., B.W., Y.R., M.C.G., G.H., S.E.A., A.R., T.H., M.G. and\nY.H. led the project and oversaw the analysis. C.A.D., X.R., B.A.W. and P.C. oversaw or\nsignificantly contributed to data generation. S.D., A.Me., A.D., T.L., A.Mo., A.T., J.L., W.L.,\nF.S., C.X., G.K.M., J.K., C.Z., J.R.,M.R., F.K. and J.H. made major contributions towards data\nprocessing and analysis. R.F.A., T.A., I.A., M.T.B., N.S.B., P.B., K.B., I.B.,S.C., X.C., J.Ch., J.Cu.,\nT.D., J.Dr., E.D., J.Du., R.D., E.F.,M.F., K.F-T., P.F., S.F., M.J.F., H.Ga., D.G.,A.G., H.Gu., C.H.,S.J.,\nR.J., P.K., B.K., C.K., O.J.L., E.P., K.P., J.B.P., P.R., B.R., D.R., M.S., L.S., L.-H.S., A.S., J.S., A.M.S.,\nH.Ta., H.Ti., D.T., N.W., H.W., J.W. and Y.Y. were responsible for data production and\nanalysis. T.R.G. and R.G. wrote the manuscript with input from all authors.\n\nPublished - nature11233.pdf
Supplemental Material - nature11233-s1.pdf
Supplemental Material - nature11233-s2.pdf
", "abstract": "Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.", "date": "2012-09-06", "date_type": "published", "publication": "Nature", "volume": "489", "number": "7414", "publisher": "Nature Publishing Group", "pagerange": "101-108", "id_number": "CaltechAUTHORS:20121025-155437375", "issn": "0028-0836", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20121025-155437375", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "U54HG004557" }, { "agency": "NIH", "grant_number": "U54HG004555" }, { "agency": "NIH", "grant_number": "U54HG004576" }, { "agency": "NIH", "grant_number": "U54HG004558" }, { "agency": "NIH", "grant_number": "R01 HG003700" }, { "agency": "NIH", "grant_number": "1RC2HG005591" }, { "agency": "NSF", "grant_number": "127375" }, { "agency": "European Research Council (ERC)", "grant_number": "249968" }, { "agency": "Ministry of Education, Culture, Sports, Science and Technology (MEXT)" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "BIO2011-26205" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "CSD2007-00050" }, { "agency": "Ministerio de Ciencia e Innovaci\u00f3n (MCINN)", "grant_number": "INB GNV-1" } ] }, "doi": "10.1038/nature11233", "pmcid": "PMC3684276", "primary_object": { "basename": "nature11233-s1.pdf", "url": "https://authors.library.caltech.edu/records/stqtp-40c75/files/nature11233-s1.pdf" }, "related_objects": [ { "basename": "nature11233-s2.pdf", "url": "https://authors.library.caltech.edu/records/stqtp-40c75/files/nature11233-s2.pdf" }, { "basename": "nature11233.pdf", "url": "https://authors.library.caltech.edu/records/stqtp-40c75/files/nature11233.pdf" } ], "resource_type": "article", "pub_year": "2012", "author_list": "Djebali, Sarah; Mortazavi, Ali; et el." } ]