Showing 21 of 21 results

• Publication

  released

  Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells

  Riccardo Calandrelli, Xingzhao We, John Lalith Charles Richard, et al.

  Nat Commun. 2023-10-16;14(1):6519.

  • doi:10.1038/s41467-023-42274-7
  • PMID:37845234
  • PMCID:PMC10579264

  Available supplemental data: website

  URL: https://data.4dnucleome.org

  Data summary: All high-throughput data supporting the current study have been deposited on the 4D Nucleome Data…See more

  Available supplemental data: website

  URL: https://github.com/Zhong-Lab-UCSD/RNA3Dgenome-code-repository

  Data summary: The codes used for the analysis have been deposited and made publicly available on GitHub at…See more

• Publication

  released

  Proper acquisition of cell class identity in organoids allows definition of fate specification programs of the human cerebral cortex

  Ana Uzquiano, Amanda J Kedaigle, Martina Pigoni, et al.

  Cell. 2022-09-29;185(20):3770-3788.e27.

  • doi:10.1016/j.cell.2022.09.010
  • PMID:36179669
  • PMCID:PMC9990683

  Available supplemental data: website

  URL: https://www.synapse.org

  Data summary: Read-level data from scRNA-seq, scATAC-seq, SHARE-seq, and Slide-seq data, supporting the findings…See more

  Available supplemental data: website

  URL: https://singlecell.broadinstitute.org/single_cell/study/SCP1756

  Data summary: The count-level data and meta-data have been deposited at the Single Cell Portal.

  Available supplemental data: website

  URL: https://doi.org/10.17632/7cxccpv4hg.1

  Data summary: Supplemental data related to Figures 1, ​,3,3, ​,4,4, ​,5,5, ​,6,6, and ​and77 has been deposited…See more

  Available supplemental data: website

  URL: https://github.com/AmandaKedaigle/OrganoidAtlas

  Data summary: Code used during data analysis is available at GitHub. d Any additional information required to…See more

  Available supplemental data: website

  URL: http://solo.bmap.ucla.edu/shiny/webapp/

  Data summary: Data from previous publications that was used in this study can be found at the Gene Expression…See more

• Publication

  released

  Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia

  Marianna Zazhytska, Albana Kodra, Daisy A Hoagland, et al.

  Cell. 2022-03-17;185(6):1052-1064.e12.

  • doi:10.1016/j.cell.2022.01.024
  • PMID:35180380
  • PMCID:PMC8808699

  Available supplemental data: website

  URL: https://doi.org/10.1101/2021.02.09.430314

  Data summary: Human and hamster RNAseq, scRNAseq, in situ HiC, supplemental spreadsheets and detailed…See more

  Data summary: This study did not generate custom computer code. Any additional information is available from…See more

• Publication

  released

  Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant complex traits

  Matthew C. Pahl, Claudia A. Doege, Kenyaita M. Hodge, et al.

  Nat Commun. 2021-11-19;12(1):6749.

  • doi:10.1038/s41467-021-27001-4
  • PMID:34799566
  • PMCID:PMC8604959

• Publication

  released

  Joint disease-specificity at the regulatory base-pair level

  Pushpanathan Muthuirulan, Dewei Zhao, Mariel Young, et al.

  Nat Commun. 2021-07-06;12(1):4161.

  • doi:10.1038/s41467-021-24345-9
  • PMID:34230488
  • PMCID:PMC8260791

• Publication

  released

  Common schizophrenia risk variants are enriched in open chromatin regions of human glutamatergic neurons

  Mads E. Hauberg, Jordi Creus-Muncunill, Jaroslav Bendl, et al.

  Nat Commun. 2020-11-04;11(1):5581.

  • doi:10.1038/s41467-020-19319-2
  • PMID:33149216
  • PMCID:PMC7643171

• Publication

  released

  Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

  Ana Viñuela, Arushi Varshney, Martijn van de Bunt, et al.

  Nat Commun. 2020-09-30;11(1):4912.

  • doi:10.1038/s41467-020-18581-8
  • PMID:32999275
  • PMCID:PMC7528108

  URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7528108/

• Publication

  released

  Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information

  Sebastian Guelfi, Karishma D’Sa, Juan A. Botía, et al.

  Nat Commun. 2020-02-25;11(1):1041.

  • doi:10.1038/s41467-020-14483-x
  • PMID:32098967
  • PMCID:PMC7042265

• Publication

  released

  Functional testing of thousands of osteoarthritis-associated variants for regulatory activity

  Jason C Klein, Aidan Keith, Sarah J Rice, et al.

  Nat Commun. 2019-06-04;10(1):2434.

  • doi:10.1038/s41467-019-10439-y
  • PMID:31164647
  • PMCID:PMC6547687

• Publication

  released

  Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization

  Elizabeth H Finn, Gianluca Pegoraro, Hugo B Brandão, et al.

  Cell. 2019-03-07;176(6):1502-1515.e10.

  • doi:10.1016/j.cell.2019.01.020
  • PMID:30799036
  • PMCID:PMC6408223

  Data summary: The Hi-C data has been deposited in GEO under ID code GSE107051, and in the 4D Nucleome data…See more

• Publication

  released

  Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

  Benjamin J Schmiedel, Divya Singh, Ariel Madrigal, et al.

  Cell. 2018-11-29;175(6):1701-1715.e16.

  • doi:10.1016/j.cell.2018.10.022
  • PMID:30449622
  • PMCID:PMC6289654

• Publication

  released

  ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

  Jie Wang, Cristina Zibetti, Peng Shang, et al.

  Nat Commun. 2018-04-10;9(1):1364.

  • doi:10.1038/s41467-018-03856-y
  • PMID:29636475
  • PMCID:PMC5893535

• Publication

  released

  Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes

  Sílvia Bonàs-Guarch, Marta Guindo-Martínez, Irene Miguel-Escalada, et al.

  Nat Commun. 2018-01-22;9(1):321.

  • doi:10.1038/s41467-017-02380-9
  • PMID:29358691
  • PMCID:PMC5778074

• Publication

  released

  Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns

  Martin Enge, H. Efsun Arda, Marco Mignardi, et al.

  Cell. 2017-10-05;171(2):321-330.

  • doi:10.1016/j.cell.2017.09.004
  • PMID:28965763

• Publication

  released

  Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms

  Victor Rusu, Eitan Hoch, Josep M Mercader, et al.

  Cell. 2017-06-29;170(1):199-212.e20.

  • doi:10.1016/j.cell.2017.06.011
  • PMID:28666119
  • PMCID:PMC5562285

• Publication

  released

  β-Glucan Reverses the Epigenetic State of LPS-Induced Immunological Tolerance

  Boris Novakovic, Ehsan Habibi, Shuang-Yin Wang, et al.

  Cell. 2016-11-17;167(5):1354-1368.e14.

  • doi:10.1016/j.cell.2016.09.034
  • PMID:27863248
  • PMCID:PMC5927328

• Publication

  released

  Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

  Chen L, Ge B, Casale FP, et al.

  Cell. 2016-11-17;167(5):1398-1414.

  • doi:10.1016/j.cell.2016.10.026
  • PMCID:PMC5119954
  • PMID:27863251

• Publication

  released

  Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

  Yohann Nédélec, Joaquín Sanz, Golshid Baharian, et al.

  Cell. 2016-10-20;167(3):657-669.e21.

  • doi:10.1016/j.cell.2016.09.025
  • PMID:27768889

• Publication

  released

  Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo

  Raymond E. Soccio, Eric R. Chen, Satyajit R. Rajapurkar, et al.

  Cell. 2015-07-02;162(1):33-44.

  • doi:10.1016/j.cell.2015.06.025
  • PMID:26140591

• Publication

  released

  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

  Suhas S.P. Rao, Miriam H. Huntley, Neva C. Durand, et al.

  Cell. 2014-12-18;159(7):1665-1680.

  • doi:10.1016/j.cell.2014.11.021
  • PMID:25497547

  URL: https://www.cell.com/cell/fulltext/S0092-8674(14)01497-4

• Publication

  released

  Comparative Epigenomic Analysis Of Murine And Human Adipogenesis

  Tarjei S. Mikkelsen, Zhao Xu, Xiaolan Zhang, et al.

  Cell. 2010-10-01;143(1):156-169.

  • doi:10.1016/j.cell.2010.09.006
  • PMID:20887899