Showing 22 of 22 results

• Publication

  released

  Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk

  Ricardo D’Oliveira Albanus, Xuming Tang, Henry J. Taylor, et al.

  bioRxiv. 2022-11-14;

  • doi:10.1101/2022.11.12.516291

• Publication

  released

  Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution

  Charles A Herring, Rebecca K Simmons, Saskia Freytag, et al.

  Cell. 2022-10-31;185(23):4428-4447.

  • doi:10.1016/j.cell.2022.09.039
  • PMID:36318921

  Available supplemental data: website

  File format: other format

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168408

  Data summary: Single-nuclei RNA-seq and single-nuclei ATAC-seq data have been deposited at GEO under accession…See more

  Available supplemental data: website

  URL: http://brain.listerlab.org/

  Data summary: Accompanying interactive browsers for this study are available at http://brain.listerlab.org.

  Available supplemental data: website

  URL: http://development.psychencode.org/

  Data summary: All data for the Velmeshev et al. study is publicly available through the Sequence Read Archive,…See more

  Available supplemental data: website

  URL: https://www.sciencedirect.com/science/article/pii/S0092867422012582?via%3Dihub#sec4.1

  Data summary: All original code has been deposited at Zenodo and is publicly available as of the date of…See more

  Available supplemental data: website

  URL: https://www.sciencedirect.com/science/article/pii/S0092867422012582?via%3Dihub#sec4.2.1

  Data summary: Any additional information required to reanalyze the data reported in this work paper is available…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

  Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

  Jiang Xu, Sanjeev Kumar, Nan Hua, et al.

  bioRxiv. 2022-02-12;

  • doi:10.1101/2022.02.03.478915

• Publication

  released

  A single-cell atlas of chromatin accessibility in the human genome

  Kai Zhang, James D. Hocker, Michael Miller, et al.

  Cell. 2021-11-08;S0092-8674(21):01279-4.

  • doi:10.1016/j.cell.2021.10.024
  • PMID:34774128
  • PMCID:PMC8664161

  Available supplemental data: website

  File format: other format

  URL: https://cmdga.org/publications/424edf8e-b0ab-4dfd-b61c-a68aae175e03/

  Data summary: sci-ATAC-seq data of human lung samples: dbGaP: phs001961

  Available supplemental data: website

  File format: other format

  URL: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002204.v1.p1

  Data summary: sci-ATAC-seq data of human heart samples: dbGaP: phs002204

  Available supplemental data: website

  File format: other format

  URL: https://cmdga.org/publications/1c27d047-15bc-46ac-bf94-e8881474d541/

  Data summary: sci-ATAC-seq data of human islet samples: GEO: GSE160472

  Available supplemental data: website

  File format: other format

  URL: https://cmdga.org/publications/7b1307ba-fbf9-4461-8c59-f8a65ee5379f/

  Data summary: sci-ATAC-seq data of human fetal tissues:…See more

  Available supplemental data: website

  File format: other format

  URL: https://cmdga.org/publications/1d94a4be-f51d-4f82-a84c-414193b0b2e3/

  Data summary: sci-ATAC-seq data of human fetal tissues:…See more

  Available supplemental data: website

  File format: other format

  URL: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002003.v1.p1

  Data summary: sci-ATAC-seq data of human fetal tissues:…See more

  Available supplemental data: website

  File format: other format

  URL: https://descartes.brotmanbaty.org/bbi/human-chromatin-during-development/

  Data summary: Human chromatin accessibility during development

• Publication

  released

  Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

  Alexandro E Trevino, Fabian Müller, Jimena Andersen, et al.

  Cell. 2021-09-16;184(19):5053-5069.

  • doi:10.1016/j.cell.2021.07.039
  • PMID:34390642

  Available supplemental data: website

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162170

  Data summary: Data used for the analyses presented in this work are available under GEO: GSE162170 and on a…See more

  Available supplemental data: website

  URL: https://github.com/GreenleafLab/Brain_ASD

  Data summary: BPNet code can be found at GitHub.

  Available supplemental data: website

  URL: https://scbrainregulation.su.domains/

  Data summary: A supplementary website with references to the data, code repositories and tools for interactive…See more

• Publication

  released

  Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes

  C.C. Robertson, J.R.J. Inshaw, S. Onengut-Gumuscu, et al.

  bioRxiv. 2020-06-20;

  • doi:10.1101/2020.06.19.158071

• Publication

  released

  Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk

  Daniel Richard, Zun Liu, Jiaxue Cao, et al.

  Cell. 2020-04-16;181(2):362-381.

  • PMID:32220312
  • PMCID:PMC7179902
  • doi:10.1016/j.cell.2020.02.057

  URL: https://www.sciencedirect.com/science/article/abs/pii/S0092867420302348

• 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

  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

• Publication

  released

  The three-dimensional chromatin structure of the major human pancreatic cell types reveals lineage-specific regulatory architecture of T2D risk

  Chun Su, Long Gao, Catherine L. May, et al.

  bioRxiv.

  • doi:10.1101/2021.11.30.470653

• Publication

  released

  Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq

  Paola Benaglio, Jacklyn Newsome, Jee Yun Han, et al.

  bioRxiv.

  • doi:10.1101/2020.12.03.387894

• Publication

  released

  Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments

  Xin Sheng, Ziyuan Ma, Junnan Wu, et al.

  bioRxiv.

  • doi:10.1101/2020.11.09.375592