Showing 25 of 30 results

• Publication

  released

  Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes

  Fan Zhang, Anna Helena Jonsson, Aparna Nathan, et al.

  Nature. 2023-11-08;623(7987):616-624.

  • doi:10.1038/s41586-023-06708-y
  • PMID:37938773
  • PMCID:PMC10651487

  URL: https://doi.org/10.7303/syn52297840

  Data summary: CITE-seq single-cell expression matrices and sequencing and bulk expression matrices are available…See more

  URL: https://arkportal.synapse.org/Explore/Datasets/DetailsPage?id=syn52297840

  Data summary: Associated genotype and clinical data are available through the Arthritis and Autoimmune and…See more

  URL: https://immunogenomics.io/ampra2/

  Data summary: A cell browser website is available to visualize our data and results.

  Data summary: AMP Phase 1 single-cell data from ref. 8 are available on Immport (SDY998). PEAC clinical trial…See more

  URL: https://github.com/Immunogenomics/RA_Atlas_CITEseq/

  Data summary: The source code for the analyses is available at GitHub

  URL: https://zenodo.org/record/8118599

  Data summary: The source code for the analyses is available at zenodo

• 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

  Cohesin-mediated loop anchors confine the locations of human replication origins

  Daniel J Emerson # 1 2 3 , Peiyao A Zhao # 4 , Ashley L Cook # 1 2 3 , et al.

  Nature. 2022-06-08;606(7915):812-819.

  • doi:10.1038/s41586-022-04803-0
  • PMID:35676475
  • PMCID:PMC9217744

  Data summary: All new raw data created in this manuscript have been uploaded to the 4D Nucleome portal and will…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

  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

  Systematic analysis of binding of transcription factors to noncoding variants

  Jian Yan, Yunjiang Qiu, André M. Ribeiro dos Santos, et al.

  Nature. 2021-1-27;

  • doi:10.1038/s41586-021-03211-0
  • PMID:33505025

• 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

  Large-scale genetic association and single cell accessible chromatin mapping defines cell type-specific mechanisms of type 1 diabetes risk

  Joshua Chiou, Ryan J Geusz, Mei-Lin Okino, et al.

  Nature. 2021-05-19;594(7863):398-402.

  • doi:10.1038/s41586-021-03552-w
  • PMID:34012112

• Publication

  released

  Genome-wide enhancer maps link risk variants to disease genes

  Joseph Nasser, Drew T. Bergman, Charles P. Fulco, et al.

  Nature. 2021-04-07;593:238–243.

  • doi:10.1038/s41586-021-03446-x

• Publication

  released

  Regulatory genomic circuitry of human disease loci by integrative epigenomics

  Carles A Boix, Benjamin T James, Yongjin P Park, et al.

  Nature. 2021-02-03;590(7845):300-307.

  • doi:10.1038/s41586-020-03145-z
  • PMID:33536621
  • PMCID:PMC7875769

• Publication

  released

  Expanded encyclopaedias of DNA elements in the human and mouse genomes

  The ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, et al.

  Nature. 2020-07-29;583(7818):699–710.

  • doi:10.1038/s41586-020-2493-4
  • PMID:32728249
  • PMCID:PMC7410828

• Publication

  released

  Index and biological spectrum of human DNase I hypersensitive sites

  Wouter Meuleman, Alexander Muratov, Eric Rynes, et al.

  Nature. 2020-07-29;584(7820):244–251.

  • doi:10.1038/s41586-020-2559-3
  • PMCID:PMC7422677
  • PMID:32728217

• 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

  Charting cellular identity during human in vitro β-cell differentiation

  Adrian Veres, Aubrey L Faust, Henry L Bushnell, et al.

  Nature. 2019-05-01;569(7756):368-373.

  • doi:10.1038/s41586-019-1168-5
  • PMCID:PMC6903417
  • PMID:31068696

• 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

  Integrative analysis of haplotype-resolved epigenomes across human tissues

  Danny Leung, Inkyung Jung, Nisha Rajagopal, et al.

  Nature. 2015-02-19;518(7539):350-354.

  • doi:10.1038/nature14217
  • PMID:25693566
  • PMCID:PMC4449149

• 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