Showing 25 of 169 results

• Publication

  released

  Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk

  Nicole E Kramer, Philip Coryell, Susan D'Costa, et al.

  bioRvix. 2024-05-05;

  • doi:10.1101/2024.05.05.592567

• Publication

  released

  Multimodal cell atlas of the ageing human skeletal muscle

  Yiwei Lai, Ignacio Ramírez-Pardo, Joan Isern, et al.

  Nature. 2024-04-22;

  • PMID:38649488
  • doi:10.1038/s41586-024-07348-6

  Data summary: All raw data have been deposited to CNGB Nucleotide Sequence Archive (CNP0004394, CNP0004395,…See more

  URL: https://db.cngb.org/cdcp/hlma/

  Data summary: All processed data are available at the Human Muscle Ageing Cell Atlas database.

  URL: https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software

  Data summary: All data were analysed using standard programs and packages, as described in the Methods. Custom…See more

  URL: https://github.com/123anjuan/HMA

  Data summary: Analysis of the generated data82.

• Publication

  released

  Human skeletal muscle aging atlas

  Veronika R. Kedlian, Yaning Wang, Tianliang Liu, et al.

  Nature Aging. 2024-04-15;

  • PMID:38622407
  • doi:10.1038/s43587-024-00613-3

  URL: https://www.muscleageingcellatlas.org

  Data summary: The processed data objects generated within this study are available for browsing

  URL: https://doi.org/10.7272/Q65X273X

  Data summary: Raw sequencing data for the newly generated libraries have been deposited to ArrayExpress…See more

  Data summary: Mouse datasets were obtained from GSE110878, GSE138707, GSE134540, GSE143476, GSE149590 and…See more

  Data summary: All other data supporting the findings of this study are available from the corresponding authors…See more

  URL: https://github.com/Teichlab/SKM_ageing_atlas

  Data summary: Code availability: All custom notebooks and scripts used in this study have been deposited to

• 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

  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

  Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions

  Renhe Luo, Jielin Yan, Jin Woo Oh, et al.

  at Genet. 2023-07-24;55(8):1336-1346.

  • doi:10.1038/s41588-023-01450-7
  • PMID:37488417

  Available supplemental data: website

  Data summary: The parental HUES8 hESC line was obtained from Harvard University under a material transfer…See more

• Publication

  released

  Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation

  Kris G Alavattam, Katie A Mitzelfelt, Giancarlo Bonora, et al.

  Stem Cell Reports. 2023-01-10;18(1):159-174.

  • doi:10.1016/j.stemcr.2022.11.003
  • PMID:36493778
  • PMCID:PMC9860068

  Available supplemental data: website

  URL: https://data.4dnucleome.org/Alavattam-Mitzelfelt-endothelial-differentiation-chromatin

  Data summary: Data have been deposited in the 4DN data portal and are publicly available at…See more

  Available supplemental data: website

  Data summary: Previously published CM differentiation data are available from GEO: GSE106690 (Bertero et al.,…See more

  Available supplemental data: website

  URL: https://github.com/Noble-Lab/

  Data summary: Source code for analyses performed in this study is available 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

  The developmental impacts of natural selection on human pelvic morphology

  Mariel Young, Daniel Richard, Mark Grabowski, et al.

  Sci Adv. 2022-08-19;8(33):eabq4884.

  • doi:10.1126/sciadv.abq4884
  • PMID:35977020
  • PMCID:PMC9385149

• Publication

  released

  Single-nucleus chromatin accessibility profiling highlights distinct astrocyte signatures in progressive supranuclear palsy and corticobasal degeneration

  Nils Briel, Viktoria C. Ruf, Katrin Pratsch, et al.

  Acta Neuropathol. 2022-08-17;144(4):615–635.

  • doi:10.1007/s00401-022-02483-8
  • PMID:35976433
  • PMCID:PMC9468099

  Available supplemental data: website

  URL: https://github.com/nes-b/snATAC-seq_psp_cbd

  Data summary: All scripts for pre-processing and analyzing the snATAC-seq data from PSP/CBD frontal cortex and…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

  Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk

  Adam W Turner, Shengen Shawn Hu, Jose Verdezoto Mosquera, et al.

  Nat Genet.. 2022-06-01;54(6):804-816.

  • doi:10.1038/s41588-022-01069-0
  • PMID:35590109
  • PMCID:PMC9203933

  File format: TSV

  URL: https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-022-01069-0/MediaObjects/41588_2022_1069_MOESM10_ESM.xlsx

  Data summary: Supplementary Data 6 Chromatin accessibility QTLs within individual coronary artery cell types,…See more

  File format: TSV

  URL: https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-022-01069-0/MediaObjects/41588_2022_1069_MOESM11_ESM.xlsx

  Data summary: Supplementary Data 7 Chromatin accessibility QTLs from bulk coronary artery ATAC-seq data,…See more

• Publication

  released

  The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans

  Tabula Sapiens Consortium*; Robert C Jones, Jim Karkanias, Mark A Krasnow, et al.

  Science. 2022-05-13;376(6594):eabl4896.

  • doi:10.1126/science.abl4896
  • PMID:35549404

  Available supplemental data: website

  URL: http://tabula-sapiens-portal.ds.czbiohub.org/

  Data summary: The entire dataset can be explored interactively at http://tabula-sapiens-portal.ds.czbiohub.org/.

  Available supplemental data: website

  URL: https://doi.org/10.5281/zenodo.6069683

  Data summary: The code used for the analysis is available from Zenodo (https://doi.org/10.5281/zenodo.6069683).

  Available supplemental data: website

  URL: https://doi.org/10.6084/m9.figshare.14267219

  Data summary: Gene counts and metadata are available from figshare…See more

  Available supplemental data: website

  URL: https://registry.opendata.aws/tabula-sapiens/

  Data summary: The raw data files are available from a public AWS S3 bucket…See more

  Available supplemental data: website

  URL: https://doi.org/10.6084/m9.figshare.14962947

  Data summary: The histology images are available from figshare (https://doi.org/10.6084/m9.figshare.14962947).

  Available supplemental data: website

  URL: https://doi.org/10.6084/m9.figshare.14977281

  Data summary: SpliZ scores are available from figshare (https://doi.org/10.6084/m9.figshare.14977281).

• Publication

  released

  A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells

  Sen Li, Xiaolin Zong, Liheng Zhang, et al.

  Adipocyte. 2022-04-17;11(1):239-249.

  • doi:10.1080/21623945.2022.2063015
  • PMID:35435105
  • PMCID:PMC9037556

• 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

  Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

  Chongyuan Luo, Hanqing Liu, Fangming Xie, et al.

  Cell Genom. 2022-03-09;2(3):100107.

  • doi:10.1016/j.xgen.2022.100107
  • PMID:35419551
  • PMCID:PMC9004682

  Available supplemental data: website

  URL: http://neomorph.salk.edu/Human_cells_snmCT-seq.php

  Data summary: Raw and processed data included in this study were deposited to NCBI GEO/SRA with accession number…See more

  Available supplemental data: website

  URL: http://neomorph.salk.edu/human_frontal_cortex_ensemble.php

  Data summary: snmCAT-seq generated from brain tissues can be visualized at…See more

  Available supplemental data: website

  URL: https://assets.nemoarchive.org/dat-s3creyz

  Data summary: snRNA-seq data is available for download from the Neuroscience Multi-omics Archive…See more

  Available supplemental data: website

  URL: https://github.com/mukamel-lab/SingleCellFusion

  Data summary: The code for SingleCellFusion is available from https://github.com/mukamel-lab/SingleCellFusion.

  Available supplemental data: website

  URL: https://github.com/lhqing/snmCAT-seq_integration

  Data summary: The code benchmarking computational integration methods are available from…See more

  Available supplemental data: website

  URL: https://github.com/FangmingXie/mctseq_over_under_splitting/blob/master/over-under-splitting-analysis.ipynb

  Data summary: The code reproducing the over- and under-splitting analysis are available from…See more

  Available supplemental data: website

  URL: https://www.protocols.io/view/snmcat-v1-bwubpesn

  Data summary: A detailed bench protocol for snmCAT-seq and future updates to the method can be found at…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

  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

  Systematic evaluation of chromosome conformation capture assays

  Betul Akgol Oksuz, Liyan Yang, Sameer Abraham, et al.

  Nat Methods. 2021-09-03;18(9):1046-1055.

  • doi:10.1038/s41592-021-01248-7
  • PMID:34480151
  • PMCID:PMC8446342

  Data summary: Data are available at GEO under accession number GSE163666. Supplementary Table 1 lists datasets…See more

  Available supplemental data: website

  URL: https://github.com/dekkerlab/matrix_paper

  Data summary: Scripts and notebooks used in this paper can be accessed at…See more

• 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

  Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci

  Tiit Örd, Kadri Õunap, Lindsey K Stolze, et al.

  Circ Res.. 2021-05-24;129(2):240-258.

  • doi:10.1161/CIRCRESAHA.121.318971
  • PMID:34024118
  • PMCID:PMC8260472

  Available supplemental data: website

  File format: other format

  URL: https://figshare.com/articles/dataset/Single-nuclei_ATAC-Seq_data_from_human_atherosclerosis/14501985

  Data summary: Single-cell ATAC-Seq data from human atherosclerosis. The files contain cells from endarterectomy…See more

• Publication

  released

  Genetic effects on liver chromatin accessibility identify disease regulatory variants

  Kevin W Currin, Michael R Erdos, Narisu Narisu, et al.

  Am J Hum Genet.. 2021-05-20;S0002-9297(21):00185-3.

  • doi:10.1016/j.ajhg.2021.05.001
  • PMID:34038741
  • PMCID:PMC8323023

• Publication

  released

  Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease

  Ilakya Selvarajan, Anu Toropainen, Kristina M Garske, et al.

  Am J Hum Genet. 2021-03-04;108(3):411-430.

  • doi:10.1016/j.ajhg.2021.02.006
  • PMID:33626337
  • PMCID:PMC8008493

• Publication

  released

  A molecular quantitative trait locus map for osteoarthritis

  Julia Steinberg, Lorraine Southam, Theodoros I. Roumeliotis, et al.

  Nature Communications. 2021-02-26;12(1):1309.

  • doi:10.1038/s41467-021-21593-7
  • PMID:33637762

  URL: https://msk.hugeamp.org/downloads.html

  URL: https://hmgubox.helmholtz-muenchen.de/d/fc1fcf65a6724152b7f9/

• 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