Showing 25 of 31 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

  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

  A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk

  Antje K Rottner, Yingying Ye, Elena Navarro-Guerrero, et al.

  Nat Genet. 2022-12-21;55(1):54-65.

  • doi:10.1038/s41588-022-01261-2
  • PMID:36543916
  • PMCID:PMC9839450

  URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9839450/

  Available supplemental data: website

  File format: text

  URL: https://hugeamp.org:8000/research.html?pageid=beta_cell_249

  Data summary: Pancreatic beta cell function and type 2 diabetes predicted effector genes (Rottner AK et al., 2023)

• Publication

  released

  Long-range chromosomal interactions increase and mark repressed gene expression during adipogenesis

  Kristina M Garske, Caroline Comenho, David Z Pan, et al.

  Epigenetics. 2022-12-01;17(13):1849-1862.

  Available supplemental data: website

  File format: other format

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129574

  Data summary: Assay for transposase accessible chromatin (ATAC) -seq libraries were produced from human primary…See more

• 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

  Genetic regulation of RNA splicing in human pancreatic islets

  Goutham Atla, Silvia Bonàs-Guarch, Mirabai Cuenca-Ardura, et al.

  Genome Biol. 2022-09-15;23(1):196.

  • doi:10.1186/s13059-022-02757-0
  • PMID:36109769
  • PMCID:PMC9479353

  URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02757-0#Sec36

  Available supplemental data: website

  File format: text

  URL: https://zenodo.org/record/6546807#.Y-wbZi-B39B

• 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

  Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease

  Hongbo Liu, Tomohito Doke, Dong Guo, et al.

  Nature Genetics. 2022-06-16;54:950–962.

  • PMID:35710981
  • doi:10.1038/s41588-022-01097-w

  Available supplemental data: website

  URL: https://github.com/hbliu/Kidney_Epi_Pri

  Data summary: Customized code used in the present study is available at github

  Available supplemental data: website

  URL: https://doi.org/10.5281/zenodo.6392494

  Data summary: Zenodo

• 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

  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

  A mechanistic framework for cardiometabolic and coronary artery diseases

  Simon Koplev, Marcus Seldin, Katyayani Sukhavasi, et al.

  Nat Cardiovasc Res. 2022-01-12;1(1):85-100.

  • doi:10.1038/s44161-021-00009-1
  • PMID:36276926
  • PMCID:PMC9583458

  Available supplemental data: website

  URL: http://starnet.mssm.edu

  Data summary: The website was developed with a Python Flask backend and a sqlite3 database, with an application…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

  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

  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

  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

  Rationale and design of the Kidney Precision Medicine Project

  Ian H de Boer, Charles E Alpers, Evren U Azeloglu, et al.

  Kidney International. 2021-03-01;99(3):498-510.

  • PMID:33637194
  • doi:10.1016/j.kint.2020.08.039
  • PMCID:PMC8330551

  Available supplemental data: website

  URL: https://www.kpmp.org

  Data summary: The Kidney Precision Medicine Project (KPMP) is an ambitious, multi-year project funded by the…See more

  Available supplemental data: website

  URL: https://www.kpmp.org/doi-collection/10-48698-92nk-e805

  Data summary: Aggregated, clustered single-cell RNA-seq data used in the KPMP Atlas Explorer v1.3 - Dataset…See more

• Publication

  released

  A human cell atlas of fetal gene expression

  Junyue Cao, Diana R O'Day, Hannah A Pliner, et al.

  Science. 2020-11-13;370(6518):eaba7721.

  • doi:10.1126/science.aba7721
  • PMID:33184181
  • PMCID:PMC7780123

  Available supplemental data: website

  File format: other format

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

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

• Publication

  released

  A human cell atlas of fetal chromatin accessibility

  Silvia Domcke, Andrew J Hill, Riza M Daza, et al.

  Science. 2020-11-13;370(6518):eaba7612.

  • doi:10.1126/science.aba7612
  • PMID:33184180
  • PMCID:PMC7785298

  Available supplemental data: website

  File format: other format

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

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

• Publication

  released

  Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes

  Allen Wang, Joshua Chiou, Olivier B Poirion, et al.

  eLife. 2020-11-09;9:e62522.

  • doi:10.7554/eLife.62522
  • PMID:33164753

  Available supplemental data: website

  File format: other format

  URL: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001961.v1.p1

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

• Publication

  released

  Transcriptional and Cellular Diversity of the Human Heart

  Nathan R. Tucker, Mark Chaffin, Stephen J. Fleming, et al.

  Circulation. 2020-08-04;142(5):466-482.

  • doi:10.1161/CIRCULATIONAHA.119.045401
  • PMID:32403949
  • PMCID:PMC7666104

  URL: https://www.ahajournals.org/doi/10.1161/CIRCULATIONAHA.119.045401

  Available supplemental data: website

  File format: other format

  URL: https://www.ahajournals.org/doi/suppl/10.1161/circulationaha.119.045401

  Data summary: The Data Supplement is available with this article.

  Available supplemental data: website

  File format: other format

  URL: https://singlecell.broadinstitute.org/single_cell/study/SCP498/transcriptional-and-cellulardiversity-of-the-human-heart

  Data summary: Processed data with interactivity for gene search functions will be available through the Broad…See more

• Publication

  released

  Ultrastructural Details of Mammalian Chromosome Architecture

  Nils Krietenstein, Sameer Abraham, Sergey V Venev, et al.

  Mol Cell. 2020-05-07;78(3):554-565.e7.

  • doi:10.1016/j.molcel.2020.03.003
  • PMID:32213324
  • PMCID:PMC7222625

  Available supplemental data: website

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

  Data summary: Raw and processed files are available in the 4DN data portal (under the accession numbers…See more

• Publication

  released

  Common DNA sequence variation influences 3-dimensional conformation of the human genome

  David U Gorkin, Yunjiang Qiu, Ming Hu, et al.

  Genome Biol. 2019-11-28;20(1):255.

  • doi:10.1186/s13059-019-1855-4
  • PMID:31779666
  • PMCID:PMC6883528

  Available supplemental data: website

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

  Data summary: All raw sequencing data and many processed data files are available through NCBI’s Gene Expression…See more

  Available supplemental data: website

  URL: http://renlab.sdsc.edu/renlab_website/download/iqtl/

  Data summary: Additional processed data are available on the Ren lab’s website, or by request.

  Available supplemental data: website

  Data summary: The following third-party datasets were also used in this study (also listed in Additional file 2:…See more