Showing 25 of 41 results

• Publication

  released

  Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2

  Sheridan H Littleton, Khanh B Trang, Christina M Volpe, et al.

  Cell Genomics. 2024-05-08;

  • doi:10.1101/2023.08.21.553157
  • PMID:37662342
  • PMCID:PMC10473629

  Data summary: Hi-C, RNA-seq, ATAC-seq, single-nucleus RNA-seq, and single-nucleus ATAC-seq data have been…See more

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241592

  Data summary: Raw and processed Hi-C data GEO: GSE241592

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241050

  Data summary: Raw and processed RNA-seq data GEO: GSE241050

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241591

  Data summary: Raw and processed ATAC-seq data GEO: GSE241591

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241594

  Data summary: Raw and processed single-nucleus RNA-seq data GEO: GSE241594

  URL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE241593

  Data summary: Raw and processed single-nucleus ATAC-seq data GEO: GSE241593;

• 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

  Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

  Linda Kachuri, Angel C. Y. Mak, Donglei Hu, et al.

  Nat Genet. 2023-05-25;55(6):952-963.

  • PMID:37231098
  • doi:10.1038/s41588-023-01377-z
  • PMCID:PMC10260401

• 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

  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

  Characterizing cis-regulatory elements using single-cell epigenomics

  Sebastian Preissl, Kyle J Gaulton, Bing Ren.

  Nat Rev Genet. 2022-07-15;

  • doi:10.1038/s41576-022-00509-1
  • PMID:35840754

• 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

  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

  TIGER: The gene expression regulatory variation landscape of human pancreatic islets

  Lorena Alonso, Anthony Piron, Ignasi Morán, et al.

  Cell Rep. 2021-10-12;37(2):109807.

  • PMID:34644572
  • doi:10.1016/j.celrep.2021.109807
  • PMCID:PMC8864863

  Data summary: RNA-seq and genotyping array data from PISA cohort Sequence data have been deposited at the…See more

• 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

  A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory Signatures

  Arushi Varshney, Yasuhiro Kyono, Venkateswaran Ramamoorthi Elangovan, et al.

  Diabetes. 2021-04-13;(db201087)

  • doi:10.2337/db20-1087
  • PMID:33849996

• Publication

  released

  Characterisation of genetic regulatory effects for osteoporosis risk variants in human osteoclasts

  Benjamin H. Mullin, Jennifer Tickner, Kun Zhu, et al.

  Genome Biology. 2020-03-26;20(1):80.

  • PMID:32216834
  • PMCID:PMC7098081
  • doi:10.1186/s13059-020-01997-2

  URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-01997-2

• Publication

  released

  Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases

  M Ryan Corces, Anna Shcherbina, Soumya Kundu, et al.

  Nat Genet. 2020 Oct 26;52(11):1158-1168.

  • doi:10.1038/s41588-020-00721-x
  • PMID:33106633
  • PMCID:PMC7606627

• Publication

  released

  CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

  Ruilin Tian, Mariam A Gachechiladze, Connor H Ludwig, et al.

  Neuron. 2019-10-23;104(2):239-255.e12.

  • doi:10.1016/j.neuron.2019.07.014
  • PMID:31422865
  • PMCID:PMC6813890

• Publication

  released

  The single-cell transcriptomic landscape of early human diabetic nephropathy

  Parker C Wilson, Haojia Wu, Yuhei Kirita, et al.

  Proc Natl Acad Sci U S A. 2019-09-24;116(39):19619-19625.

  • PMID:31506348
  • PMCID:PMC6765272
  • doi:10.1073/pnas.1908706116

• Publication

  released

  Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

  Thomas M Norman, Max A Horlbeck, Joseph M Replogle, et al.

  Science. 2019-08-23;365(6455):786-793.

  • doi:10.1126/science.aax4438
  • PMID:31395745
  • PMCID:PMC6746554

• 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

  Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

  Fan Zhang#, Kevin Wei#, Kamil Slowikowski#, et al.

  Nat Immunol. 2019-05-06;20(7):928-942.

  • doi:10.1038/s41590-019-0378-1
  • PMID:31061532
  • PMCID:PMC6602051

  URL: https://www.immport.org/shared/study/SDY998

  Data summary: The single-cell RNA-seq data, bulk RNA-seq data, mass cytometry data, flow cytometry data, and the…See more

  URL: https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001457.v1.p1

  Data summary: The raw single-cell RNA-seq data are deposited in dbGaP.

  URL: https://github.com/immunogenomics/amp_phase1_ra

  Data summary: The source code repository of the computational and statistical analysis is located at…See more

  URL: https://immunogenomics.io/ampra

  Data summary: Data can also be viewed on three different websites 1/3.

  URL: https://immunogenomics.io/cellbrowser/

  Data summary: Data can also be viewed on three different websites 2/3.

  URL: https://portals.broadinstitute.org/single_cell/study/amp-phase-1

  Data summary: Data can also be viewed on three different websites 3/3.

• 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

  Gain-of-Function Mutations of SLC16A11 Contribute to the Pathogenesis of Type 2 Diabetes

  Yongxu Zhao, Zhuanghui Feng, Yongxian Zhang, et al.

  Cell Rep. 2019-01-22;26(4):884-892.e4.

  • doi:10.1016/j.celrep.2018.12.100
  • PMID:30673611

• Publication

  released

  High-throughput characterization of genetic effects on DNA-protein binding and gene transcription

  Cynthia A Kalita, Christopher D Brown, Andrew Freiman, et al.

  Genome Res. 2018-09-25;28(11):1701-1708.

  • doi:10.1101/gr.237354.118
  • PMID:30254052
  • PMCID:PMC6211638

• Publication

  released

  Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

  Tahsin Stefan Barakat, Florian Halbritter, Man Zhang, et al.

  Cell Stem Cell. 2018-08-02;23(2):276-288.e8.

  • doi:10.1016/j.stem.2018.06.014
  • PMID:30033119
  • PMCID:PMC6084406

• Publication

  released

  Single-cell RNA-seq analysis reveals the progression of human osteoarthritis

  Quanbo Ji, Yuxuan Zheng, Guoqiang Zhang, et al.

  Ann Rheum Dis. 2018-07-19;78(1):100-110.

  • doi:10.1136/annrheumdis-2017-212863
  • PMID:30026257
  • PMCID:PMC6317448