Search – Common Metabolic Diseases Genome Atlas

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Publication
released
Systematic Functional Characterization of Candidate Causal Genes for Type 2 Diabetes Risk Variants
Thomsen SK, Ceroni A, van de Bunt M, et al.
December 2016;(65(12)):3805-3811.
- PMID:27554474
- doi:10.2337/db16-0361
Publication
released
Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
Kevin W Currin, Hannah J Perrin, Gautam K Pandey, et al.
Genome Res. 2025-05-20;
- doi:10.1101/gr.279741.124
- PMID:40393811
Publication
released
A comprehensive spatio-cellular map of the human hypothalamus
John A. Tadross, Lukas Steuernagel, Georgina K. C. Dowsett, et al.
Nature. 2025-02-05;639(8055):708-716.
URL: https://www.nature.com/articles/s41586-024-08504-8
Publication
released
Response splicing QTLs in primary human chondrocytes identifies putative osteoarthritis risk genes
Seyoun Byun, Philip Coryell, Nicole Kramer, et al.
bioRxiv. 2024-11-12;
- doi:10.1101/2024.11.11.622754
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;
Data summary: Hi-C, RNA-seq, ATAC-seq, single-nucleus RNA-seq, and single-nucleus ATAC-seq data have been…
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
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,…
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…
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…
Data summary: Mouse datasets were obtained from GSE110878, GSE138707, GSE134540, GSE143476, GSE149590 and…
Data summary: All other data supporting the findings of this study are available from the corresponding authors…
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
Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes
Norbert Bittner, Chenfu Shi, Danyun Zhao, et al.
Ann Rheum Dis. 2024-03-13;:ard-2023-224945.
- PMID:38479789
- doi:10.1136/ard-2023-224945
Publication
released
An integrated map of cell type-specific gene expression in pancreatic islets
Ruth M Elgamal, Parul Kudtarkar, Rebecca L Melton, et al.
Diabetes. 2023-15-08;(db230130)
- PMID:37582230
- doi:10.2337/db23-0130
Publication
released
Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation
Arushi Varshney Arushi Varshney, Nandini Manickam, Peter Orchard, et al.
bioRxiv. 2023-12-15;
URL: https://www.biorxiv.org/content/10.1101/2023.12.15.571696v2
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.
URL: https://doi.org/10.7303/syn52297840
Data summary: CITE-seq single-cell expression matrices and sequencing and bulk expression matrices are available…
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…
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…
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
Cell-Type Composition Affects Adipose Gene Expression Associations With Cardiometabolic Traits
Sarah M Brotman, Anniina Oravilahti, Jonathan D Rosen, et al.
Diabetes. 2023-11-01;72(11):1707-1718.
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.
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…
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…
Publication
released
Plasma proteomic associations with genetics and health in the UK Biobank
Benjamin B Sun, Joshua Chiou, Matthew Traylor, et al.
Nature. 2023-10-04;622(7982):329-338.
URL: http://ukb-ppp.gwas.eu
Data summary: Proteo-genomic results and summary association data are available through an interactive portal.
URL: https://www.ukbiobank.ac.uk/enable-your-research
Data summary: Underlying NPX measures are available through the UK Biobank Research Analysis Portal.
URL: https://biobank.ndph.ox.ac.uk/showcase/label.cgi?id=1839
Data summary: UKB has catalogued the dataset in Category 1839, under ‘Field 30900’, described in greater detail…
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…
Publication
released
An atlas of healthy and injured cell states and niches in the human kidney
Blue B. Lake, Rajasree Menon, Seth Winfree, et al.
Nature. 2023-07-19;619(7970):585-594.
URL: https://www.nature.com/articles/s41586-023-05769-3
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.
Publication
released
Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression
Katia K. Mattis, Nicole A. J. Krentz, Christoph Metzendorf, et al.
Diabetologia. 2023-01-12;
- doi:10.1007/s00125-022-05856-6
- PMID:36633628
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.
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…
Available supplemental data: website
Data summary: Previously published CM differentiation data are available from GEO: GSE106690 (Bertero et al.,…
Available supplemental data: website
URL: https://github.com/Noble-Lab/
Data summary: Source code for analyses performed in this study is available at…
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.
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
Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines
Paola Benaglio, Han Zhu, Mei-Lin Okino, et al.
Cell Genomics. 2022-12-14;2(12):100214.
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…
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…
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,…
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…
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…

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Showing 25 of 257 results