Search – Common Metabolic Diseases Genome Atlas

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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
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
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
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
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.
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.
Data summary: All new raw data created in this manuscript have been uploaded to the 4D Nucleome portal and will…
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.
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,…
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,…
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…
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…
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
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells
Kousuke Mouri, Michael H. Guo, Carl G. de Boer, et al.
Nat Genet. 2022-05-01;54(5):603-612.
- doi:10.1038/s41588-022-01056-5
- PMID:35513721
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.
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.
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…
Data summary: This study did not generate custom computer code. Any additional information is available from…
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.
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.
Data summary: Data are available at GEO under accession number GSE163666. Supplementary Table 1 lists datasets…
Available supplemental data: website
URL: https://github.com/dekkerlab/matrix_paper
Data summary: Scripts and notebooks used in this paper can be accessed at…
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.
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.
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…
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.
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.
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
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics
Houda Belaghzal, Tyler Borrman, Andrew D Stephens, et al.
Nat Genet. 2021-02-11;53(3):367-378.
Data summary: All sequencing data have been submitted to a public data repository (GEO; accession number…

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Showing 25 of 137 results