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Riccardo Calandrelli, Xingzhao We, John Lalith Charles Richard, et al.
Nat Commun. 2023-10-16;14(1):6519.
Available supplemental data: websiteData summary: All high-throughput data supporting the current study have been deposited on the 4D Nucleome Data…Available supplemental data: websiteData summary: The codes used for the analysis have been deposited and made publicly available on GitHub at…Publication
released
Renhe Luo, Jielin Yan, Jin Woo Oh, et al.
at Genet. 2023-07-24;55(8):1336-1346.
Available supplemental data: websiteData 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 differentiationKris G Alavattam, Katie A Mitzelfelt, Giancarlo Bonora, et al.
Stem Cell Reports. 2023-01-10;18(1):159-174.
Available supplemental data: websiteData summary: Data have been deposited in the 4DN data portal and are publicly available at…Available supplemental data: websiteData summary: Previously published CM differentiation data are available from GEO: GSE106690 (Bertero et al.,…Available supplemental data: websiteData summary: Source code for analyses performed in this study is available at…Publication
released
Antje K Rottner, Yingying Ye, Elena Navarro-Guerrero, et al.
Nat Genet. 2022-12-21;55(1):54-65.
Available supplemental data: websiteFile format: textData summary: Pancreatic beta cell function and type 2 diabetes predicted effector genes (Rottner AK et al., 2023)Publication
released
Kristina M Garske, Caroline Comenho, David Z Pan, et al.
Epigenetics. 2022-12-01;17(13):1849-1862.
Available supplemental data: websiteFile format: other formatData summary: Assay for transposase accessible chromatin (ATAC) -seq libraries were produced from human primary…Publication
released
Charles A Herring, Rebecca K Simmons, Saskia Freytag, et al.
Cell. 2022-10-31;185(23):4428-4447.
Available supplemental data: websiteFile format: other formatData summary: Single-nuclei RNA-seq and single-nuclei ATAC-seq data have been deposited at GEO under accession…Available supplemental data: websiteData summary: Accompanying interactive browsers for this study are available at http://brain.listerlab.org.Available supplemental data: websiteData summary: All data for the Velmeshev et al. study is publicly available through the Sequence Read Archive,…Available supplemental data: websiteData summary: All original code has been deposited at Zenodo and is publicly available as of the date of…Available supplemental data: websiteData summary: Any additional information required to reanalyze the data reported in this work paper is available…Publication
released
Goutham Atla, Silvia Bonàs-Guarch, Mirabai Cuenca-Ardura, et al.
Genome Biol. 2022-09-15;23(1):196.
Available supplemental data: websiteFile format: textPublication
released
Nils Briel, Viktoria C. Ruf, Katrin Pratsch, et al.
Acta Neuropathol. 2022-08-17;144(4):615–635.
Available supplemental data: websiteData summary: All scripts for pre-processing and analyzing the snATAC-seq data from PSP/CBD frontal cortex and…Publication
released
Hongbo Liu, Tomohito Doke, Dong Guo, et al.
Nature Genetics. 2022-06-16;54:950–962.
Available supplemental data: websiteData summary: Customized code used in the present study is available at githubPublication
released
Tabula Sapiens Consortium*; Robert C Jones, Jim Karkanias, Mark A Krasnow, et al.
Science. 2022-05-13;376(6594):eabl4896.
Available supplemental data: websiteData summary: The entire dataset can be explored interactively at http://tabula-sapiens-portal.ds.czbiohub.org/.Available supplemental data: websiteData summary: The code used for the analysis is available from Zenodo (https://doi.org/10.5281/zenodo.6069683).Available supplemental data: websiteData summary: Gene counts and metadata are available from figshare…Available supplemental data: websiteData summary: The raw data files are available from a public AWS S3 bucket…Available supplemental data: websiteData summary: The histology images are available from figshare (https://doi.org/10.6084/m9.figshare.14962947).Available supplemental data: websiteData summary: SpliZ scores are available from figshare (https://doi.org/10.6084/m9.figshare.14977281).Publication
released
Marianna Zazhytska, Albana Kodra, Daisy A Hoagland, et al.
Cell. 2022-03-17;185(6):1052-1064.e12.
Available supplemental data: websiteData 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
Chongyuan Luo, Hanqing Liu, Fangming Xie, et al.
Cell Genom. 2022-03-09;2(3):100107.
Available supplemental data: websiteData summary: Raw and processed data included in this study were deposited to NCBI GEO/SRA with accession number…Available supplemental data: websiteData summary: snmCAT-seq generated from brain tissues can be visualized at…Available supplemental data: websiteData summary: snRNA-seq data is available for download from the Neuroscience Multi-omics Archive…Available supplemental data: websiteData summary: The code for SingleCellFusion is available from https://github.com/mukamel-lab/SingleCellFusion.Available supplemental data: websiteData summary: The code benchmarking computational integration methods are available from…Available supplemental data: websiteData summary: The code reproducing the over- and under-splitting analysis are available from…Available supplemental data: websiteData summary: A detailed bench protocol for snmCAT-seq and future updates to the method can be found at…Publication
released
Simon Koplev, Marcus Seldin, Katyayani Sukhavasi, et al.
Nat Cardiovasc Res. 2022-01-12;1(1):85-100.
Available supplemental data: websiteData summary: The website was developed with a Python Flask backend and a sqlite3 database, with an application…Publication
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Kai Zhang, James D. Hocker, Michael Miller, et al.
Cell. 2021-11-08;S0092-8674(21):01279-4.
Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human lung samples: dbGaP: phs001961Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human heart samples: dbGaP: phs002204Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human islet samples: GEO: GSE160472Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human fetal tissues:…Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human fetal tissues:…Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human fetal tissues:…Available supplemental data: websiteFile format: other formatData summary: Human chromatin accessibility during developmentPublication
released
Alexandro E Trevino, Fabian Müller, Jimena Andersen, et al.
Cell. 2021-09-16;184(19):5053-5069.
Available supplemental data: websiteData summary: Data used for the analyses presented in this work are available under GEO: GSE162170 and on a…Available supplemental data: websiteData summary: BPNet code can be found at GitHub.Available supplemental data: websiteData summary: A supplementary website with references to the data, code repositories and tools for interactive…Publication
released
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: websiteData summary: Scripts and notebooks used in this paper can be accessed at…Publication
released
Tiit Örd, Kadri Õunap, Lindsey K Stolze, et al.
Circ Res.. 2021-05-24;129(2):240-258.
Available supplemental data: websiteFile format: other formatData summary: Single-cell ATAC-Seq data from human atherosclerosis. The files contain cells from endarterectomy…Publication
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Ian H de Boer, Charles E Alpers, Evren U Azeloglu, et al.
Kidney International. 2021-03-01;99(3):498-510.
Available supplemental data: websiteURL: https://www.kpmp.orgData summary: The Kidney Precision Medicine Project (KPMP) is an ambitious, multi-year project funded by the…Available supplemental data: websiteData summary: Aggregated, clustered single-cell RNA-seq data used in the KPMP Atlas Explorer v1.3 - Dataset…Publication
released
Junyue Cao, Diana R O'Day, Hannah A Pliner, et al.
Science. 2020-11-13;370(6518):eaba7721.
Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human fetal tissues:…Publication
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Silvia Domcke, Andrew J Hill, Riza M Daza, et al.
Science. 2020-11-13;370(6518):eaba7612.
Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human fetal tissues:…Publication
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Allen Wang, Joshua Chiou, Olivier B Poirion, et al.
eLife. 2020-11-09;9:e62522.
Available supplemental data: websiteFile format: other formatData summary: sci-ATAC-seq data of human lung samples: dbGaP: phs001961Publication
released
Nathan R. Tucker, Mark Chaffin, Stephen J. Fleming, et al.
Circulation. 2020-08-04;142(5):466-482.
Available supplemental data: websiteFile format: other formatData summary: The Data Supplement is available with this article.Available supplemental data: websiteFile format: other formatData summary: Processed data with interactivity for gene search functions will be available through the Broad…Publication
released
Nils Krietenstein, Sameer Abraham, Sergey V Venev, et al.
Mol Cell. 2020-05-07;78(3):554-565.e7.
Available supplemental data: websiteData summary: Raw and processed files are available in the 4DN data portal (under the accession numbers…Publication
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David U Gorkin, Yunjiang Qiu, Ming Hu, et al.
Genome Biol. 2019-11-28;20(1):255.
Available supplemental data: websiteData summary: All raw sequencing data and many processed data files are available through NCBI’s Gene Expression…Available supplemental data: websiteData summary: Additional processed data are available on the Ren lab’s website, or by request.Available supplemental data: websiteData summary: The following third-party datasets were also used in this study (also listed in Additional file 2:…Publication
released
Kristin Abramo, Anne-Laure Valton, Sergey V Venev, et al.
Nat Cell Biol. 2019-11-04;21(11):1393-1402.
Data summary: Sequencing data generated in this study have been deposited in the Gene Expression Omnibus (GEO)…Available supplemental data: websiteData summary: Data from this publication can also be accessed in the 4DN Data Portal with link…