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Showing 18 of 18 results
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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
Ana Uzquiano, Amanda J Kedaigle, Martina Pigoni, et al.
Cell. 2022-09-29;185(20):3770-3788.e27.
Available supplemental data: websiteData summary: Read-level data from scRNA-seq, scATAC-seq, SHARE-seq, and Slide-seq data, supporting the findings…Available supplemental data: websiteData summary: The count-level data and meta-data have been deposited at the Single Cell Portal.Available supplemental data: websiteData summary: Supplemental data related to Figures 1, ,3,3, ,4,4, ,5,5, ,6,6, and and77 has been deposited…Available supplemental data: websiteData summary: Code used during data analysis is available at GitHub. d Any additional information required to…Available supplemental data: websiteData summary: Data from previous publications that was used in this study can be found at the Gene Expression…Publication
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
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
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
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
released
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…Publication
released
Judhajeet Ray, Paul R Munn, Anniina Vihervaara, et al.
Proc Natl Acad Sci U S A. 2019-09-24;116(39):19431-19439.
Available supplemental data: websiteData summary: Hi-C. Human K562 and Drosophila S2 cells were subjected to HS or not (NHS) and cross-linked with…Publication
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Yanxiao Zhang, Ting Li, Sebastian Preissl, et al.
Nat Genet. 2019-08-19;51(9):1380-1388.
Available supplemental data: websiteData summary: All sequencing datasets have been deposited on GEO with the accession number GSE116862.Publication
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Madhusudhan Bysani, Rasmus Agren, Cajsa Davegårdh, et al.
Sci Rep. 2019-05-23;9(1):7785.
Available supplemental data: websiteData summary: Supplementary MaterialsPublication
released
Mete Civelek, Ying Wu, Calvin Pan, et al.
AJHG. 2017-03-02;100(3):428–443.
Available supplemental data: websiteData summary: Supplemental Data include 8 figures and 14 tables and can be found with this article.