The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data
<jats:title>Abstract</jats:title><jats:p>The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (<jats:ext-link xmlns:xlink="h...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Springer Science and Business Media LLC
2023
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| Online Access: | https://hdl.handle.net/1721.1/150492 |
| _version_ | 1811071005393682432 |
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| author | Reiff, Sarah B Schroeder, Andrew J Kırlı, Koray Cosolo, Andrea Bakker, Clara Mercado, Luisa Lee, Soohyun Veit, Alexander D Balashov, Alexander K Vitzthum, Carl Ronchetti, William Pitman, Kent M Johnson, Jeremy Ehmsen, Shannon R Kerpedjiev, Peter Abdennur, Nezar Imakaev, Maxim Öztürk, Serkan Utku Çamoğlu, Uğur Mirny, Leonid A Gehlenborg, Nils Alver, Burak H Park, Peter J |
| author2 | Harvard-MIT Program in Health Sciences and Technology |
| author_facet | Harvard-MIT Program in Health Sciences and Technology Reiff, Sarah B Schroeder, Andrew J Kırlı, Koray Cosolo, Andrea Bakker, Clara Mercado, Luisa Lee, Soohyun Veit, Alexander D Balashov, Alexander K Vitzthum, Carl Ronchetti, William Pitman, Kent M Johnson, Jeremy Ehmsen, Shannon R Kerpedjiev, Peter Abdennur, Nezar Imakaev, Maxim Öztürk, Serkan Utku Çamoğlu, Uğur Mirny, Leonid A Gehlenborg, Nils Alver, Burak H Park, Peter J |
| author_sort | Reiff, Sarah B |
| collection | MIT |
| description | <jats:title>Abstract</jats:title><jats:p>The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://data.4dnucleome.org/">https://data.4dnucleome.org/</jats:ext-link>), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.</jats:p> |
| first_indexed | 2024-09-23T08:44:38Z |
| format | Article |
| id | mit-1721.1/150492 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T08:44:38Z |
| publishDate | 2023 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1504922023-04-13T03:50:47Z The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data Reiff, Sarah B Schroeder, Andrew J Kırlı, Koray Cosolo, Andrea Bakker, Clara Mercado, Luisa Lee, Soohyun Veit, Alexander D Balashov, Alexander K Vitzthum, Carl Ronchetti, William Pitman, Kent M Johnson, Jeremy Ehmsen, Shannon R Kerpedjiev, Peter Abdennur, Nezar Imakaev, Maxim Öztürk, Serkan Utku Çamoğlu, Uğur Mirny, Leonid A Gehlenborg, Nils Alver, Burak H Park, Peter J Harvard-MIT Program in Health Sciences and Technology <jats:title>Abstract</jats:title><jats:p>The 4D Nucleome (4DN) Network aims to elucidate the complex structure and organization of chromosomes in the nucleus and the impact of their disruption in disease biology. We present the 4DN Data Portal (<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://data.4dnucleome.org/">https://data.4dnucleome.org/</jats:ext-link>), a repository for datasets generated in the 4DN network and relevant external datasets. Datasets were generated with a wide range of experiments, including chromosome conformation capture assays such as Hi-C and other innovative sequencing and microscopy-based assays probing chromosome architecture. All together, the 4DN data portal hosts more than 1800 experiment sets and 36000 files. Results of sequencing-based assays from different laboratories are uniformly processed and quality-controlled. The portal interface allows easy browsing, filtering, and bulk downloads, and the integrated HiGlass genome browser allows interactive visualization and comparison of multiple datasets. The 4DN data portal represents a primary resource for chromosome contact and other nuclear architecture data for the scientific community.</jats:p> 2023-04-12T18:04:42Z 2023-04-12T18:04:42Z 2022 2023-04-12T17:58:32Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/150492 Reiff, Sarah B, Schroeder, Andrew J, Kırlı, Koray, Cosolo, Andrea, Bakker, Clara et al. 2022. "The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data." Nature Communications, 13 (1). en 10.1038/S41467-022-29697-4 Nature Communications Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | Reiff, Sarah B Schroeder, Andrew J Kırlı, Koray Cosolo, Andrea Bakker, Clara Mercado, Luisa Lee, Soohyun Veit, Alexander D Balashov, Alexander K Vitzthum, Carl Ronchetti, William Pitman, Kent M Johnson, Jeremy Ehmsen, Shannon R Kerpedjiev, Peter Abdennur, Nezar Imakaev, Maxim Öztürk, Serkan Utku Çamoğlu, Uğur Mirny, Leonid A Gehlenborg, Nils Alver, Burak H Park, Peter J The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data |
| title | The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data |
| title_full | The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data |
| title_fullStr | The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data |
| title_full_unstemmed | The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data |
| title_short | The 4D Nucleome Data Portal as a resource for searching and visualizing curated nucleomics data |
| title_sort | 4d nucleome data portal as a resource for searching and visualizing curated nucleomics data |
| url | https://hdl.handle.net/1721.1/150492 |
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