Dataset: Transparent Danionella translucida as a genetically tractable vertebrate brain model.
This repository contains data linked to Schulze, Henninger, et al., 2018.
http://doi.org/10.1038/s41592-018-0144-6
Jörg Henninger
e65cab1054
updated read maps
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6 роки тому | |
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| DT_GRCz10_SRA.bam | 6 роки тому | |
| DT_GRCz10_SRA.bam.bai | 6 роки тому | |
| DT_MRI.zip | 6 роки тому | |
| DT_coronal_sections.zip | 6 роки тому | |
| Danio_rerio.GRCz10.dna_rm.toplevel.fa.gz | 6 роки тому | |
| LICENSE | 6 роки тому | |
| README.md | 6 роки тому | |
| datacite.yml | 6 роки тому |
Original data ressources published alongside Schulze, Henninger et al., 2018, titled:
Transparent Danionella translucida as a genetically tractable vertebrate brain model
High-resolution 35 µm MRI of Danionella translucida (83 MB zipped DICOM file): Data descriptor: Acquired with preclinical 7T MRT (BioSpec 70/20 USR; Bruker) with a 20 cm horizontal bore magnet and a 12 cm (inner diameter) shielded gradient with a 1H-resonance-frequency of 300 MHz and a maximum gradient strength of 440 mT/m. Protocol: T1_FLASH_3D at 35 µm3 isovoxel resolution. TR/TE = 50/9.5 ms, flip angle 20°, 8 averages, FOV (field of view) coronal 14.0 x 12.6 x 12.6 mm, MD (matrix dimension) 400 x 360 x 360, scan time 14h24min. Data can be explored with any freely available DICOM viewer. Filename: DT_MRI.zip
Histological Nissl-stained sections of Danionella translucida head (2.8 GB zip file): Data descriptor: 280 Nissl-stained transverse sections (8 µm thickness) of the Danionella translucida head scanned on an Axio Scan.Z1 (Zeiss) at 40x resolution and stored in the CZI format of Zeiss, all metadata included. Data can be explored with any CZI viewer, such as ‘ZEN’ by Zeiss (tested on version 2.3 blue edition), FIJI and many others. A second file (TIFF) includes the aligned coronal sections of the brain. Data can be explored with any TIFF viewer, such as FIJI. Filename: DT_coronal_sections.zip
Danionella translucida sequence read alignment (3.6 GB BAM file): Data descriptor: Danionella translucida sequencing reads aligned to the Danio rerio genome (reference genome assembly GRCz10). Submitted to the NCBI SRA database with submission number SUB3071063. Data can be browsed with the freely available Integrative Genomics Viewer. Filename: DT_GRCz10_SRA.bam
| datacite.yml | |
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| Title | Dataset: Transparent Danionella translucida as a genetically tractable vertebrate brain model. |
| Authors |
Schulze,Lisanne;Charité Universitätsmedizin Berlin and Humboldt University, Einstein Center for Neuroscience, NeuroCure Cluster of Excellence, Berlin, Germany;https://orcid.org/0000-0001-7875-3107
Henninger,Jörg;Charité Universitätsmedizin Berlin and Humboldt University, Einstein Center for Neuroscience, NeuroCure Cluster of Excellence, Berlin, Germany;AuthorID1 (e.g. ORCID) Faustino,Ana Isabel;Charité Universitätsmedizin Berlin and Humboldt University, Einstein Center for Neuroscience, NeuroCure Cluster of Excellence, Berlin, Germany;https://orcid.org/0000-0002-7307-1569 Chaigne,Thomas;Charité Universitätsmedizin Berlin and Humboldt University, Einstein Center for Neuroscience, NeuroCure Cluster of Excellence, Berlin, Germany Kadobianskyi,Mykola;Charité Universitätsmedizin Berlin and Humboldt University, Einstein Center for Neuroscience, NeuroCure Cluster of Excellence, Berlin, Germany Hakiy,Nahid;Charité Universitätsmedizin Berlin and Humboldt University, Einstein Center for Neuroscience, NeuroCure Cluster of Excellence, Berlin, Germany Albadri,Shahad;Institut Curie, Neuronal Circuit Development Group, Paris, France Schuelke,Markus;Charité Universitätsmedizin Berlin and Humboldt University, Einstein Center for Neuroscience, NeuroCure Cluster of Excellence, Berlin, Germany;https://orcid.org/0000-0003-2824-3891 Maler,Leonard;Brain and Mind Research Institute, Faculty of Medicine, University of Ottawa, Canada Del Bene,Filippo;Institut Curie, Neuronal Circuit Development Group, Paris, France Judkewitz,Benjamin;Charité Universitätsmedizin Berlin and Humboldt University, Einstein Center for Neuroscience, NeuroCure Cluster of Excellence, Berlin, Germany |
| Description | Original data ressources published alongside Schulze, Henninger, et al., 2018: 1. High-resolution 35 µm isovoxel MRI scan of a DT specimen (83 MB), 2. Nissl-stained histological sections across the head, covering the entire brain (1.4 GB) 3. Danionella translucida sequence read alignment (3.6 GB) |
| License | CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/) |
| References | |
| Funding |
Einstein Foundation Berlin
DFG, EXC 257 NeuroCure Human Frontiers Science Program |
| Keywords |
Neuroscience
Danionella translucida, MRI Anatomy Histology |
| Resource Type |
Dataset |
