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danionella
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Schulze_Henninger_et_al_2018
DOI
10.12751/g-node.230a07
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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

Branch: master
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Schulze_Henn...
Jörg Henninger e65cab1054 updated read maps 6 years ago
DT_GRCz10_SRA.bam e65cab1054 updated read maps 6 years ago
DT_GRCz10_SRA.bam.bai e65cab1054 updated read maps 6 years ago
DT_MRI.zip 00c7d4c9b2 uploaded raw data 6 years ago
DT_coronal_sections.zip 00c7d4c9b2 uploaded raw data 6 years ago
Danio_rerio.GRCz10.dna_rm.toplevel.fa.gz e65cab1054 updated read maps 6 years ago
LICENSE 4d11a93ad1 license added 6 years ago
README.md d36d6f3ca8 modified title 6 years ago
datacite.yml f4095084ea modified title 6 years ago

README.md

Dataset: Transparent Danionella translucida as a genetically tractable vertebrate brain model.

Original data ressources published alongside Schulze, Henninger et al., 2018, titled:

Transparent Danionella translucida as a genetically tractable vertebrate brain model

  1. 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

  2. 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

  3. 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
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