Data resources

G-Node (data) repositories: https://gin.g-node.org/danionella

GitHub (code) repositories: https://github.com/danionella

Schulze* L, Henninger* J, Kadobianskyi M, Chaigne T, Faustino AI, Hakiy N, Albadri S, Schuelke M, Maler L, Del Bene F, Judkewitz B (2018) Transparent Danionella translucida as a genetically tractable vertebrate brain model, Nature Methods 2018, doi:10.1038/s41592-018-0144-6

  • High-resolution 35 µm MRI of DT (79 MB zipped DICOM file: DT_MRI.zip)
    Acquired with preclinical 7T MRI at 35 µm³ isovoxel resolution. Data can be explored with any DICOM viewer, including the freely available FIJI and OsiriX Lite (for mac).

  • Histological Nissl-stained sections of DT head (2.8 GB zip file: DT_coronal_sections.zip)
    280 Nissl-stained transverse sections (8 µm thickness) of the DT head in CZI format. Data can be explored with any CZI viewer, such as ZEN Lite by Zeiss, FIJI and many others. A TIFF file including the aligned transverse sections of the brain. Data can be explored with any TIFF viewer, such as Fiji/ImageJ.

  • DT sequencing reads aligned to the ZF genome (3.6 GB BAM file: DT_GRCz10_SRA.bam)
    Data can be browsed with the freely available Integrative Genomics Viewer. NCBI SRA accession number SRR6906431.

Kadobianskyi M, Schulze L, Schuelke M, Judkewitz B (2019)
Hybrid genome assembly and annotation of Danionella translucida, Scientific Data 2019, doi:10.1038/s41597-019-0161-z

  • Short- and long-read sequencing data (all sequencing runs are part of NCBI Bioproject 445947)
    Short-read sequencing libraries acquired using Illumina HiSeq 4000 for DNA libraries and BGI BGISEQ-500 for RNA libraries. Long-read libraries were generated with Oxford Nanopore MinION (R9.4 flow cells).

  • All genome assembly, annotation and data analysis files are available on figshare as well as in following public repositories:

  • Genome assembly (NCBI GenBank ASM722483v1)
    Assembled using MaSuRCA v3.2.6 pipeline and polished with Pilon v1.22.

  • Transcriptome assembly (NCBI TSA GHNV00000000)
    Assembled using Trinity v2.8.4 pipeline.

  • Genome annotation (NCBI WGS SRMA00000000)
    Annotated using MAKER v2.31.10 pipeline.