Published dataset

These dataset combine data from multiple of our papers.

• Ribosome profiling

  • Ribo-seq and mRNA-seq
  • Translation rate
  • Translation efficiency
  • Genome tracks

Published data from our recent papers

• Strayer et al. NaP-TRAP reveals the regulatory grammar in 5’UTR-mediated translation regulation during zebrafish development.

  Nature Communications 2024

  • NaP-TRAP data

• Pownall et al. Chromatin expansion microscopy reveals nanoscale organization of transcription and chromatin

  Science 2023

  • Microscopy movies
  • Trackhub for ChIP-seq datasets
  • Contigs

• Tornini et al. linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells

  eLife 2023

  • Trackhubs for ATAC-seq and ChIP-seq datasets

• Miao et al. The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation

  Molecular Cell 2022

  • Trackhub for all Omni-ATAC, ChIP-seq, Cut&Tag, RNA-seq and Click-iT-seq datasets
  • Categories of all accessible regions and zygotic genes

• Vejnar et al. Genome wide analysis of 3’-UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic in zebrafish

  Genome Research 2019

  • mRNA-seq embryonic development timecourse
    • Gene counts (RPKM)
    • Trackhub
  • iCLIP trackhub
  • Source code (FIRE, Random Forest model)

• Beaudoin et al. mRNA structure dynamics identifies embryonic gene regulatory programs.

  Nature Structural Molecular Biology 2018

  • RNA structure DMS-seq
  • Ribo-seq
  • mRNA-seq

• Fernandez et al. RES complex is associated with intron definition and required for zebrafish early embryogenesis

  PLOS Genetics 2018

  • mRNA-seq snip1, rbmx2, bud13 KO

Gene annotations in FON1 format

FONtools combines the JSON-based FON (Feature Object Notation) format and tools to simplify genomic annotations usage. We provide FON1 files for main model species generated using the FONtools. They can easily be imported in a project. Only a JSON parser is required to import FON1 files.

FON1 files are available at https://data.giraldezlab.org/pub/annots.

Download

All data described above is publicly available at https://data.giraldezlab.org/pub.