Onimaru_et_al_Supplementary_Data

This folder contains Supplementary data for

Title: “Developmental hourglass and heterochronic shifts in fin and limb development”

Authors: Koh Onimaru*1,2, Kaori Tatsumi1, Chiharu Tanegashima1, Mitsutaka Kadota1, Osamu Nishimura1, Shigehiro Kuraku*1

Affiliations:

1. Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan

2. Laboratory for Bioinformatics Research, RIKEN BDR, 1-2 Hirosawa, Wako city, Saitama, 351-0198, Japan

*Corresponding authors. Email: koh.onimaru@riken.jp, shigehiro.kuraku@riken.jp

doi: https://doi.org/10.1101/2020.01.10.901173

===file descriptions===

Onimaru_et_al_Supplementary_data_amino_acid_seqs_based_on_gene_model.fa.gz: Amino acid sequences of the genes in the bamboo shark genome

Onimaru_et_al_Supplementary_data_ATAC_seq_GO_analysis.zip: the source data of Supplementary file 12 (GO analysis of clusterd ATAC-seq peaks). c1 to c8 correspond to Figure 5A.

Onimaru_et_al_Supplementary_data_ATAC_seq_motifs.zip: the source data of Figure 5A and Figure 5-figure supplement 2 and 3.

Onimaru_et_al_supplementary_data_ATAC_seq_peaks_by_clusters.sip: peak regions sorted by the clusters in Figure 5A.

Onimaru_et_al_Supplementary_data_bamboo_shark_genome.fa.gz: a bambooshark genome assembly used in this paper. This assembly is equal to https://transcriptome.riken.jp/squalomix/resources/01.GCA_003427335.1_Cpunctatum_v1.0_genomic.rn.fna.gz except that scaffold ids are named scaffold_XXXXX in this file.

Onimaru_et_al_Supplementary_data_bamboo_shark_transcriptome_assembly.fa.gz: a bamboo shark transcriptomic assembly used in this paper.

Onimaru_et_al_Supplementary_data_bamboo_shark_transcriptome_assembly_amino_acid_seq.fa.gz: amino acid sequences of the above transcriptome.

Onimaru_et_al_Supplementary_data_gene_model_with_orthology_annotation.gff3.gz: a gff3 file based on orthology annoation in this paper. This file is prepared to visualize ATAC-seq peak data and RNA-seq data on the bambooshark genome provided in this folder.