Onimaru_et_al_Supplementary_Data

This folder contains Supplementary data forTitle: “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*1Affiliations:1. Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan2. Laboratory for Bioinformatics Research, RIKEN BDR, 1-2 Hirosawa, Wako city, Saitama, 351-0198, Japan*Corresponding authors. Email: [e-mail], [e-mail]: 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 genomeOnimaru_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.

本文件夹收录了题为《鳍和肢体发育中的发育沙漏与异时性转变》的补充数据。该研究由 Koh Onimaru 等作者完成，分别隶属于日本神户市中央区神户町 2-2-3 的理化研究所生物系统动力学研究中心（BDR）的演化信息学实验室（1）和埼玉县瓦町的理化研究所生物信息学研究室（2），其中 Koh Onimaru 和 Shigehiro Kuraku 为通讯作者。联系邮箱分别为 [e-mail] 和 [e-mail]。DOI：https://doi.org/10.1101/2020.01.10.901173。

===文件描述===
Onimaru_et_al_Supplementary_data_amino_acid_seqs_based_on_gene_model.fa.gz：竹鲨基因组中基因的氨基酸序列。
Onimaru_et_al_Supplementary_data_ATAC_seq_GO_analysis.zip：补充文件12（针对聚类ATAC-seq峰值的GO分析）的原始数据。c1至c8分别对应图5A。
Onimaru_et_al_Supplementary_data_ATAC_seq_motifs.zip：图5A以及图5图补充2和3的原始数据。
Onimaru_et_al_supplementary_data_ATAC_seq_peaks_by_clusters.sip：根据图5A中的聚类对峰区域进行排序。
Onimaru_et_al_Supplementary_data_bamboo_shark_genome.fa.gz：本文中使用的竹鲨基因组组装，与https://transcriptome.riken.jp/squalomix/resources/01.GCA_003427335.1_Cpunctatum_v1.0_genomic.rn.fna.gz提供的组装相同，唯一区别在于本文件中scaffold的标识为scaffold_XXXXX。
Onimaru_et_al_Supplementary_data_bamboo_shark_transcriptome_assembly.fa.gz：本文中使用的竹鲨转录组组装。
Onimaru_et_al_Supplementary_data_bamboo_shark_transcriptome_assembly_amino_acid_seq.fa.gz：上述转录组的氨基酸序列。
Onimaru_et_al_Supplementary_data_gene_model_with_orthology_annotation.gff3.gz：基于本文同源注释的gff3文件。此文件旨在可视化本文件夹中提供的竹鲨基因组上的ATAC-seq峰值数据和RNA-seq数据。