Data Downloads
UTGB/Medaka Genome Browser
Raw Reads
Raw reads
Supporting Online Tables
Supporting Online Tables for Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites
Supporting Data
"Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites" (Science 2009)
- fig1B_fracXY.fasta
- fig1B_X.fasta
- fig1B_Y.fasta
- figS1_tss.embryo.25bp.all.vmf
VMF format file generated by ELAND. (25bp 5'-end tags were mapped to Hd-rR version1.0.)
- figS1_tss.embryo.25bp.fasta
All 25bp 5'-end tags.
"AGCCACTGGCACAATAAAGATTCAC_0_1_1_0_0_0_0" means:
0 tag in 1-day-embryos,
1 tag in 2-day-embryos,
1 tag in 3-day-embryos,
0 tag in 5-day-embryos,
0 tag in 10-day-embryos,
0 tag in 14-day-embryos,
0 tag in 2-day-embyos (8cycle, FigS2).
- figS3A_tss.txt
Columns indicate scaffold name, cluster start, cluster end, representative start position, strand, total of expression tags in this cluster, and number of tags at the representative start position.
- figS3B_tss.txt
TSS clusters with >=100 tags.
- figS3C_tss.txt
TSS clusters with >=50 tags.
- nucleosome.blastula.25bp.all.vmf
VMF format file generated by ELAND. (25bp nucleosome tags were mapped to Hd-rR version1.0.)
- nucleosome.blastula.25bp.fasta
All 25bp nucleosome tags. "TCCTGAAACAACCAAAACCGAGGTC_1" means read frequency is 1.
"Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates" (Genome Res. 2007)
- CvlBlockIDs_humanChromosomeName_and_memberGeneIDs(Ensembl-v35).txt
- genesInCvlBlocks_and_theirOhnologGenes(Ensembl-v35).txt
UTGB/Medaka Track Data
The following files, except for genetic marker information, are compressed with gzip
5'SAGE:
The raw sequences of 5' SAGE (5'-end serial analysis of gene expression) tags in multi-FASTA format.
See also 5'SAGE Track Information
- SAGE5Prime.fasta.gz
- mappedSAGE_ver0.9.gff.gz
- mappedSAGE_ver1.0.gff.gz
ASSEMBLY:
The assembly sequence of medaka genome. All files are in multi-FASTA format
- medakaAssembly_version0.9.fasta.gz
- medakaAssembly_version1.0.fasta.gz
- medakaAssembly_version0.9.fasta.masked (repeat masked sequences)
- medakaAssembly_version1.0.fasta.masked (repeat masked sequences)
- medakaAssembly_version1.0.qual.fasta (Quality Values of the assembly. One integer for each nucleotide.)
- medakaAssembly_version1.0.coverage.fasta (Read coverage of the assembly. One integer for each nucleotide.)
REPEAT:
The newly identified repetitive sequences. The file is in FASTA format
BAC:
The raw BAC end sequences are in multifasta format.
See also BAC end Track Information
- version1.0.bac_end.fasta.gz
EST:
Sequence data is available in the multi-FASTA format
See also Medaka Transcript Track Information
- Cab_Gastrula_fasta.txt.gz
- Cab_Neurula_fasta.txt.gz
- Cab_organogenesis_fasta.txt.gz
- Cab_ovary_fasta.txt.gz
- Cab_stage18-36_fasta.txt.gz
- MF01ALA_fasta.txt.gz: Hd-rR Adult liver (female & male)
- MF01ASD_fasta.txt.gz: Hd-rR, adult female whole body
- MF01FFA_fasta.txt.gz: Hd-rR whole embryo at stage 40
- MF01SSA_fasta.txt.gz: Hd-rR whole embryo at stage 20
- MF01SSB_fasta.txt.gz: Hd-rR whole embryo at stage 20
- MF015DA_fasta.txt.gz: Hd-rR whole embryo at stage 35
- OL30VN_fasta.txt.gz: Orange Red, anterior head of stage 30-31 embryo
- OLa_fasta.txt.gz: HNI, male and female adult whole body
- OLb_fasta.txt.gz: HNI, cultured medaka cell derived from caudal fin of adult male
- OLc_fasta.txt.gz: HNI, cultured medaka cell derived from caudal fin of adult male (with 20J/m2 UV +- PR)
- OLd_fasta.txt.gz: HNI, ovary
- OLe_fasta.txt.gz: HNI, liver (female & male)
- OLf_fasta.txt.gz: HNI, cultured medaka cell derived from caudal fin of adult male (with gamma-irradiation)
- SNK01_fasta.txt.gz: Wild population from Okayama Pref. (Southern part of Japan), eye.
- br_fasta.txt.gz: HNI Brain (female & male)
- olrf_fasta.txt.gz: Cab regenerating fin 3dpa or 10dpa
FOSMID:
The raw fosmid end sequences are in multi-FASTA format.
See also Fosmid end Track Information
- version1.0.fosmid_end.fasta.gz
GENE:
The genes that are predicted by Medaka Genome Project.
See also Predicted gene Track Information
- predictedgenever0.9.egtc.gz: EasyGeneTrack* file for medaka ver0.9
- predictedgenever0.9.fasta.gz: muli-FASTA format file medaka ver0.9
- predictedgenever1.0.egtc.gz: EasyGeneTrack* file for medaka ver1.0
- predictedgenever1.0.fasta.gz: muli-FASTA format file for medaka ver1.0
*The EasyGeneTrack is a format used for drawing UTgenome browser tracks.
GeneticMarkers:
PCR primers, aneal temperature and restiriction enzemes informations (only in the case of RFLP marker) are shown in the tables (Excel 97-2003 format).
See also Genetic Marker Track Information
- Mbase_Markersl.xls: This file is an alias of Mbase data.
- Microsatelite_markers.xls: This file is an alias of the supplementary table 1 in Kimura et. al, Gene 363 24-31 (2005), Copyright Elsevier.
- SNPs_markers(TUN_series).xls: The list of SNPs_markers which are mapped using MassArray system.
- SSLP&RFLP_markers.xls: The list of SSLP and RFLP markers that are mapped using conventional polyacrylamide gel electrophoresis.
KaKs
- medaka-SN-KaKs_human-chimp-KaKs used in main paper.tsv
- medaka-SN-KaKs_over300bp-GO_Evalue10_Cover0(1).3_4775_median_1666GOcategories.tsv
- medaka-SN-KaKs_over300bp-GO_Evalue10_Cover0(1).3_4775_members_1666GOcategories.tsv
- ver0(1).9.medaka.KaKs.tsv
Alignment between Hd-rR and HNI. Polymorphic informations including SNPs are here
See also HNI alignment Track Information and file information
- HdrR_v0.9_HNI_v1.0.polymorphisms.xml.gz
- HdrR_v1.0-HNI_v1.0.axt.tar.gz
- HdrR_v1.0_HNI_v1.0.polymorphisms.xml.gz