Aniseed - Downloads

Data

Aniseed Data

C.robusta
C.savignyi
H.roretzi
P.mammillata
B.villosa
B.Schlosseri
B.leachii
M.Oculata
M.Occulta
M.Occidentalis
H.aurantium
P.fumigata
O.dioica

Genomic data

Assembly
	Joined Scaffold (Fasta)
	Joined Scaffold (GFF3)

Coding Gene Models
	KH2012 complete with NCBI gene features (GFF3)
	KH2012 complete with NCBI Gene Model to Best Blast Hit mapping

sgRNA
	CionaWholeGenome_sgRNA_score_primer

Transcript Models
	KH2012 complete with NCBI (Nucleotides Fasta)
	KH2012 complete with NCBI (Proteins Fasta - from Met)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	GOSlim ontology
	InterPro annotations
	UniProt Blast

Genes Phylogeny
	Ciona robusta Orthology Trees (v11, SiLiX)

Old Transcript Models
	Ensembl [Obsolete]
	JGI v1.0 [Obsolete]
	Kyoto Grail 2005 [Obsolete]
	KH2012 vs Ensembl (Blast)
	KH2012 vs JGI (Blast)
	KH2012 vs Kyoto Grail (Blast)

cDNA sequences
	cDNA Sequences including ESTs (fasta)
	ESTs <—> Genome (Exonerate GFF3)
	ESTs <—> KH Transcript Models (Blast)

cDNA clone collections
	Ciona Gateway full ORF plate coordinates
	Ciona gene collection 1 Satoh file
	Ciona Gene Clones Correspondence file

Libraries
	Sequenced cDNA Libraries
	Libraries <—> cDNA Clones

Selex seq
	SELEX-seq table S1-S3, Nitta et al. 2019
	SELEX-seq all rounds 6-mer enrichments and PWMs
	SELEX-seq best round 6-mer enrichments

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)

Biometry data
	Biometry data for the whole embryo collection

Contact Surface
	Contact surface data
	Surface/Volume data

Expression data

In situ data
	ISH

Regulatory Regions
	Cis-regulatory modules

RNASeq data
	FPKM/RLE data

Genomic data

Assembly
	Ciona savignyi genome ENS81 fasta and gff3

Coding Gene Models
	Ciona savignyi transcript fasta and gff3

Transcript Models
	Ciona savignyi (Proteins Fasta)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	GOSlim ontology
	InterPro annotations
	UniProt Blast

cDNA sequences
	cDNA Sequences including ESTs (fasta)
	ESTs <—> Genome (Exonerate GFF3)
	ESTs <—> Transcript Models (Blast)

Genes Phylogeny
	Ciona savignyi Orthology Trees (v11, SiLiX)

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)

Expression data

Genomic data

Assembly
	Halocynthia roretzi genome MTP2014 fasta and gff3

Coding Gene Models
	Halocynthia roretzi transcripts MTP2014 fasta and gff3

Transcript Models
	Halocynthia roretzi (Proteins Fasta)

cDNA sequences
	ESTs (fasta)

Functional annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	GOSlim ontology
	InterPro annotations
	UniProt Blast

Genes Phylogeny
	Halocynthia roretzi Orthology Trees (v11, SiLiX)

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)
Biometry data
	Biometry data for the whole embryo collection

Surface
	Contact surface data
	Surface/Volume data

Expression data

In situ data
	ISH

RNASeq data
	FPKM/RLE data

Genomic data

Assembly
	Phallusia mammillata genome MTP2014 fasta

Coding Gene Models
	Phallusia mammillata transcript fasta and gff3

Transcript Models
	Phallusia mammillata (proteins Fasta)

cDNA sequences
	ESTs (fasta)

Functional annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	GOSlim ontology
	InterPro annotations
	UniProt Blast

Genes Phylogeny
	Phallusia mammillata Orthology Trees (v11, SiLiX)

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)
Biometry data
	Biometry data for the whole embryo collection

Surface
	Contact surface data
	Surface/Volume data

Expression data

RNASeq data
	FPKM/RLE data

Genomic data

Anatomy data

Biometry data
	Biometry data for the whole embryo collection

Surface
	Contact surface data
	Surface/Volume data

Expression data

Genomic data

Assembly
	Botryllus schlosseri genome fasta and gff3

Coding Gene Models
	Botryllus schlosseri transcript fasta and gff3

Transcript Models
	Botryllus schlosseri (Proteins Fasta)

cDNA sequences
	cDNA Sequences including ESTs (fasta)
	ESTs <—> Genome (Exonerate GFF3)
	ESTs <—> Transcript Models (Blast)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	GOSlim ontology
	InterPro annotations
	UniProt Blast

Genes Phylogeny
	Botryllus schlosseri Orthology Trees (v11, SiLiX)

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)

Expression data

Genomic data

Assembly
	Botrylloides leachii genome fasta and gff3

Coding Gene Models
	Botrylloides leachii transcript fasta and gff3

Transcript Models
	Botrylloides leachii (Proteins Fasta)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	InterPro annotations
	UniProt Blast

Training Sets
	Training set for Augustus (Gene Model Prediction)
	Training set for Repeat Modeler (Repeat Elements Prediction)
	Training set for SNAP

Anatomy data

Expression data

Genomic data

Assembly
	Molgula oculata genome fasta and gff3

Coding Gene Models
	Molgula oculata transcript fasta and gff3

Transcript Models
	Molgula oculata (Proteins Fasta)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	GOSlim ontology
	InterPro annotations
	UniProt Blast

Genes Phylogeny
	Molgula oculata Orthology Trees (v11, SiLiX)

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)

Expression data

Genomic data

Assembly
	Molgula occulta genome fasta and gff3 (august 2015)

Functional Annotations
	GO annotations(GAF)
	InterPro annotations
	UniProt Blast

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)

Expression data

Genomic data

Assembly
	Molgula occidentalis genome fasta and gff3 (august 2015)

Coding Gene Models
	Molgula occidentalis transcript fasta and gff3

Transcript Models
	Molgula occidentalis (Proteins Fasta)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	InterPro annotations
	UniProt Blast

Genes Phylogeny
	Molgula occidentalis Orthology Trees (v11, SiLiX)

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)

Expression data

Genomic data

Assembly
	Halocynthia aurantium genome MTP2014 fasta

Coding Gene Models
	Halocynthia aurantium transcript fasta and gff3

Transcript Models
	Halocynthia aurantium (proteins Fasta)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	InterPro annotations
	UniProt Blast

Genes Phylogeny
	Halocynthia aurantium Orthology Trees (v11, SiLiX)

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)

Expression data

Genomic data

Assembly
	Phallusia fumigata genome MTP2014 fasta

Coding Gene Models
	Phallusia fumigata transcript fasta and gff3

Transcript Models
	Phallusia fumigata (proteins Fasta)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	InterPro annotations
	UniProt Blast

Genes Phylogeny
	Phallusia fumigata Orthology Trees (v11, SiLiX)

Anatomy data

Ontologies
	Anatomical territories - Developmental stages (OBO)

Expression data

Genomic data

Assembly
	Oikopleura dioica genome fasta

Coding Gene Models
	Oikopleura dioica transcript fasta and gff3

Transcript Models
	Oikopleura dioica (proteins Fasta)

Functional Annotations
	GO annotations(GAF)
	GOSlim annotations(GAF)
	InterPro annotations
	UniProt Blast

Anatomy data

Expression data