IMORI

The sequence resource for the Japanese fire bellied newt

Last Updated: 2016-03-29 

 The Japanese fire bellied newt (Cynops pyrrhogaster), called eAkahara Imorif in Japan, is one of the most studied amphibians in a broad spectrum of life science fields.

Here, to accelerate studies using this animal, particularly those concerning stem-cell/development, metamorphosis, regeneration, reproduction, sense, and evolution, the Japan Newt Research Community (JNRC) provides ground information for transcriptomic and proteomic approaches.

 

 

Materials and Methods

Toride Imori, a race of the C. pyrrhogaster newt, that was originally caught from a restricted area (~25 km in diameter) in Japan (Kamogawa city, Chiba prefecture), and reared in the laboratory or a field Imori-no-Sato (Kaizuka/Kamitakai, Toride city, Ibaraki prefecture), was utilized in this project.

Standard or normalized cDNA libraries for mRNA-seq were constructed from total RNA samples collected from target tissues. Paired-end sequencing (100bp x2) was carried out by Illumina HiSeq2000.

Three algorisms, Trinity, Trans-ABySS and Velvet-Oases, were applied to de novo assembly.

 

 

Results

 

1)  Eyes at 0-14 days after removal of both the neural retina and the lens

 

Reference

 

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS515156

   Accession : SRX391946


De novo assembled transcriptome  

 Assembler  Fasta file (gzip compressed)
 Trinity  Download
 Trans-ABySS  Download
 Velvet-Oases  Download

 

Inferred proteome

  Download

 

Annotation (Blastx with NR data in NCBI)

  Download



2)  Eyes at 20 days after removal of both the neural retina and the lens


Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685592

   Accession : SRX682058


De novo assembled transcriptome

  Download 

Annotation (Blastx with NR data in NCBI)

  Download



3)  Eyes at 25 days after removal of both the neural retina and the lens

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685593

   Accession : SRX682059


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



4)  Eyes at 30 days after removal of both the neural retina and the lens

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685594

   Accession : SRX682061


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



5)  Eyes at 50 days after removal of both the neural retina and the lens

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685595

   Accession : SRX682062


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



6)  Eyes at 20, 25, 30 and 50 days after removal of both the neural retina and the lens

Reference

(Under construction)

De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



7)  Lens

Reference


Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685588, SRS685589

   Accession : SRX682054, SRX682055


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



8)  Normal and regenerating brains

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685590

   Accession : SRX682056


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



9)  Normal and regenerating hearts

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685591

   Accession : SRX682057


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



10)  Limb blastema


Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685577

   Accession : SRX682042


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



11) 
Limb

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685579

   Accession : SRX682043


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download        Under construction



12) 
Testis


Reference


Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS589430
   Accession : SRX512608

De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download


13)  Testis (apoptotic condition)

Reference

(Under construction)


Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685575

   Accession : SRX682040


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



14)  Ovary

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685578

   Accession : SRX682044


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download 



15)  Oviduct

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685581

   Accession : SRX682046


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



16)  Olfactory epithelium + Vomeronasal organ (VNO)

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685576

   Accession : SRX682041


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



17)  Viscera (lung, Intestine, Pancreas, Liver, Kidney)

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685587

   Accession : SRX682053


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



18)  Embryo at Stage 5 (16-cell stage)

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685583

   Accession : SRX682049


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



19)  Embryo at Stage 18 (Neurula stage)

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685585

   Accession : SRX682051


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



20)  Embryo at Stage 29 (Tail bud stage)

Reference

(Under construction)

Clean reads data deposited at NCBI

Sequence Read Archive ID : SRP034152

BioProject ID : PRJNA231688

BioSample ID : SRS685586

   Accession : SRX682052


De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



21)  Embryos at Stage 5, 18 and 29

Reference

(Under construction)

De novo assembled transcriptome

  Download

Annotation (Blastx with NR data in NCBI)

  Download



22)  All samples [1-21]

Reference

(Under construction)

De novo assembled transcriptome (a reference transcriptome for Cynops pyrrhogaster)

  Download        Under construction

Annotation (Blastx with NR data in NCBI)

  Download        Under construction




*The data can be used for research purposes only.

Contact us imori@imori-net.org, if you use the data for commercial purposes.

 

 

 

 

Copyright (C) 2013- Japan Newt Research Community. All rights reserved.