IMORI

IMORI

The sequence resource for the Japanese fire bellied newt

Last Updated: 2018-06-04

The Japanese fire bellied newt (Cynops pyrrhogaster), called ‘Akahara Imori’ 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 HiSeq2000/2500.

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

BLAST search

You can use our BLAST server to align a given sequence to transcripts.

GO to BLAST search page

Results

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

Reference

Islam, M.R., Nakamura, K., Casco-Robles, M.M., Kunahong, A., Inami, W., Toyama, F., Maruo, F. and Chiba, C. (2014) The newt reprograms mature RPE cells into a unique multipotent state for retinal regeneration. Sci Rep 4: 6043. doi: 10.1038/srep06043
[link to the paper]
Nakamura, K., Islam, M.R., Takayanagi, M., Yasumuro, H., Inami, W., Kunahong, A., Casco-Robles, R.M., Toyama, F. and Chiba, C. (2014) A transcriptome for the study of early processes of retinal regeneration in the adult newt, Cynops pyrrhogaster. PLoS ONE 9(10): e109831. doi:10.1371/journal.pone.0109831
[link to the paper]
Inami, W., Islam. M.R., Nakamura, K., Yoshikawa, T., Yasumuro, H., Casco-Robles, M.M., Toyama, F., Maruo, F. and Chiba, C. (2016) Expression of two classes of Pax6 transcripts in reprogramming retinal pigment epithelium cells of the adult newt. Zool. Sci. 33: 21-30. doi: 10.2108/zs150111
[link to the paper]

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

Annotation (Blastx with NR data in NCBI)

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)

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)

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)

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)

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)

7) Lens

Reference

Sousounis, K., Qi, F., Yadav, M.C., Millan, J.L., Toyama, F., Chiba, C., Eguchi, Y., Eguchi, G. and Tsonis, P.A. (2015) A robust transcriptional program in newts undergoing multiple events of lens regeneration. eLife 2015;10.7554/eLife.09594. doi: http://dx.doi.org/10.7554/eLife.09594
[link to the paper]

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)

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)

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)

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)

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

Yokoe, M., Sano, M., Shibata, H., Shibata, D., Takayama-Watanabe, E., Inaba, K. and Watanabe, A. (2014) Sperm proteases that may be involved in the initiation of sperm motility in the newt, Cynops pyrrhogaster. Int. J. Mol. Sci. 15: 15210-15224. doi:10.3390/ijms150915210
[link to the paper]

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)

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)

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)

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)

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)

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)

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)

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)

21) Embryos at Stage 5, 18 and 29

Reference

(Under construction)

De novo assembled transcriptome

Download

Annotation (Blastx with NR data in NCBI)

22) TOTAL [1-21]

Reference

(Under construction)

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

Download

Annotation (Blastx with NR data in NCBI)

GO classification

*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.

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