Imperial College London

ProfessorBorisLenhard

Faculty of MedicineInstitute of Clinical Sciences

Professor of Computational Biology
 
 
 
//

Contact

 

+44 (0)20 3313 8353b.lenhard Website

 
 
//

Assistant

 

Mr Alastair Douglas Ivor Williams +44 (0)20 3313 4318

 
//

Location

 

230ICTEM buildingHammersmith Campus

//

Summary

 

Publications

Citation

BibTex format

@article{Kolder:2016:10.1186/s12864-016-3038-y,
author = {Kolder, IC and van, der Plas-Duivesteijn SJ and Tan, G and Wiegertjes, GF and Forlenza, M and Guler, AT and Travin, DY and Nakao, M and Moritomo, T and Irnazarow, I and den, Dunnen JT and Anvar, SY and Jansen, HJ and Dirks, RP and Palmblad, M and Lenhard, B and Henkel, CV and Spaink, HP},
doi = {10.1186/s12864-016-3038-y},
journal = {BMC Genomics},
title = {A full-body transcriptome and proteome resource for the European common carp.},
url = {http://dx.doi.org/10.1186/s12864-016-3038-y},
volume = {17},
year = {2016}
}

RIS format (EndNote, RefMan)

TY  - JOUR
AB - BACKGROUND: The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies. RESULTS: Here we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data. CONCLUSIONS: The identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes.
AU - Kolder,IC
AU - van,der Plas-Duivesteijn SJ
AU - Tan,G
AU - Wiegertjes,GF
AU - Forlenza,M
AU - Guler,AT
AU - Travin,DY
AU - Nakao,M
AU - Moritomo,T
AU - Irnazarow,I
AU - den,Dunnen JT
AU - Anvar,SY
AU - Jansen,HJ
AU - Dirks,RP
AU - Palmblad,M
AU - Lenhard,B
AU - Henkel,CV
AU - Spaink,HP
DO - 10.1186/s12864-016-3038-y
PY - 2016///
SN - 1471-2164
TI - A full-body transcriptome and proteome resource for the European common carp.
T2 - BMC Genomics
UR - http://dx.doi.org/10.1186/s12864-016-3038-y
UR - http://hdl.handle.net/10044/1/40085
VL - 17
ER -