NFINtb Nothobranchius furzeri transcriptome browser

The Nothobranchius furzeri Information Network transcriptome browser (NFINtb) is a database of cDNA contig assemblies of the short-lived teleost fish Nothobranchius furzeri supplemented with the best currently available annotation.

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Catalogues:

The following assemblies are currently maintained in the NFINtb Nothobranchius furzeri transcriptome browser:

AssemblyMaterialTechnologyTranscript contigsTotal lengthGenesGenes with full CDS
2010/03 8 GRZ, 8 - 10 weeks old, whole body Sanger, 454/Roche 118,795 87 Mb 18,065 3,909 (22%)
2011/09 30 GRZ and MZM-0403, 1 - 31 weeks old, whole body, brain, skin Sanger, 454/Roche, Solexa/Illumina 213,621 253 Mb 19,875 14,170 (71%)
2011/09 30 GRZ and MZM-0403, 1 - 31 weeks old, whole body, brain, skin, embryo Sanger, 454/Roche, Solexa/Illumina 224461 304 Mb 20,388 14,384 (71%)

Sequencing:

RNA was isolated from brain, skin, embryo and whole body samples obtained from several N. furzeri GRZ and MZM-0403 individuals. Most of them were males, except for the embryos where sex was unknown. Initially, RNA samples were converted into cDNA using oligo-dT priming. These cDNA libraries were then normalised and sequenced with Sanger and 454/Roche. After switching to Solexa/Illumina, poly(A)-enriched RNA samples were converted into cDNA libraries for sequencing using random hexamer priming.

Assembly:

The first assembly, based on Sanger and 454/Roche data, was done with PAVE. This program first groups overlapping reads into clusters using BLAST and then incrementally assembles the clusters with CAP3. It additionally includes pairing information to validate assembly integrity and to split incorrect joins. The other two assemblies include Solexa/Illumina data which cannot be processed in this way. For the second, a new assembly strategy was developed. PAVE contigs of the first assembly were assembled together with the Illumina libraries using the De Bruijin graph-based assembler CLC assembly cell. Hereby, individual Solexa/Illumina libraries were iteratively integrated, i.e. the reads were mapped onto an existing assembly and only the unmapped reads were assembled together with the contigs of the assembly thus extending/improving it. The third assembly was done with Trinity, which then already had become a kind of gold standard for de novo transcriptome assembly.

Annotation:

We provide an annotation based on BLAST-searches against all protein coding genes/transcripts of pufferfish (Tetraodon nigroviridis), medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio) as currently annotated in the ENSEMBL genome browser.

Queries:

A complex query mask allows to quickly find cDNA contigs of interest. You may search by annotation, full coding sequence (CDS), transcript length, ... .

Blast:

A BLAST server allows to search for N. furzeri cDNA contigs of interest.

Last Update: 31.11.2015

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