Transcription Data

Transcription Data

Data available at URGI

  • RNA-Seq expression data from JIC (C. Uauy). The transcriptome atlas was developed from 850 RNA-Seq datasets representing a diverse range of tissues, development stages and environmental condition
  • Deep Triticum aestivum transcriptome sequence data generated by INRA GDEC (L. Pingault, E. Paux) from five wheat tissues. Data were generated from two RNA-Seq libraries (non-oriented and oriented) and have been used to annotate chromosome 3B and the Chromosome Survey Sequence. The libraries are described in: Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome. Pingault, L. Choulet, F., Alberti, A., Glover, N., Wincker, P., Feuillet, C., Paux, E. Genome Biology 2015 16:29. DOI:10.1186/s13059-015-0601-9

Wheat expression browser (JIC)

  • A total of 850 RNA-Seq samples derived from 32 tissues at different growth stages and/or challenged by different stress treatments were mapped to the IWGSC RefSeq Annotations v1.0 and v1.1.The visualisation interface allows users to group, filter, sort and download the data according to the categories specified above. This design provides control over precise categories to be used in the database and the visualisation interface will adjust accordingly. The interface allow users to query one gene, compare two genes or visualise up to 50 genes in a heatmap interface. A detailed tutorial can be found here and all the analysed data and source code is also available here.

WheatExp (UC Davis)

  • Quality and adapter-trimmed RNA-seq reads were mapped to the full cDNA set of wheat transcripts from the International Wheat Genome Sequencing Consortium which are hosted by the Ensembl database . Diploid datasets were mapped to A-genome (32,091 cDNAs), tetraploid datasets were mapped to the A- and B-genomes (68,166 cDNAs) and hexaploid datasets were mapped to the A-, B- and D- genomes (101,245 cDNAs). Current expression data is generated from Ensembl release 26. Reference FASTA and GTF files, as well as all expression data in tabular format, are available for download from the following FTP site.

Modification date: 16 August 2023 | Publication date: 10 December 2020 | By: ic