Transcriptome data

Submitted by jaiswalp on


If you are accessing and using this data in your projects and resources, you are required to cite the following publications.

  • Gupta P, Geniza M, Naithani S, Phillips J, Haq E and Jaiswal P. (2021) Chia (Salvia hispanica) Gene Expression Atlas Elucidates Dynamic Spatio-Temporal Changes Associated With Plant Growth and Development. Front. Plant Sci. 12:667678. doi: 10.3389/fpls.2021.667678 (
  • Pankaj Jaiswal (2017). Comparative analysis of reference transcriptome atlas and insight into essential fatty acids and terpenoid biosynthesis pathways from Chia (Salvia hispanica). CyVerse Data Commons. DOI 10.7946/P2192W (


The raw transcriptome sequence reads and the metadata was deposited in the EMBL-EBI ArrayExpress with an accession #E-MTAB-5515 (ArrayExpress Link). 

The same can be accessed from NCBI Bioproject #PRJEB19614 (Bioproject link)


All the following processed and analyzed transcriptome data is available from the CyVerse Data Commons and the Jaiswal Lab file share site under the CC BY 4.0 license and the Public Domain Dedication and License v1.0.

  • Assembly (cDNAs): All tissues combined and tissue-specific assemblies
  • Annotation: Gene Ontology, Pathway, and InterPro assignments
  • Expression: All Vs All and Each sample Vs All.
  • KEGG Pathway: Transcript assembly matches to the reference Arabidopsis and tomato pathways from KEGG
  • SSR markers: Simple Sequence Repeat (SSR) markers identified in the assembled transcripts
  • Transdecoder results
  • BLAST results queried against various genomes

Additional supplementary files and data (Zip archive) published in the transcriptome paper (Gupta et al, 2021) can be accessed from the following link.