The NCBI Transcriptome Shotgun Assembly (TSA) Database

Scientists determine transcriptomes using a variety of computational techniques to assemble sequences from transcribed RNAs into longer transcripts that may represent a complete expressed gene.  By analyzing an organism's transcriptome, researchers can determine expression levels of genes in different cells and tissue types to better understand health and disease. 

The Transcriptome Shotgun Assembly (TSA) division of GenBank was developed specifically for high-throughput shotgun assemblies of RNASeq data.  The database serves as an archive of computationally assembled transcripts from primary sequence reads  deposited in the Sequence Read Archive (SRA).  Sequences are deposited to TSA through the NCBI Submission Portal.  Submitting rich contextual metadata along with the transcriptome data is important for providing users with a complete understanding of the source of the biological data.  This information is captured in two databases designed specifically to house contextual metadata, BioProject for project-specific information and BioSample for sample-specific attributes. All data associated with a transcriptome project is linked via the BioProject ID.  The data can be retrieved by both  Entrez and the Shotgun Assembly Sequences browser.   TSA  is a resource for scientists to retrieve and analyze transcriptomic data to make important scientific discoveries.

Also, the NCBI's eukaryotic genome annotation pipeline, uses transcript sequences including TSAs for genome mapping and to compensate for gaps in genome assemblies. The pipeline automatically constructs model RefSeq transcripts and proteins (XM_ and XP_ accession prefixes) that combine genome and transcript sequence, resulting in a more accurate and complete model than is possible from using only the genome sequence.