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Transcriptome Shotgun Assembly (TSA)

TSA is an open access archive of computationally assembled transcribed RNA sequences from next generation sequencing technologies. Unassembled reads must be submitted to Sequence Read Archive (SRA) before starting the TSA submission.

What You Should Expect

This tool is for submitting computationally assembled transcribed RNA sequences representing a transcriptome. The computationally assembled transcripts are derived from overlapping sequence reads submitted to the Sequence Read Archive (SRA). When you submit, you will need to:

  1. Submit your sequence reads to the SRA prior to submitting your transcriptome. Note your BioProject, BioSample and SRA run accession number(s):
    • BioProject (PRJNAXXXXXX)
    • BioSample (SAMNXXXXXXXX)
    • SRA accession number (SRRXXXXXX)
  2. Prepare your file in ASN.1 or FASTA format and upload your data file according to the instructions.
    Note that if you submit an ASN.1 format file, your data will be autopopulated in the submission workflow.
  3. Review or provide a BioProject and BioSample that have already been registered for an SRA submission.
  4. Select a ‘Release Date’ for your submission.
  5. Review or provide the SRA run accession(s) for the sequence reads used to generate this assembly.
  6. Review or provide metadata on the sequencing and assembly of the transcriptome.
  7. Indicate whether your submission is an update to an existing submission.

Prepare and upload your data files.

  • If there is no annotation, you can upload a FASTA file
  • If there is annotation, you will need to create an ASN.1 or .sqn file. The submission tool will automatically scan ASN.1 or .sqn files after your upload and prepopulate any provided fields with your data.

Read more here.

Review or provide the following requirements. If you have included required information in the ASN.1 file then check that the auto-populated data is correct and edit as necessary.

You will also need to indicate the release date and whether your submission is an update.

Project/Sample

Review or provide a BioProject and BioSample that have already been registered for an SRA submission.

  • The BioProject contains the description of the research effort, relevant grant(s), and has links to the public data. A transcriptome must belong to a BioProject, and transcriptomes sequenced as part of the same research effort can belong to a single BioProject. Use the same BioProject for the sequence reads and transcriptome assembly made from those reads; do not create duplicate BioProjects.The SRA run accessions were provided when you submitted to the Sequence Read Archive (SRA).
  • The BioSample contains the source information of the sample sequenced. Use the same BioSample for the sequence reads and transcriptome assembly made from those reads; do not create duplicate BioSamples.

Primary data

Review or provide SRA run accessions (SRRXXXXXX) for the sequence reads used to create your assembly. The SRA run accessions were provided when you submitted to the Sequence Read Archive (SRA).

Assembly metadata

Review or provide the following information to submit as metadata:

  • Assembly method: name of the assembly algorithm(s)
  • Version or date program was run
  • Assembly name (optional)
  • Coverage (optional)
  • Description of assembly method: brief description of the assembly process
  • Sequencing technology or technologies

Annotation is optional.

If you plan to submit a transcriptome with annotation, it must show the focus of the study. Annotation must be biologically valid. If coding regions are provided, the product names should follow the International Protein Nomenclature Guidelines.

Submit your sequence data on desktop. The desktop view allows you to easily:

  • Enter your information
  • Enter or upload metadata
  • Upload large source files
  • Review your submission

Email me a link to get started

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TSA FAQ

  • SRA archives the raw, unassembled reads that act as the basis for generating the assembled transcriptome. TSA stores the assembled transcriptome.

  • Submit the unassembled reads to Sequence Read Archive (SRA). This is the required first step to TSA submission.

GenBank

GenBank is the world's largest nucleotide archive containing sequences from all branches of life. The archive is a foundation for medical and biological discovery.

  • Submit assembled ribosomal RNA (rRNA), rRNA-ITS, SARS-CoV-2, Influenza, Norovirus or metazoan COX1 sequences.

  • Submit mRNA, genomic DNA, organelle, ncRNA, plasmids, other viruses, phages, synthetic constructs.

  • Submit assembled eukaryotic and prokaryotic genomes (WGS or Complete).

Sequence Read Archive (SRA)

SRA is the largest publicly-available repository of high throughput sequencing data. The archive accepts data from all branches of life as well as metagenomic and environmental surveys.

Other Tools

  • TSA

    Submit computationally assembled, transcribed RNA sequences after submitting unassembled reads to SRA. Learn more

  • GEO

    Submit RNA-seq, ChIP-seq, and other types of gene expression and epigenomics datasets. Learn more

  • BioProject & BioSample

    Choose a tool above if submitting sequence data. Learn more

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Submit clinical data, small & large human genomics variants, and genotype & phenotype data.

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