Documentation PlantQTLdb Assistant Finding Sequencing Data with ENA
Browse Documentation
Getting Started with Assistant Gene Structure and Sequence Extraction Variant Annotation and Local QTL Evidence Functional Enrichment with g:Profiler Network Analysis with STRING Finding Sequencing Data with ENA Sequence Similarity Search with BLAST Plant Motif Analysis with JASPAR and FIMO DNA Analysis with Evo2 External Biological Evidence Sources Troubleshooting and Limitations

PlantQTLdb Assistant

Finding Sequencing Data with ENA

locate public sequencing runs and source records without downloading large read files

Requires Research mode

Open PlantQTLdb Assistant

When to use it

Find candidate RNA-seq, WGS or other sequencing datasets for reuse. Specify species, an experimental keyword and sequencing strategy. Search results are metadata matches, not a quality assessment of the experiment.

How to ask and what you receive

Find drought RNA-seq data

ask
Search ENA for rice drought RNA-seq datasets

what you receive

A preview of matching runs with study/sample accessions, titles, library strategy and source links. The result card offers JSON and CSV; FASTQ addresses and MD5 checksums appear when supplied by ENA.

Find resequencing data

ask
Search ENA for rice WGS datasets

what you receive

Whole-genome sequencing run metadata for rice. The default result limit is 20 and the maximum is 50; a truncated result is not the total number of datasets in ENA.

Read the returned identifiers

Study
The project or experiment collection; several samples and runs may belong to one study.
Sample
The biological material described by the submitter.
Run
A sequencing run or submitted read set. Several returned runs can represent one study or sample.

Before reuse

  • Follow the source record and inspect treatment, tissue, controls, replicates, read layout and reference compatibility.
  • The tool does not download FASTQ files, align reads or run differential expression.
  • English keywords search study and sample titles. Use a condition such as drought, or provide an explicit keywords parameter for a different search term. Relevant studies may be missed if their titles use different wording.