Quick Start guide

  1. Experiments table
  2. Single experiment overview
  3. Samples table
  4. Files for download
  5. BAM files for RNA-seq experiments
  6. More help

Under each topic, click on the screenshot or help link to get bite-size guide in EBI Train Online tutorials (will open in a new browser window or tab).

 

1. Experiments table

This is the table of experiments you'll see when you go to the ArrayExpress Experiments tab, one row per experiment. The experiments displayed depend on search terms you've entered or filters you've selected.

Tour the experiments table in section 2 of Train Online tutorial "How to search ArrayExpress"Search results table

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2. Single experiment overview

When you click on an experiment on the Experiments table, e.g. "http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-777", you will come to this page which summarises all the information and data download links for an experiment. There are also links to GenomeSpace and R ExpressionSet objects.

Discover features of this overview in section 5 of Train Online tutorial "How to search ArrayExpress"Single experiment view

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3. Samples table

You'll get to this table from the link "Click for detailed sample information and links to data" on the Single experiment overview page, e.g. http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-674/samples.html. Here, samples are in rows and sample attributes are in columns. You'll also find direct link to data files for each sample in the last column.

To download the full samples table, just use the link at the bottom of the table. The downloaded file is tab-delimited text file, which can be opened in any spreadsheet programme.

See annotated samples table in section 6 of Train Online tutorial "How to search ArrayExpress"Experiment samples view

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4. Files for download

On the Single experiment overview page, you can download all files (e.g. sample annotations, raw data files) for the experiment using links in the "Files" section, e.g. http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-674/files/".

Find out more about data files in Train Online tutorial "How to get data from ArrayExpress"Experiment files view

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5. BAM files for RNA-seq experiments

For a subset of RNA-seq experiments in ArrayExpress, e.g. https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-822/samples/, we created BAM files by processing the experimental raw FASTQ data files with the ArrayExpressHTS BioConductor package as part of the RNA-seq data processing pipeline. The BAM files are available for download and can also be viewed in Ensembl.

Find out about the BAM files in Train Online tutorial "High-throughput sequencing" sections 3-4BAM files in Ensembl Genome Browser

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6. More help

For a comprehensive guide on using ArrayExpress, please try our free, online tutorial:

Train Online tutorial - ArrayExpress: Exploring functional genomics data with the ArrayExpress

If you are submitting data to us for the first time, you will find guidelines and tips in:

ArrayExpress experiment or array design submission overview
How to use Annotare webform tool to submit an experiment

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