Help with downloading data
Method 1: Downloading data from the submission archive
- The original data submitted to GUDMAP (unedited) is available from the original submission archive.
- Note: only raw microarray data is available for public download. No ISH or IHC data is available.
- Support for download is available from the GUDMAP editors if you wish to analyse large quantities of GUDMAP expression data. Contact them by e-mail: gudmap-editors@gudmap.org.
The archive table has columns detailing the source of the submission (Source Lab), the date it was received, the type of data it contains, the filename(s) and status plus any other relevant notes. The date column provides a link to the page where data can be downloaded from (example, below). For text based files (eg. TXT or RPT) clicking on them will cause them to open in the browser. To download these file types you will have to either CTRL+click OR right-click and select 'Save Link as' from the menu. This is the case if using Firefox on a Mac. Other browsers may give different options such as 'Download linked file' or 'Download linked target'.
Method 2: Downloading data via the microarray series page
Downloading via the microarray series page is perhaps the most informative download method. Follow the steps below to go to the GUDMAP gene expression page and navigate to the microarray series page via Browse > Array > Series.
Step 1: Go to the GUDMAP gene expression page and click on Browse > Array > Series.
Step 2: This page lists the microarray series that are available. Click on the series name of interest. For example 'Gene expression in whole ovary at gd 11, 12, 14, 16, 18 and pnd2'.
Step 3: A full description of the series is given along with a list of the samples available. Click on the sample you wish to download, in this example GUDMAP:2217 (pnd 2 whole ovary).
Step 4: Download data from the individual sample page
by clicking on the 'Supplemental Data Files' section. Files are available in .CEL, .CHP, .RPT and .TXT format.
Note: As before, for text based files (eg. TXT or RPT) clicking on them will cause them to open in the browser. To download these file types you will have to either CTRL+click OR right-click and select 'Save Link as' from the menu. This is the case if using Firefox on a Mac. Other browsers may give different options such as 'Download linked file' or 'Download linked target'.
