Download microarray data from GEO

Question

[tolsma.joseph]

I am trying to download raw data from this https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81442 (GSE81442) microarray experiment.

I am comfortable using SRA but this doesn't have an SRA number.

The reason I need the data is to eventually use it in the MEME suite so if someone has a way to use MEME suite without FASTA files that would work too. Getting the differentially expressed gene IDs is no problem but I don't think MEME suite will accept those like HOMER will.

[Kevin Blighe]

That study was conducted with an A. thaliana microarray. The raw data comprises CEL files. The link to the raw data is at the bottom of the page:

Supplementary file                         Size     Download        File type/resource
GSE81442_RAW.tar                           28.7 Mb  (http)(custom)  TAR (of CEL)
GSE81442_Statistical_analysis_dataset.xlsx 8.5 Mb   (ftp)(http)     XLSX

[GenoMax]

As @Kevin notes this is not sequence data so there are no fasta files.

[tolsma.joseph]

Thanks. Was hoping to get the sequence data but I'll have to go from the CEL to get sequences myself.

[Kevin Blighe]

If you search the Affymetrix / ThermoFisher website for the array type, then you may find a FASTA file of the probe sequences. You cannot have a FASTA file of the measured intensities that are stored in the CEL files, though - that makes no sense.