Download microarray data from GEO

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5.7 years ago

tolsma.joseph ▴ 20

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.

microarray GEO • 1.6k views

ADD COMMENT • link 5.7 years ago by tolsma.joseph ▴ 20

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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

ADD REPLY • link 5.7 years ago by Kevin Blighe 88k

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

ADD REPLY • link 5.7 years ago by GenoMax 148k

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

ADD REPLY • link 5.7 years ago by tolsma.joseph ▴ 20

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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.

ADD REPLY • link 5.7 years ago by Kevin Blighe 88k

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