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Rna Seq Data In Geo Datasets

Hi Experts, I am lost in GEO data sets and cannot figure out if the data is RNA seq or Micro array.

Most of the times it is written: Experiment Type Expression profiling by high throughput sequencing Platforms: Illumina Genome Analyzer IIx (Homo sapiens)

Experiment type Expression profiling by array Platforms Affymetrix Mouse Genome 430 2.0 Array

Experiment type Expression profiling by array Platforms Affymetrix Human Genome U133 Plus 2.0 Array and so on.

I am confused and cannot proceed. Guidance will be highly appreciated.

rnaseq geo
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updated by Sean Davis Sean Davis • written by Bioinformatics_NewComer Bioinformatics_NewComer

your link refers to the data series representing the entire list of data sets (samples) for that particular work. each sample you can access by clicking on the link provided. In your example they want to compare mirna expression in normal kidney (eg:K1N miRNA-Seq) and cancer tissue (eg:K1C miRNA-Seq).

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written by ancient_learner ancient_learner

By the way you are suppose to post this as a question not as a tutorial.

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written by ancient_learner ancient_learner

Could someone remove this from the "how to" section?

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written by Devon Ryan Devon Ryan

What exactly is your question and can you give us some examples of GEO datasets that you find confusing in this regard? In general, RNAseq datasets should have "expression profiling by high throughput sequencing" as the "DataSet Type" and "high throughput sequencing" as the "Platform Technology Type".

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written by Devon Ryan Devon Ryan

1 answer

You'll want to look at the GEO platform record associated with the GSM. For example, for your GSM932904, you'll see that it is associated with GPL11002:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11002

If you look at GPL11002, you'll notice that the platform technology is high throughput sequencing.

The GEOmetadb bioconductor package can be useful for bulk metadata searches of NCBI GEO if you need that kind of capability.

http://www.bioconductor.org/packages/release/bioc/html/GEOmetadb.html

• 754 views • link
written by Sean Davis Sean Davis

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