Rna Seq Data In Geo Datasets

Question

[Bioinformatics_NewComer]

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.

[ancient_learner]

I think you can check the Title, Extraction protocol, Library strategy headers for further information! eg: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM932904

[Bioinformatics_NewComer]

@ ancient_learner - Thank your reply and help.

I was looking at GEO series http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24457

And the URL you pinged shows SAMPLES. Can you please help me understand what represents what?

[ancient_learner]

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).

[ancient_learner]

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

[Devon Ryan]

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

[Michael]

Moved to question.

[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".

Answer 1

[Sean Davis]

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

[Bioinformatics_NewComer]

@seniors- sorry for late reply. Thank you for your help and time.