Question: Rna Seq Data In Geo Datasets
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gravatar for Bioinformatics_NewComer
6.6 years ago by
Genomic Island
Bioinformatics_NewComer320 wrote:

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 • 4.6k views
ADD COMMENTlink modified 6.6 years ago by Sean Davis26k • written 6.6 years ago by Bioinformatics_NewComer320
1

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

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by ancient_learner620

@ 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?

ADD REPLYlink written 6.6 years ago by Bioinformatics_NewComer320
1

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).

ADD REPLYlink written 6.6 years ago by ancient_learner620
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By the way you are suppose to post this as a question not as a tutorial.

ADD REPLYlink written 6.6 years ago by ancient_learner620
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Could someone remove this from the "how to" section?

ADD REPLYlink written 6.6 years ago by Devon Ryan95k
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Moved to question.

ADD REPLYlink written 6.6 years ago by Michael Dondrup47k
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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".

ADD REPLYlink written 6.6 years ago by Devon Ryan95k
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gravatar for Sean Davis
6.6 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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

ADD COMMENTlink written 6.6 years ago by Sean Davis26k

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

ADD REPLYlink written 6.6 years ago by Bioinformatics_NewComer320
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