Accessing Expression Levels for Genes of Interest from GEO Experiments

Question

[a.aiezza]

I have a list of 100 lncRNAs. For each of these RNAs, I would like to query GEO to find any experiments that used a high throughput sequencing platform and detected expression levels of that RNA in FPKM. To filter further, I'd like to have those expression levels found in controls only. The last filter is to find experiments which found the specific RNA's expression in smooth muscle tissue.

Here are some example lncRNAs:

• CDC37L1-AS1
• LCMT1-AS1
• FLJ21408
• CDIPT-AS1
• LINC00920
• TAT-AS1
• SUZ12P1

Is there any way to do any of this? Any help would be appreciated.

Thanks.

Answer 1

[anthonycor]

You may want to look at the Human Body Map 2.0 dataset to see if there are any samples/datasets that may answer your question.

Try something like this search expression in GEO:

expression profiling by high throughput sequencing[DataSet Type] AND "smooth muscle"[Sample Source]

You'll have to then download the soft files for experiments of interest and parse sample characteristics or sample names for controls. Sometimes this information is not structured well in GEO.

Answer 2

[Mikael Huss]

The EMBL-EBI Baseline Expression Atlas offers a convenient interface for looking gene by gene (put your gene name in the search bar where it says "Enter gene query"). It summarized information from studies such as the already mentioned BodyMap and others. There is a column for smooth muscle (scroll right when you get the result table).

Also, you might want to check out bgee.