How To Find The Strand-Specific Info In The Public Data From The Illumina Human Body Map 2.0 Project

Question

[camelbbs]

Hi,

Anyone can guide a while how to find if this public rnaseq data are prepared by strand-specific assay. Thanks a lot!

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30611

Ch

[Istvan Albert]

I have sent an email to the submitter, hopefully she will respond here.

Answer 1

[matted]

If you read the PDF at the bottom of the page you linked, you will find the answer to your question (page 15):

"The samples used for the 2X50 and 1X75 bp runs are prepared using the Illumina mRNA-Seq kit.

– They are made with a random priming process and are not stranded."

"The sample prep used for the 1X100 bp run is the Illumina Pre- Released Directional RNA-Seq protocol.

– These data are stranded."

In general, you can usually make a quick guess by loading up aligned reads in some viewer and looking for agreement (or differences) between strands. You could also imagine doing something more sophisticated like looking at a correlation coefficient across binned read counts between the two strands... higher would indicate unstranded and lower would indicate strand-specificity.

[camelbbs]

Thanks a lot! I am still not very understanding the method you said to check if the seq are stranded or not. But the PDF gives the clear info. That' very helpful. I also have two other datasets from ENCODE project and I can't figure out the stranded info:

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34820

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37592

[Istvan Albert]

The mind boggling part is that one needs to go to the 15th page of an associated PDF. Whereas the file itself is hosted on a supposedly science oriented website that is full of seemingly useless information:

Overall design    

Experimental Design: organism_part_comparison_design
Experimental Design: co-expression_design
Experimental Design: optimization_design
Experimental Factor Name: ORGANISMPART
Experimental Factor Name: LIBRARYPREP
Experimental Factor Name: PHENOTYPE
Experimental Factor Type: organism_part
Experimental Factor Type: protocol
Experimental Factor Type: phenotype

[camelbbs]

Thanks. I wonder how to look for the agreement or differences between strands in IGV browser with input bam files.