Anatomic Structures ISH Survey

I am trying to understand the pipeline of Ivy GAP anatomic structures studies and wondering how the 343 gene probe in the initial Anatomic Structures ISH Survey was used in the subsequent Anatomic Structures RNA-Seq and Anatomic Structures ISH for Enriched Genes studies.

I realize that the Anatomic Structures RNA-Seq study was designed to profile expression in the anatomical structures identified by H&E staining through which we subsequently identify 37 genes for the later enriched genes ISH study. If so, how was the initial study performing ISH on 343 gene probes helpful for later studies?

Thanks for the clarification.

Hi @kasthuri,
I have a partial answer that may or may not be satisfactory. The 343 “genes were selected in 2009 based on their known or presumed relevance to glioblastoma and expression levels in glioblastoma relative to other tissues.” The 37 “genes were selected in 2014 based on the specificity of their expression patterns in the 5 major anatomic structures of glioblastomafrom RNA-seq and are mostly independent of the 343. However, many of the 343 genes were used in the stem cell ISH study. This is laid out in more detail in the overview documentation.

If you still have questions after reading the documentation, I would suggest contacting one of the corresponding authors of our platform paper.

Hi @jeremyinseattle,

Yes, I tried to see the intersection of the 37 with 343 and found hardly any and that is when I got this question. Thanks for confirming my hunch. I will try contacting the corresponding authors.