Are the following type of data available for schizophrenia in the Synapse project?
1. RNA-Seq summary data (gene level).
2. Microarrays.
Created by Assif Yitzhaky assify Hi al,
I was wondering whether there is kind of case/control data on chip-seq or atac-seq from schizophrenia vs controls in the Synapse project?
thnx It really depends on your specific analysis. Like I mentioned in [this thread](https://www.synapse.org/#!Synapse:syn2759792/discussion/threadId=5728), normalized and non-normalized gene counts are available and described in detail in the Capstone paper. Additionally, I recommend this [resource](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0881-8)for RNA-seq best practices. I have a question regarding the *quant.genes.results files from PEC Capstone Collection. I am not sure which gene level count column it is acceptable to use when performing gene expression analysis. Is it "expected_count"? There is gene expression data available in the form of RNAseq, but no microarray. Some of the studies have provided counts, but not all. To see a listing of all individual studies that have contributed data see here: https://www.synapse.org/#!Synapse:syn4921369/wiki/390659. The majority of the RNAseq from these studies has been reprocessed using a common pipeline into what is called the "Capstone collection'. That dataset includes gene and isoform counts. See here: https://www.synapse.org/#!Synapse:syn12080241 - follow the link to the Data Table -> select assay-rnaSeq and fileFormat-tsv. Diagnosis can be found in the clinical data table: https://www.synapse.org/#!Synapse:syn12118229/tables/