I am writing to ask where I might be able to find a list of all of the datasets generated for the PsychENCODE project. Specifically, we would like to know how many single-cell and bulk RNA-seq datasets were generated, and what the sex and age is of the samples used to generate these datasets. I was not able to find this information in the supplementary materials from your 2018 Science paper or on the PsychENCODE website, but perhaps I am missing something. Before we start the application process to access the raw data, it would be very helpful to have this information.
You should be able to find a list of all datasets used for Wang et al.
(’18) from resource.psychencode.org . Please contact Prashant (copied)
Please refer to http://resource.psychencode.org/Datasets/RawData/RAW-01_PEC_Table_of_Datasets.xlsx
This contains the set of datasets associated with the analysis in the Wang et al paper, focusing on the adult samples. Of course, this is a subset of the total PsychENCODE datasets. I can see if there is a simple resource for you to access to get the information from the superset. I will let you know soon.
I am going to answer your question in two parts. Here is Part 1:
The metadata for the prenatal and adult single-nuclei datasets is available at http://development.psychencode.org/ under the "Processed Data" heading, "Single cell/nucleus RNA-seq". The ages and sexes of the sampled individuals can be found in the .xlsx files with the labels "QC" appended.
Can you tell me if additional single-cell RNA-seq datasets will be generated in the next phase of this project and what the timeframe might be?
There will definitely be a significant expansion of the single-cell/nucleus datasets in the next phase, though it is as yet uncertain as to how long that would take. I am hesitant to take a guess right now, but please check back in a couple of months and we may have a better answer.