Information about datasets from PsychENCODE

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 . Please contact Prashant (copied)

Please refer to

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 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.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s