Q1:
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.

A1:
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.

Q2:
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?

A2:
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.

Q1:
I am looking at
http://resource.psychencode.org/#Derived
under
Derived Data Types
there are a couple of gene expression matrices. What are the columns (samples), ie which ones are which cases and which controls in the header file:
http://resource.psychencode.org/Datasets/Derived/Header_DER-01_PEC_Gene_expression_matrix_normalized.txt

What is the difference between
DER-01_PEC_Gene_expression_matrix_normalized
and
DER-02_PEC_Gene_expression_matrix_TPM
besides the fact that one has 43,886 lines and the other has 57,821 lines and that one has 1,932 columns and the other 1,867 columns.

A1:
1) "What are the columns (samples), ie which ones are which cases and which controls in the header file"

I am unable to pass on this information, as our DCC mentioned that diagnosis information would only be available upon application to Synapse for approval by the NIMH and investigators. Please contact them for access approval.

2)
"What is the difference between
DER-01_PEC_Gene_expression_matrix_normalized
and
DER-02_PEC_Gene_expression_matrix_TPM"

The difference in the numbers is simply between FPKM and TPM units in expression.
3)
"besides the fact that one has 43,886 lines and the other has 57,821 lines"
There is very likely a difference in the thresholding of gene expression applied to these two datasets. I have reached out to my colleague who processed these matrices and will get back to you with a more definite response soon.

4) "that one has 1,932 columns and the other 1,867 columns."

The column number differences arise from the following: 1931 is the original number of DFC samples considered, which includes both adult and non-adult individuals. Once we filtered out the 65 non-adult samples, we obtained the 1866 individuals in the second matrix. Unfortunately, this was not made clear on the website. I will be updating this soon.

Q2:
But wait a minute, these files are useless without at least knowing who the cases and who the controls are?

A2:
Here is the rationale:
PsychENCODE placed restrictions on the dissemination of metadata. While adhering to those restrictions, we endeavored to put out as many of the processed datasets from our analyses as possible to allow for reproduction or downstream usage. This includes several intermediate files. Some may require protected data obtained with the permission of the consortium to perform downstream analyses, but even then the files on our website are in a format that would aid such analyses, and that are not available elsewhere.

For completeness, here are the answers to your original questions:
1) Method for generating DER-01: Using the original FPKM file, we filtered on >=10 individuals with >0.1 FPKM (though GTEx also applied a filter of requiring raw read counts greater than 6 — we did not have the raw data from GTEx, so we didn’t apply a filter on raw read counts).

2) Quantile normalization was performed to bring the expression profile of each sample onto the same scale.

3) To protect from outliers, inverse quantile normalization was performed for each gene, mapping each set of expression values to a standard normal.
2) Method for generating DER-02: The TPM file was converted directly from the original FPKM file