Stanley NGS Data Download Portal (SNDDP)

Stanley Medical Research Institute NGS Data Repository contains high-quality next-generation sequencing (NGS) data from multiple brain regions of the Stanley Brain Collection provided by the Stanley Brain Research Laboratory.

Currently available NGS data

For some datasets, data is not available for all samples specified in the tissue collection.

Bulk RNA-Seq data

1. The Neuropathology Consortium (15 each schizophrenia, bipolar disorder, depression and controls)

Prefrontal cortex · Orbitofrontal cortex · Hippocampus · Cerebellum

2. The Array Collection (35 each schizophrenia, bipolar disorder and controls)

Prefrontal cortex · Cingulate cortex · Choroid plexus · Hippocampus

3. The Stanley New Collection (19 each schizophrenia, bipolar disorder and controls)

Choroid plexus

4. The Depression Collection (12 each depression with psychosis, depression without psychosis and controls)

Prefrontal cortex · Cingulate cortex

5. Combined Collections

Liver

snRNA-Seq data

The Array Collection (35 each schizophrenia, bipolar disorder and controls)

Midbrain

Whole exome sequencing data

The Array Collection (35 each schizophrenia, bipolar disorder and controls)

Prefrontal cortex

Demographic Data

Demographic metadata are available for the following collections:

The Neuropathology Consortium (n=60; schizophrenia, bipolar disorder, depression, controls)
The Array Collection (n=105; schizophrenia, bipolar disorder, controls)
The Stanley New Collection (n=57; schizophrenia, bipolar disorder, controls)
The Depression Collection (n=36; psychotic depression, non-psychotic depression, controls)
Combined tissue collections (n=73; liver)

sFTP NGS raw data access

How to request NGS raw data

Access to NGS raw data is provided after approval. To request access, please follow the steps below:

Log in to https://sncid.stanleyresearch.org/
Navigate to the RAW DATA menu and select NGS.
Complete and submit the RNA-Seq Data Request form.
After review and approval, we will provide you with an sFTP username and password by email.

sFTP download

Once you receive your sFTP credentials, you can download the approved NGS raw data using an sFTP client.

Your assigned sFTP username and password
An sFTP client program (e.g., FileZilla)
Sufficient local disk space for the data

Connection information

Host: sftp://143.248.30.179/
Port: 4000
Username: (provided after approval)
Password: (provided after approval)

Note: sFTP credentials are issued on a per-request basis and are time-limited for security reasons.