Scientific Computing and Data / Research Data Services / Data Ark: Data Commons / The Living Brain Project

The Living Brain Project

Overview

The Living Brain Project (LBP) is a multiscale, data-driven investigation of the human brain, conducted by the Laboratory of Brain and Data Sciences, wherein a single living population is being studied using all of the tools available for human-subject neuroscience, including the tools of molecular and cellular neurobiology that to date have been applied primarily in the post-mortem setting. The LBP cohort consists of prefrontal cortex (PFC) samples from a living brain cohort (LIV) matched for age and sex to a post-mortem brain cohort (PM).

The LIV samples are collected from individuals (N=306) undergoing a deep brain stimulation (DBS) electrode implantation surgery at the Icahn School of Medicine at Mount Sinai. Batteries of the neuropsychological testing survey all domains of cognition and mental health, while electronic medical records create a high-resolution digital record of the health of each participant. Brain structure and function are recorded through multi-modal neuroimaging, and during each of two DBS electrode implantation surgeries (one per hemisphere) specimens are obtained from the participant’s brain, blood and skin for cutting-edge multi-omic analyses.

Most of the LIV samples were obtained from individuals (N=230) with Parkinson’s Disease (PD), the most common indication for DBS. Non-PD LIV samples were obtained from individuals (N=76) undergoing the DBS procedure for indications other than PD. The PM samples (N=246) were obtained from three different brain banks: Harvard Brain and Tissue Resource Center, the New York Brain Bank at Columbia University, and the University of Miami Brain Endowment Bank. A total of 766 brain samples have been collected to date from 486 individuals (520 living and 246 post-mortems). Of the 520 living samples, 268 are from the left hemisphere and 246 are from the right hemisphere.

With this unique cohort, the LBP aims to discover how interactions between the various levels of neurobiology, neurophysiology, and neuroanatomy assessed give rise not only to the chronic traits that have been probed in post-mortem studies (e.g., depression, dementia), but also acute states that can only be assessed in a living cohort (e.g., sadness, working memory).”

Currently, on the Data Ark, we are hosting the following RNAseq data files that have passed the quality control test. RNA sequencing was performed on 289 living brain samples from 172 subjects and 248 post-mortem samples from 248 individuals.

1.lbp_covariates.tsv —Covariate table – covariates can influence the outcome of a given statistical trial but is not of direct interest

2.lbp_featureCounts.tsv –featureCounts – used to quantify reads generated from sequencing in terms of any genomic feature

3.lbp_residuals.tsv — Residuals table – residual measures how far a subject’s observation is from expectation

LBP is an ongoing project; the numbers may change due to the enrollment of future patients.

Access

To use this data, you must read, agree and sign the Data Use Agreement (you must be logged in through the Mount Sinai campus network or secure remote VPN). On Minerva, you can load module $ module load dataark to see the path variables.

More Information

If you have questions about the terms of the Data Use Agreement, please contact Steven Ascolillo at steven.ascolillo@mssm.edu

Data Ark Data Sets

Please visit the Data Ark Data Set webpage to explore other data sets.