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Study Description

The NeuroLINCS Center is part of the NIH Common Fund's Library of Integrated Network-based Cellular Signatures (LINCS) program, which aims to characterize how a variety of human cells, tissues and the entire organism respond to perturbations by drugs and other molecular factors.

As Part of the LINCS program, the NeuroLINCS study concentrates on human brain cells, which are far less understood than other cells in the body. Our initial focus is to produce diseased motor neurons from patients by utilizing high-quality induced pluripotent stem cell (iPSC) lines from Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA) patients in addition to unaffected normal healthy controls. Using state-of-the-art OMICS methods (genomics, epigenomics, transcriptomics, and proteomics), we intend to create a wealth of cellular data that is patient-specific in the context of their baseline genetic perturbations and in the presence of other genetic and environmental perturbagens (e.g. endoplasmic reticulum stress). The primary data will be used to build cell signatures that convey the key features that distinguish the state of a cell and determine its behavior. Ultimately, the analysis of these datasets will lead to the identification of a network of unique signatures relevant to each of these motor neuron diseases. The datasets represented in this study are generated from assays interrogating RNA expression (RNA-seq), chromatin accessibility (ATAC-seq) and whole genome sequencing.

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Publicly Available Data (Public ftp)

Connect to the public download site. The site contains release notes and manifests. If available, the site also contains data dictionaries, variable summaries, documents, and truncated analyses.

Study Inclusion/Exclusion Criteria

Case samples were included if clinical history description included ALS (C9, SOD1 or sporadic) or SMA (SMN 1 deletion) diagnosis. Control cohort had no history of ALS or SMA phenotype.

Molecular Data
TypeSourcePlatformNumber of Oligos/SNPsSNP Batch IdComment
RNA Sequencing Illumina HiSeq 2500 N/A N/A
RNA Sequencing Illumina HiSeq 4000 N/A N/A
Whole Genome Sequencing Illumina HiSeq X N/A N/A New York Genome Center
ATAC Sequencing Illumina HiSeq 2000 N/A N/A
Selected publications
Diseases/Traits Related to Study (MESH terms)
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Study Attribution