ID
45701
Description
Principal Investigator: Leslie Thompson, PhD, University of California, Irvine, CA, USA MeSH: Amyotrophic Lateral Sclerosis,Muscular Atrophy, Spinal,Spinal Muscular Atrophies of Childhood https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001231 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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Versions (1)
- 5/14/23 5/14/23 - Chiara Middel
Copyright Holder
Leslie Thompson, PhD, University of California, Irvine, CA, USA
Uploaded on
May 14, 2023
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License
Creative Commons BY 4.0
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dbGaP phs001231 NeuroLINCS
This subject phenotype table contains subject IDs, sex, race, tissue type, source aliases, diagnosis, and age.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, subject aliases, and case control status of the subject for Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA) disease.
- This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample use and sample aliases.
- This subject phenotype table contains subject IDs, sex, race, tissue type, source aliases, diagnosis, and age.
- This sample attributes table contains sample IDs, subject IDs, histological type, IPS (Induced Pluripotent Stem Cell ) passage number, sample source, sequencing information (n=9 variables: analyte type, RNA integrity number, library prep kit, fragment size, sequencing type, strand, sequencing cycle number, sequencing platform, sequencing center which conducted sequencing), tumor status, days cells were differentiated into motor neurons, protocol, and cell markers .
Similar models
This subject phenotype table contains subject IDs, sex, race, tissue type, source aliases, diagnosis, and age.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs, consent information, subject aliases, and case control status of the subject for Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA) disease.
- This data table contains a mapping of study subject IDs to sample IDs. Samples are the final preps submitted for genotyping, sequencing, and/or expression data. For example, if one patient (subject ID) gave one sample, and that sample was processed differently to generate 2 sequencing runs, there would be two rows, both using the same subject ID, but having 2 unique sample IDs. The data table also includes sample use and sample aliases.
- This subject phenotype table contains subject IDs, sex, race, tissue type, source aliases, diagnosis, and age.
- This sample attributes table contains sample IDs, subject IDs, histological type, IPS (Induced Pluripotent Stem Cell ) passage number, sample source, sequencing information (n=9 variables: analyte type, RNA integrity number, library prep kit, fragment size, sequencing type, strand, sequencing cycle number, sequencing platform, sequencing center which conducted sequencing), tumor status, days cells were differentiated into motor neurons, protocol, and cell markers .
C2348585 (UMLS CUI [1,2])
C3847505 (UMLS CUI [1,2])
C1301820 (UMLS CUI [1,3])
C0007600 (UMLS CUI [1,4])
C0449416 (UMLS CUI [1,2])
C0007600 (UMLS CUI [1,3])
C0026882 (UMLS CUI [1,2])
C0449560 (UMLS CUI [1,3])
C0012634 (UMLS CUI [1,4])
C0011900 (UMLS CUI [1,5])
C0011008 (UMLS CUI [1,2])
C0200345 (UMLS CUI [1,3])