ID
45599
Description
Principal Investigator: Christopher K. Glass, MD, PhD, University of California, San Diego, CA, USA MeSH: Epilepsy,Brain Neoplasms,Hypoxia-Ischemia, Brain https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001373 These studies map the epigenetic landscape of microglia, neurons, astrocytes and oligodendrocytes. The initial study compared acutely isolated microglia to cultured microglia from the same donors, to identify changes that occur when microglia are removed from the brain microenvironment. In collaboration with the Rady Children's hospital, we obtained brain tissue samples from pediatric patients representing putative normal tissue resected to gain access to brain tumors as well as tissue resected to remove epileptic foci. We assayed microglia isolated from these samples using RNA-seq, ATAC-seq and ChIP-seq for PU.1, H3K4me2, and H3K27ac. For patients from whom a sufficient cell number was obtained, we additionally cultured their microglia for up to 7 days and subjected these to the same suite of assays. In a follow-up study, we obtained brain tissue from a comparable cohort of pediatric epilepsy patients from Rady Children's hospital. We isolated nuclei from microglia, neurons, astrocytes and oligodendrocytes, and assayed for ATAC-seq, ChIP-seq for H3K4me3, and H3K27ac, and PLAC-seq (Proximity Ligated ChIP-seq).
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Versions (1)
- 2/9/23 2/9/23 - Simon Heim
Copyright Holder
Christopher K. Glass, MD, PhD, University of California, San Diego, CA, USA
Uploaded on
February 9, 2023
DOI
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License
Creative Commons BY 4.0
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dbGaP phs001373 Mechanisms Controlling Gene Expression of Human Microglia
The subject consent file includes subject IDs and consent information.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs and consent information.
- 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.
- This subject phenotype table contains subject ID, age, sex, race, primary diagnosis, and pathology.
- This sample attributes table contains sample ID, body site, analyte type, tumor status, histological type, name of the center which conducted sequencing, brain region, resected tissue, number of isolated microglia, assays, and isolation of whole cells or nuclei.
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The subject consent file includes subject IDs and consent information.
- StudyEvent: SEV1
- Eligibility Criteria
- The subject consent file includes subject IDs and consent information.
- 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.
- This subject phenotype table contains subject ID, age, sex, race, primary diagnosis, and pathology.
- This sample attributes table contains sample ID, body site, analyte type, tumor status, histological type, name of the center which conducted sequencing, brain region, resected tissue, number of isolated microglia, assays, and isolation of whole cells or nuclei.