EXPERIMENT_TITLE: GSM6255136: Stimulated microglia - pcHi-C_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were harvested, fixed in 1% formaldehyde, snap frozen in dry ice, then stored at -80C. Nuclei extraction was performed prior to further processing. In situ Hi-C was performed using the standard protocol, then 500 ng of the resulting libraries were used to prepare pcHi-C using a custom biotinylated RNA probe set. In In situ Hi-C followed by pcHi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Alzheimer's disease (AD) is an age-related neurodegenerative progressive disorder affecting 10% of people over 65. Less than 5% of patients have known causal genetic mutations while the exact cause of AD for the majority of patients, especially the late onset form, is unknown. Large scale epigenomic studies revealed that disease associated SNPs are highly enriched in cell-type-specific cis-regulatory elements. In AD, SNPs are more significantly enriched in the regulatory regions of myeloid lineages rather than the neuronal cells. However, how AD SNPs affect microglia enhancers, and more interestingly differentially affect state-specific enhancers such as activated upon stimulation, e.g. viral infection, remain largely unexplored. In this study we identified cis-regulatory elements in both resting and IFN-beta stimulated microglia and further functionally characterized how regulatory SNPs lead to immune response dysregulation in the pathogenesis of AD. Overall design: Examination of chomatin interactions in both resting and IFN-beta stimulated human iPSC derived microglia
SAMPLE_TITLE: Stimulated microglia - pcHi-C_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "WTC11 iPSC-derived Microglia"}, {"TAG": "cell type", "VALUE": "Microglia"}, {"TAG": "cell line", "VALUE": "WTC11 iPSC-derived Microglia"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Stimulated microglia - pcHi-C_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Stimulated microglia - pcHi-C_rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR19754377.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR019/19754/SRR19754377/SRR19754377.lite.1", "size": "19774536631", "date": "2022-10-18 03:10:22", "md5": "14a0a38dca93f202fabc025b16b6d3ed", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR19754377", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR19754377/SRR19754377", "size": "24954078227", "date": "2022-06-20 21:15:49", "md5": "12aad870663c15c958d9c74acccc442c", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "IJ382_S15_L002_R2_001.fastq.gz", "size": "21291463379", "date": "2022-06-20 21:13:57", "md5": "c8c07a04270c38cf202168ef394f28c4", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "IJ382_S15_L002_R1_001.fastq.gz", "size": "20190938687", "date": "2022-06-20 21:12:55", "md5": "29e6a65991ea34bb1073d597b544b46b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]