characteristics.text: 3
characteristics.characteristic: BIOLOGICAL_REPLICATES
characteristics.text: ncim:C0549184
characteristics.characteristic: DISEASE_ONTOLOGY_CURIE
characteristics.text: https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI Metathesaurus&code=C0549184
characteristics.characteristic: DISEASE_ONTOLOGY_URI
characteristics.text: month
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UO_0000035
characteristics.characteristic: DONOR_AGE_UNIT
characteristics.text: ncim:C0549184
characteristics.characteristic: DONOR_HEALTH_STATUS_ONTOLOGY_CURIE
characteristics.text: https://ncim.nci.nih.gov/ncimbrowser/ConceptReport.jsp?dictionary=NCI Metathesaurus&code=C0549184
characteristics.characteristic: DONOR_HEALTH_STATUS_ONTOLOGY_URI
characteristics.text: adult
characteristics.characteristic: DONOR_LIFE_STAGE
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2022-01-24T00:26:33Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2022-01-24T00:26:33Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA11469579
characteristics.characteristic: External Id
characteristics.text: Center for Epigenomics Research, HKUST
characteristics.characteristic: INSDC center name
characteristics.text: 2022-01-24T00:26:33Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-01-24T00:26:33Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: uberon:0002421
characteristics.characteristic: SAMPLE_ONTOLOGY_CURIE
characteristics.text: http://purl.obolibrary.org/obo/UBERON_0002421
characteristics.characteristic: SAMPLE_ONTOLOGY_URI
characteristics.text: ERS9115484
characteristics.characteristic: SRA accession
characteristics.text: 93M_HIPPOCAMPUS
characteristics.characteristic: Submitter Id
characteristics.text: 3
characteristics.characteristic: biological replicate
characteristics.text: Leung lab, Hong Kong University of Science and Technology
characteristics.characteristic: biomaterial provider
characteristics.text: Primary Tissue
characteristics.characteristic: biomaterial type
characteristics.text: Hippocampus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0002421
characteristics.characteristic: brain_region_name
characteristics.text: MA:0000189
characteristics.characteristic: brain_region_ontology
characteristics.text: The animal was deeply anesthetized with Avertin (0.03 ml/g); the depth of anesthesia was assessed by the absence of deep tendon reflexes following a strong foot pinch. Once adequate anesthesia was achieved, the chest cavity was opened. The right atrium was clipped to allow exsanguination and the mouse was perfused through the left ventricle with PBS. Whole brain was obtained and cut into the left and right hemispheres. Each half was then dissected separately by eye. Hindbrain and cerebellum was first separated from the hemispheres, then cerebellum was obtained. The olfactory bulb was removed, along with brain stem regions until hippocampus was clearly visible. Hippocampus was obtained, and the remaining tissue was labelled as cerebral cortex. All collected tissue was snap frozen and stored at -80°C until nuclei extraction. For nuclei extraction, frozen tissue was added to 1 mL cold 1X homogenization buffer (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 16.7 μM PMSF, 167 μM β-mercaptoethanol, 1U/mL RNAse inhibitor in nuclease-free water) (modified from Corces et al., 2017). Tissue was dounced 10 strokes using loose pestle and 5 strokes using tight pestle (WHEATON® Dounce Tissue Grinder, 1 mL). Homogenate was filtered through a 40 μm cell strainer and spun down at 4°C, 1000g for 10 mins. Pellet was resuspended in 3mL of low sucrose buffer (0.32M sucrose, 10mM HEPES pH 8, 5mM CaCl2, 3mM Mg(Ac)2, 0.1mM EDTA, 1mM DTT, 0.2U/μL RNAse inhibitor in nuclease-free water) (modified from Matson et al., 2018). 12.5 mL of sucrose density buffer (1M sucrose, 10mM HEPES pH 8, 3mM Mg(Ac)2, 1mM DTT in nuclease-free water) was added slowly underneath the low sucrose buffer homogenate. The sucrose gradient was then centrifuged in a swing-bucket rotor at 4°C, 3200g for 20 min. The supernatant was decanted and pelleted purified nuclei was resuspended in buffer for sorting (0.2U/μL RNAse inhibitor, 1% BSA in PBS). Nuclei was stained with Hoechst at 2μg/uL.
characteristics.characteristic: collection method
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Hippocampus of mouse 93M
characteristics.characteristic: description
characteristics.text: 3
characteristics.characteristic: donor age
characteristics.text: 93M
characteristics.characteristic: donor id
characteristics.text: Male
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000384
characteristics.characteristic: donor sex
characteristics.text: 93M
characteristics.characteristic: mouse id
characteristics.text: 2020-11-07
characteristics.characteristic: mouse_sacrificial_date
characteristics.text: The most inclusive ontology term was used, but not all regions in the ontology are present in the tissue. Under hippocampal formation (ontology hierarchy), this sample is best represented by dentate gyrus, hippocampus region and hippocampus layer hippocampus.
characteristics.characteristic: notes_on_tissue
characteristics.text: 2021-01-06
characteristics.characteristic: nuclei_extraction_date
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: C57BL/6J
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000606
characteristics.characteristic: strain
characteristics.text: Hippocampal formation
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0002421
characteristics.characteristic: tissue depot
characteristics.text: Hippocampal formation
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0002421
characteristics.characteristic: tissue type
characteristics.text: 93M_HIPPOCAMPUS
characteristics.characteristic: title