EXPERIMENT_TITLE: GSM3453680: 24hr_donor1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Naïve CD4 T cells were fixed by culture medium containing 1% formaldehyde for 5 minutes at room temperature and quenched by Tris (pH8.0). Nuclei were then isolated and subjected to SDS permeabilization followed by TritonX-100 to quench SDS. After that, nuclei pellets were subjected to HindIII digestion and re-ligation, at which step the biotin-dCTP was induced into the de novo ligation sites. Newly re-ligated genomic DNA were purified and sheared into 200bp fragments and fragments containing biotin-labeled de novo ligation sites were purified by M280 streptavidin beads (Invitrogen) and subjected to library preparation. DNA fragment was subjected to end-repair and biotin-remove by a master mix containing T4 DNA ligase buffer, dNTP mix, T4 PNK, T4 DNA Polymerase I and DNA polymerase I Large (Klenow) Fragment. Then dATP was attached to fragment end by Klenow exo minus enzyme. Resulted DNA fragment was ligated with Illumina indexed adaptors and amplified using Illumina PCR primer 1 and 2.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We report chromatin interaction changes before and early after naïve CD4 T cell activation. Overall design: Human naïve CD4 T cells were isolated from periphery blood of 4 healthy donors. Cells were activated by CD3/CD28 beads for 0, 8 or 24 hours. 10 million cells were collected for HiC sequencing library preparation at each time point.
SAMPLE_TITLE: 24hr_donor1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human na\u00efve CD4 T cells"}, {"TAG": "individual", "VALUE": "donor1"}, {"TAG": "cell type", "VALUE": "naive CD4 T cells"}, {"TAG": "treatment", "VALUE": "activated by CD3/CD28 beads"}, {"TAG": "time", "VALUE": "24hr"}]
Pool_Member_@attributes_sample_title: 24hr_donor1
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