EXPERIMENT_TITLE: GSM5582264: Ortho-E_HiC_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cell populations of distinct differentiation stages were isolated by the following cell surface markers: Pro-E cells are CD235a+CD71+CD45lowCD36+CD117highCD105high; Baso-E cells are CD235a+CD71+CD45lowCD36+CD117dimCD105dim; Poly-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSChigh; Ortho-E cells are CD235a+CD71+CD45lowCD36+CD117-CD105-FSClow. Hi-C assay was carried out using the in-situ method as described before with minor modifications17. Half a million FACS-purified primary erythroblasts were used for each reaction. In brief, after fixation with 1% formaldehyde, cells were digested overnight at 37°C using 50U of MboI (NEB, Cat. #R0147). After biotin filling, proximity ligation was carried out overnight at 25 °C with 1600U T4 DNA Ligase (Vazyme, Cat. # N103-01). After reverse-crosslinking, DNA was purified and sheared to 300-500bp fragments using Covaris M220 sonicator. Ligation fragments containing biotin were immobilized on MyOne Streptavidin C1 beads (ThermoFisher Cat. #: 65602), and then library preparation was performed using the DNA library preparation kit (Vazyme, Cat.# ND607) as per the manufacturer's protocol. DNA was then subjected to double-size selection using DNA Clean Beads (Vazyme, Cat. # N411) in order to isolate fragments between 300 and 600bp.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Erythropoiesis in mammalian involves chromatin compaction which is initiated in the early stage of terminal differentiation. The proper condensation of chromatin is essential for the subsequent enucleation of erythroblast, but the characteristics of chromatin compaction and chromatin architecture changes in erythropoiesis are poorly understood. Here, we show that the formation of H3K9me3 long-range interactions which mediated heterochromatin three-dimensional rewiring participant in human erythroid chromatin condensation. TADs structure attenuated and boundary strength weakened globally but selectively maintaining in active chromatin region during terminal erythropoiesis. We demonstrate that the erythroid master regulators GATA1 safeguard the active chromatin structure and ensure the appropriate gene expression, under the chromatin condensation of human terminal erythropoiesis Overall design: Hi-C was performed on human Pro-, Ortho-erythroblast, KO-GATA1 and KO-control samples, and each sample has 2 replicates. The KO-KLF1 sample only has one replicate.
SAMPLE_TITLE: Ortho-E_HiC_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "cord blood"}, {"TAG": "cell type", "VALUE": "orthochromatic erythroblast"}, {"TAG": "tissue", "VALUE": "cord blood"}, {"TAG": "treatment", "VALUE": "no"}]
Pool_Member_@attributes_sample_title: Ortho-E_HiC_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Ortho-E_HiC_rep2
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