EXPERIMENT_TITLE: GSM6846888: BLaER cells non-induced, rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were collected by centrifugation and wahed twice with fresh medium Cells were collected and crosslinked with 1% formaldehyde. Nuclei were digested with MboI followed by fill-in with bio-dATP, in-situ ligation and DNA extraction. DNA was sonicated and libraries were constructed using the the NEBNext DNA Library Prep Kit (New England Biolabs). Libraries were amplified for 8-12 cycles using Illumina TruSeq primers. Amplified libraries were purified and size-selected (>250bp) using Ampure XP beads.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Cell identity is orchestrated through an interplay between transcription factor (TF) action and genome architecture. The mechanisms used by TFs to shape three-dimensional (3D) genome organization remain incompletely understood. Here we present evidence that the lineage-instructive TF CEBPA drives extensive chromatin compartment switching and promotes the formation of long-range chromatin hubs during induced B cell to macrophage transdifferentiation. A large intrinsically disordered region (IDR) enables CEBPA to undergo in vitro phase separation and to co-condense with transcriptional partners, which is at least partially mediated by aromatic residues. Furthermore, CEBPA forms visible nuclear condensates in transdifferentiating B cells that co-localize with co-activator condensates and recover rapidly upon photobleaching. Finally, native CEBPA-expressing cell types such as primary granulocyte-macrophage progenitors (GMPs), liver cells and trophectoderm cells also reveal nuclear CEBPA condensates and long-range 3D chromatin hubs at CEBPA-bound regions. These findings support a model in which CEBPA acts as a 3D genome structural organizer and suggest that this effect is mediated at least in part by its phase-separation capacity. Overall design: HiC datasets were generated from BLaER cells knocked out for a CEBPA binding site in the FGGY locus  before and after 24h of CEBPA induction (n=2)
SAMPLE_TITLE: BLaER cells non-induced, rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "BLaER KO"}, {"TAG": "cell line", "VALUE": "BLaER KO"}, {"TAG": "cell type", "VALUE": "B cells"}, {"TAG": "treatment", "VALUE": "none"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: BLaER cells non-induced, rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: BLaER cells non-induced, rep1
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