EXPERIMENT_TITLE: GSM5258489: WT_T47D_HiC_3; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For the in situ Hi-C, adherent cells were crosslinked with 1% formaldehyde in PBS for 10 min at room temperature. Glycine 0.125M was added for 5 min at room temperature and for 15 min at 4ºC to stop the crosslink reaction. Before permeabilization, cells were treated for 5 min with trypsin. Nuclei digestion was performed with 400 units of MboI restriction enzyme. The ends of the restriction fragments were labeled using biotinylated nucleotides and ligated with T4 DNA ligase. After reversal of crosslinks, DNA was purifed and sheared (Diagenode BioruptorPico) to obtain fragments of around 300-500 bp and ligation junctions were pull-down with streptavidin beads. Hi-C libraries were finally amplified, controlled for quality, and prepared for sequencing using standard Illumina protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The combined depletion of histones H1.2 and H1.4 in T47D-MTVL human breast cancer cells has a strong deleterious effect, deregulates gene expression, promotes the appearance of genome-wide accessibility sites, and triggers the interferon response. We have further analyzed the consequences of multiple H1 variants depletion at the topological level by performing Hi-C experiments on T47D-MTVL cancer cells expressing a Dox-inducible shRNA against multiple H1 variants. Overall design: Stable breast cancer-derived cell lines expressing an shRNA against different histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the presence or absence of Dox. Three Hi-C libraries were subsequently prepared and high-throughput sequenced.
SAMPLE_TITLE: WT_T47D_HiC_3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Breast cancer cell line"}, {"TAG": "tissue", "VALUE": "Breast cancer ductal carcinoma"}, {"TAG": "cell line", "VALUE": "T47D-MTVL"}, {"TAG": "dox treatment", "VALUE": "Untreated"}]
Pool_Member_@attributes_sample_title: WT_T47D_HiC_3
RUN_SET_RUN_Pool_Member_@attributes_sample_title: WT_T47D_HiC_3
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