EXPERIMENT_TITLE: GSM7496018: in situ Hi-C of DSMZ's NB-4 cell line with no stimulation; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Sample was processed using Arima-HiC Kit, Library Preparation using Swift Biosciences® Accel-NGS® 2S Plus DNA Library Kit [Arima A510008] . Sample was lysed and crosslinked followed by restriction enzyme digestion and ligation. Ligated DNA was purified, sheared, and used for library generation using Active Motif Next Gen DNA Library Kit [Active Motif 53216].
STUDY_DESCRIPTOR_STUDY_ABSTRACT: This Hi-C experiment was a part of a research which analyzed chromosomal structural aberrations in hematological malignancies. First, the author conducted comprehensive detection of fusion transcripts in RNA-seq data of DSMZ's 99 cell lines, and then picked up cell lines with characteristic complex karyotype. NB-4 cell line is one of them, which shows characteristic fusion cluster in 8q24 region in the fusion detection step. This Hi-C experiment revealed amplifications of MYC, PVT1, and CCDC26 in 8q24 region. Additionally, several structural aberrations were found by scanning the whole genome. Overall design: in situ Hi-C of DSMZ's NB-4 cell line with no treatment
SAMPLE_TITLE: in situ Hi-C of DSMZ's NB-4 cell line with no stimulation
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "bone marrow"}, {"TAG": "tissue", "VALUE": "bone marrow"}, {"TAG": "cell line", "VALUE": "NB-4"}, {"TAG": "cell type", "VALUE": "acute promyelocytic leukemia"}, {"TAG": "genotype", "VALUE": "WT"}, {"TAG": "treatment", "VALUE": "no treatment"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: in situ Hi-C of DSMZ's NB-4 cell line with no stimulation
RUN_SET_RUN_Pool_Member_@attributes_sample_title: in situ Hi-C of DSMZ's NB-4 cell line with no stimulation
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