EXPERIMENT_TITLE: GSM3753209: Biosample_8606_4132_58664_HYL2CBGX2_K562_InSituHiC_NHS_1_ATCACG; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were crosslinked with 1% formaldehyde for 10 min, quenched and permeabilized. Nuclei were digested with MboI and ends were biotinylated with biotin-14-dATP followed by in-situ ligation. Crosslinks were reversed and DNA was purified, sonicated and pulled down by streptavidin beads. DNA was end repaired with T4 DNA polymerase, DNA polymerase I large (Klenow) polymerase and T4 polynucleotide kinase. DNA ends were adenylated by dATP and Klenow (3'-5' exo-) polymerase. Illumina Truseq adapters were ligated to the DNA ends and PCR amplified for 10 cycles. Library was purified with Qiaquick PCR purfication kit and sequenced on Illumina Nextseq 500.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Heat shock (HS) causes dramatic and rapid changes in transcription of thousands of genes in metazoans. We have used insitu Hi-C in Drosophila S2 and human K562 cells to determine the effects of HS upon chromatin conformation. Our study shows that topologically associated domains (TADs), compartments and distal regulatory interactions remain unchanged upon HS. Overall design: Investigate changes in chromatin conformation upon acute HS in Drosophila S2 and human K562 cells by insitu Hi-C. Two biological replicates were done for Non heat shock (NHS) or HS conditions in each organism.
SAMPLE_TITLE: Biosample_8606_4132_58664_HYL2CBGX2_K562_InSituHiC_NHS_1_ATCACG
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "K562 immortalized cell line"}, {"TAG": "cell line", "VALUE": "K562"}]
Pool_Member_@attributes_sample_title: Biosample_8606_4132_58664_HYL2CBGX2_K562_InSituHiC_NHS_1_ATCACG
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Biosample_8606_4132_58664_HYL2CBGX2_K562_InSituHiC_NHS_1_ATCACG
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