EXPERIMENT_TITLE: GSM3380628: control sample for ActD treatment rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C libraries were generated with the in-situ ligation using the HindIII restriction enzyme (PMID: 28435001), Briefly, after crosslinking the cells with 1% formaldehyde for 10 minutes at room temperature, the nuclei were extracted by dounce homogenization. Next, the chromatin was digested with HindIII either in the presence of 500μg RNase A (Qiagen #19101), or 30U of RNase Inhibitor (NEB, #M0314L).  These samples that are treated after formaldehyde crosslinking (aXL) are referred as “aXL RNase A” and “aXL CTRL”, respectively. The bXL samples were processed according to the original protocol(PMID: 28435001). The digested chromatin was then end-labelled with biotin-14-dCTP (Thermo Fisher 19519016), and in-situ ligation was performed. Extraction of the DNA was performed by phenol-chloroform extraction, and the biotin was removed from unligated ends, followed by shearing of the DNA by using a Covaris S220 instrument to 100-500bp size range. After A-tailing, biotin pull-down and adapter ligation, paired-end sequencing was performed on a HiSeq instrument. Hi-C libraries for each condition were generated in two biological replicates.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Nuclear RNA and the act of transcription have been implicated in nuclear organization. However, their global contribution to shaping fundamental features of higher-order genome structure such as topologically associated domains (TADs) and genomic compartments remains unclear. To investigate these questions, we perform Hi-C genome-wide chromatin conformation capture in the presence and absence of RNase before and after crosslinking, or a transcriptional inhibitor. TAD boundaries are largely unaffected by RNase treatment, whereas transcriptional inhibition leads to higher inter-TAD interactions. Collectively, our findings demonstrate differences in the relative contribution of RNA and transcription to the formation of TAD boundaries detected by the widely used Hi-C methodology. Overall design: Hi-C in RNase treated and transcriptionally inhibited K562 cells Please note that the processed data was generated from both replicates together and is linked to the corresponding *rep1 sample records.
SAMPLE_TITLE: control sample for ActD treatment rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "control sample for ActD treatment"}, {"TAG": "cell line", "VALUE": "K562"}, {"TAG": "condition", "VALUE": "control sample for ActD treatment"}]
Pool_Member_@attributes_sample_title: control sample for ActD treatment rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: control sample for ActD treatment rep2
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