EXPERIMENT_TITLE: GSM7104841: NK92_SAHA_HiC_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Fixed chromatin was digested using DpnII enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and captured with Streptavidin C-1 beads. Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500 platform.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Purpose: The aim of this study is to examine the complex transcriptional network of NK cells in the context of 3D chromatin architecture. Conclusions: HDAC inhibitor reshape transcriptional profile through long-range enhancer-promoter interactions in natural killer cells Overall design: Hi-C profiles of untreated control and SAHA treated cells with biological replicates.
SAMPLE_TITLE: NK92_SAHA_HiC_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "NK92"}, {"TAG": "cell type", "VALUE": "NK Cells"}, {"TAG": "passages", "VALUE": "12 passages"}, {"TAG": "cell line", "VALUE": "NK92"}, {"TAG": "treatment", "VALUE": "SAHA treated"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: NK92_SAHA_HiC_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: NK92_SAHA_HiC_rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR23908065.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-3/SRR023/23908/SRR23908065/SRR23908065.lite.1", "size": "16019203855", "date": "2023-06-02 08:40:07", "md5": "b59fdcf9b04e5f5d4cac2233a0d05c11", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR23908065", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR23908065/SRR23908065", "size": "24345921287", "date": "2023-03-19 16:58:00", "md5": "9ec6c69e8057327d086f551c6e31c2dc", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NK92_SAHA_HiC_rep2_2.fastq.gz", "size": "19337635109", "date": "2023-03-19 16:54:14", "md5": "1786ff2a34284b653daa518e1cf12b99", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "NK92_SAHA_HiC_rep2_1.fastq.gz", "size": "18282810466", "date": "2023-03-19 16:54:47", "md5": "852388889f3de6dade8ff41ef911ff5f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]