EXPERIMENT_TITLE: Illumina HiSeq 3000 paired end sequencing; H3K4me3 HiChIP for L3.6pl cells (parental and paclitaxel-resistant)
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Briefly, cells were washed with PBS and trypsinized. As a spike-in control, 1.25 millions of mouse NIH/3T3 cells were added to 5 million cells of Par and PacR cells in duplicates. Cells were fixed for 10 minutes with 1% Formaldehyde and suspended in ice-cold Hi-C Lysis Buffer . Streptavidin-C1 beads (Thermo Fisher) were used to capture biotinylated DNA, library preparation was performed using the MicroPlex Library Preparation Kit v2 (Diagenode)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Identification of TSS-centric interaction
SAMPLE_TITLE: HiChIP PacR
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "ENA-FIRST-PUBLIC", "VALUE": "2023-01-01"}, {"TAG": "ENA-LAST-UPDATE", "VALUE": "2023-01-01"}, {"TAG": "External Id", "VALUE": "SAMEA14381944"}, {"TAG": "INSDC center alias", "VALUE": "Mayo Clinic"}, {"TAG": "INSDC center name", "VALUE": "Mayo Clinic"}, {"TAG": "INSDC first public", "VALUE": "2023-01-01T00:28:00Z"}, {"TAG": "INSDC last update", "VALUE": "2023-01-01T00:28:00Z"}, {"TAG": "INSDC status", "VALUE": "public"}, {"TAG": "Submitter Id", "VALUE": "E-MTAB-11732:HiChIP PacR"}, {"TAG": "broker name", "VALUE": "ArrayExpress"}, {"TAG": "cell_line", "VALUE": "L3.6pl"}, {"TAG": "common name", "VALUE": "human"}, {"TAG": "developmental stage", "VALUE": "adult"}, {"TAG": "disease", "VALUE": "pancreatic adenocarcinoma"}, {"TAG": "genotype", "VALUE": "wild type genotype"}, {"TAG": "isolate", "VALUE": "not applicable"}, {"TAG": "organism part", "VALUE": "pancreatic duct"}, {"TAG": "phenotype", "VALUE": "paclitaxel resistant"}, {"TAG": "sample name", "VALUE": "E-MTAB-11732:HiChIP PacR"}, {"TAG": "sampling site", "VALUE": "celiac lymph node"}]
Pool_Member_@attributes_sample_title: HiChIP PacR
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiChIP PacR
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiChIP_H3K4me3_PacR.FCHHCJYBBXY_L8_R1_IGTGCTA.fastq.gz", "size": "3266936485", "date": "2023-01-10 04:28:52", "md5": "f1c6f6bd7bdd434471f0c4c6b451ae1a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiChIP_H3K4me3_PacR.FCHHCJYBBXY_L8_R2_IGTGCTA.fastq.gz", "size": "3758424679", "date": "2023-01-10 04:28:41", "md5": "6dbc7c3bead8cf3654f40f1d1ea5e5cf", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ERR9723959", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR9723959/ERR9723959", "size": "4216801091", "date": "2023-01-10 04:29:29", "md5": "0ac4fcbf15792c0e5a5370ad11275ea1", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "ERR9723959.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/ERR009/9723/ERR9723959/ERR9723959.lite.1", "size": "2607349171", "date": "2023-01-10 05:29:50", "md5": "c0998a276188b0c0a2d5062c8ac3549c", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]