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 Par
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": "SAMEA14381945"}, {"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 Par"}, {"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 susceptible"}, {"TAG": "sample name", "VALUE": "E-MTAB-11732:HiChIP Par"}, {"TAG": "sampling site", "VALUE": "celiac lymph node"}]
Pool_Member_@attributes_sample_title: HiChIP Par
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiChIP Par
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiChIP_H3K4me3_L3_6.FCHHCJYBBXY_L8_R1_IACTTGA.fastq.gz", "size": "3750731249", "date": "2023-01-10 04:56:58", "md5": "7dd95b531deb4c318ce638601c255101", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiChIP_H3K4me3_L3_6.FCHHCJYBBXY_L8_R2_IACTTGA.fastq.gz", "size": "4261337741", "date": "2023-01-10 04:57:38", "md5": "5b2c1986b43fb5e6de11de6d0050aeab", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ERR9723960", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/ERR9723960/ERR9723960", "size": "4814295512", "date": "2023-01-10 04:59:31", "md5": "5ee5aab24b5537c7006a97587cf7ef37", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "ERR9723960.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/ERR009/9723/ERR9723960/ERR9723960.lite.1", "size": "3050055948", "date": "2023-01-10 05:32:44", "md5": "e69bd8a1f6cd6942cbeb3e2620cad665", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]