EXPERIMENT_TITLE: GSM5912783: pancreatic cancer PATC53 replicate 1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Extraction of cell nucleus and DNA were performed as described (Rao et al. 2014). Hi-C was performed as described (Rao et al. 2014).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Inhibition of histone acetyltransferase has been widely used to be effectively treat cancers in many studies. However, it's not clear how the downstream signaling responds to the inhibitor in pancreatic cancer. Here we performed Hi-C experiments to canonical and patient-derived pancreatic cancer cells with the treatment of small molecule inhibitor ICG-001 which has dual function to block both WNT signaling and histone acetyltransferase. This is in situ Hi-C dataset. Overall design: Pancreatic cancer cell line PANC1, and newly established cell lines from patient-derived tumor xenograft (PATX) program PATC53 were treated with ICG-001 at the concentration of 10 µM for 48 hours. Then in situ Hi-C experiments were performed for these cells.
SAMPLE_TITLE: pancreatic cancer PATC53 replicate 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "PATC53"}, {"TAG": "cell line", "VALUE": "PATC53"}, {"TAG": "cell type", "VALUE": "immortalized pancreatic cell line"}, {"TAG": "treatment", "VALUE": "untreated"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: pancreatic cancer PATC53 replicate 1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: pancreatic cancer PATC53 replicate 1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "PATC53_Rep1_R1.fastq.gz", "size": "11187392501", "date": "2022-02-24 03:49:09", "md5": "16b42edebe39b03dada7001c6511c5cd", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "PATC53_Rep1_R2.fastq.gz", "size": "12200403607", "date": "2022-02-24 04:20:27", "md5": "abaa9991ea80d6bfec9f487dd0ada9d4", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18115318", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18115318/SRR18115318", "size": "14111886230", "date": "2022-02-24 04:59:44", "md5": "5c090c24e9302330354f651929e8065b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18115318.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR018/18115/SRR18115318/SRR18115318.lite.1", "size": "8568494190", "date": "2022-10-20 06:50:36", "md5": "c26d447825bd72de3d26d9aba05aa8b8", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]