EXPERIMENT_TITLE: GSM7035853: MOLM-13 shCTRL rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: After fixating the cells, cell lysis and isolation of nuclei, chromatin was restriction-digested, followed by Klenow fill-in and ligation of DNA fragments.DNA ligation products were sheared by sonication, repaired, and immunoprecipitated. DNA fragments were ligated to adapters, and the products were amplified by PCR.The amplified library was size-selected, enriched for promoter-containing ligation products, and amplied by PCR.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To investigate chromatin remodeling in AML cells following loss of P-bodies, we knocked down DDX6 in MOLM-13 cells. Overall design: Low input capture Hi-C of MOLM-13 cells
SAMPLE_TITLE: MOLM-13 shCTRL rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "MOLM-13"}, {"TAG": "cell line", "VALUE": "MOLM-13"}, {"TAG": "cell type", "VALUE": "AML"}, {"TAG": "genotype", "VALUE": "WT"}, {"TAG": "treatment", "VALUE": "shCTRL"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: MOLM-13 shCTRL rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: MOLM-13 shCTRL rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "MOLM13_shCTRL_1_R1.fq.gz", "size": "40239601367", "date": "2023-02-10 07:02:49", "md5": "90e1d4f9999e61de4d9dbc64b568b6b2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "MOLM13_shCTRL_1_R2.fq.gz", "size": "43580424844", "date": "2023-02-10 07:05:41", "md5": "7c86560b886258507e82af565025a6df", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR23381543", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR23381543/SRR23381543", "size": "57190932536", "date": "2023-02-10 07:25:19", "md5": "89310107059f05447e82f48af61b8aec", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR23381543.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR023/23381/SRR23381543/SRR23381543.lite.1", "size": "35959671720", "date": "2023-05-08 17:12:06", "md5": "9e0b4263267d3de24a39122c462a1399", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]