EXPERIMENT_TITLE: Hi-C for LMNB1_untreated_rep3
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The goal is to assess how gene expression changes upon auxin-induced loss of lamins B1 and B2. The time points assessed for RNA-seq are 0-hour auxin, 12-hour auxin, 48-hour auxin, and 48-hour auxin with 6 days of auxin withdrawn. For Hi-C, the conditions tested are 0-hour auxin, 24-hour auxin, and 24-hour auxin with 6 days of auxin withdrawn. These were collected for auxin-induced loss of lamin B1, lamin B2, and both lamin B1 and B2. The 48-hour auxin condition was only tested for auxin-induced loss of lamin B1 and B2.
SAMPLE_TITLE: LMNB1_untreated_rep3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "LMNB1 untreated 3"}, {"TAG": "age", "VALUE": "adult"}, {"TAG": "biomaterial_provider", "VALUE": "Erez Lieberman Aiden (Baylor College of Medicine); Masato Kanemaki (National Institute of Genetics); Vadim Backman (Northwestern University)"}, {"TAG": "collection_date", "VALUE": "2018-04-25"}, {"TAG": "geo_loc_name", "VALUE": "USA"}, {"TAG": "sex", "VALUE": "male"}, {"TAG": "tissue", "VALUE": "Large intestine; Colon"}, {"TAG": "cell_line", "VALUE": "HCT116 Lamin(B1)-AID"}, {"TAG": "cell_type", "VALUE": "epithelial"}, {"TAG": "disease", "VALUE": "Carcinoma; Colorectal"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
Pool_Member_@attributes_sample_title: LMNB1_untreated_rep3
RUN_SET_RUN_Pool_Member_@attributes_sample_title: LMNB1_untreated_rep3
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180330_HKN7M_SRLaminPool2-1_L002_R1.fastq.gz", "size": "439202726", "date": "2024-02-27 00:31:27", "md5": "32f0c465f9020aca0e01c60390e52edd", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180330_HKN7M_SRLaminPool2-1_L002_R2.fastq.gz", "size": "467743450", "date": "2024-02-27 00:31:31", "md5": "aaa20ab8d245c5159ae697265389e222", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-1_L006_R1.fastq.gz", "size": "406375495", "date": "2024-02-27 00:31:20", "md5": "761b9f8d45c1ad70fd0ccdb7f9188235", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-1_L006_R2.fastq.gz", "size": "433371824", "date": "2024-02-27 00:31:21", "md5": "9ab505624da73cb11cfeef6a9ae24ec7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-1_L007_R1.recovered.cleaned.matched.fastq.gz", "size": "344027024", "date": "2024-02-27 00:31:26", "md5": "d431f2fe1551216da3a7440ad502b640", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-1_L007_R2.matched.fastq.gz", "size": "369727703", "date": "2024-02-27 00:31:23", "md5": "5a0276d6e937f2dcf0f0fd3c4c02ccec", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-1_L008_R1.recovered.cleaned.matched.fastq.gz", "size": "323280394", "date": "2024-02-27 00:31:24", "md5": "e0abe0541e131127731dd7917b66f118", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-1_L008_R2.recovered.cleaned.matched.fastq.gz", "size": "349762877", "date": "2024-02-27 00:31:29", "md5": "b6c7c03d3419f8569114f8274867e4c1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR28106344", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR28106344/SRR28106344", "size": "2191200389", "date": "2024-02-27 00:31:45", "md5": "0d29b04ae6217f0f8615bf237370ecbf", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR28106344.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR028/28106/SRR28106344/SRR28106344.lite.1", "size": "1392656845", "date": "2024-02-27 02:08:52", "md5": "bea8274b38b0664277f3f0ea47a74557", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]