EXPERIMENT_TITLE: Hi-C for LMNB1_untreated_rep1
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time points assessed for RNA-seq are 0-hour auxin, 12-hour auxin, 48-hour auxin, and 48-hour auxin with 6 days of auxin withdrawn. For Hi-C, the conditions tested are 0-hour auxin, 24-hour auxin, and 24-hour auxin with 6 days of auxin withdrawn.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_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "LMNB1 untreated 1"}, {"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_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: LMNB1_untreated_rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180330_HKN7M_SRLaminPool3-1_L003_R1.fastq.gz", "size": "2162462553", "date": "2024-02-27 00:52:01", "md5": "cc1c25b97d94e976b20ba5d72b6c126b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180330_HKN7M_SRLaminPool3-1_L003_R2.fastq.gz", "size": "2433899705", "date": "2024-02-27 00:52:32", "md5": "6d7e0e04595a2b01b581ff49e3fad87e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMT7_SRLaminPool3-1_L001_R1.recovered.cleaned.matched.fastq.gz", "size": "1614089211", "date": "2024-02-27 00:51:01", "md5": "e1767c0ef42d84e9c203de9c91d7e186", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMT7_SRLaminPool3-1_L001_R2.recovered.cleaned.matched.fastq.gz", "size": "1886971389", "date": "2024-02-27 00:51:35", "md5": "13c1b17ece9a230b935601dc28884d2d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMT7_SRLaminPool3-1_L002_R1.recovered.cleaned.matched.fastq.gz", "size": "1558320928", "date": "2024-02-27 00:51:18", "md5": "95489a93bde7d08aeab314d927491927", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMT7_SRLaminPool3-1_L002_R2.recovered.cleaned.matched.fastq.gz", "size": "1808101990", "date": "2024-02-27 00:53:06", "md5": "c5e691d9bc32e6dff949f16de23ebf7c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMT7_SRLaminPool3-1_L003_R1.recovered.cleaned.matched.fastq.gz", "size": "1553137455", "date": "2024-02-27 00:52:48", "md5": "9d54854cd4ad9dc7e41921faba1d63fb", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMT7_SRLaminPool3-1_L003_R2.recovered.cleaned.matched.fastq.gz", "size": "1785930136", "date": "2024-02-27 00:53:24", "md5": "477167fb9205b39f3386dd763bdb4f65", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR28106364", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR28106364/SRR28106364", "size": "10707294548", "date": "2024-02-27 00:56:48", "md5": "099ea62156a7480242f9dcc3d779272d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR28106364.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR028/28106/SRR28106364/SRR28106364.lite.1", "size": "6266336544", "date": "2024-02-27 02:14:46", "md5": "c37abce90c7865abb90dba537e660fac", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]