EXPERIMENT_TITLE: Hi-C for LMNB2_treated24hrs_rep4
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time points assessed for RNA-seq are 0-hour auxin, 12-hour auxin, 48-hour auxin, and 48-hour auxin with 6 days of auxin withdrawn. For Hi-C, the conditions tested are 0-hour auxin, 24-hour auxin, and 24-hour auxin with 6 days of auxin withdrawn.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: LMNB2_treated24hrs_rep4
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "LMNB2 24 hours 4"}, {"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(B2)-AID"}, {"TAG": "cell_type", "VALUE": "epithelial"}, {"TAG": "disease", "VALUE": "Carcinoma; Colorectal"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
Pool_Member_@attributes_sample_title: LMNB2_treated24hrs_rep4
RUN_SET_RUN_Pool_Member_@attributes_sample_title: LMNB2_treated24hrs_rep4
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180330_HKN7M_SRLaminPool2-8_L002_R1.fastq.gz", "size": "452125387", "date": "2024-02-27 00:33:34", "md5": "a765cc325958d14dd07bb892f3198862", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180330_HKN7M_SRLaminPool2-8_L002_R2.fastq.gz", "size": "469810428", "date": "2024-02-27 00:33:36", "md5": "a414bc923615be58507e888191fcda0e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-8_L006_R1.recovered.cleaned.matched.fastq.gz", "size": "333592767", "date": "2024-02-27 00:33:29", "md5": "aaa6085e34a1864300d8e3b6a9359888", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-8_L006_R2.recovered.cleaned.matched.fastq.gz", "size": "347668827", "date": "2024-02-27 00:33:31", "md5": "c0e89edb5dd9b4d20b82314c163835e1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-8_L007_R1.recovered.cleaned.matched.fastq.gz", "size": "336241299", "date": "2024-02-27 00:33:39", "md5": "686c35641d45a6807e68a124c4fa04b1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-8_L007_R2.recovered.cleaned.matched.fastq.gz", "size": "352087419", "date": "2024-02-27 00:33:41", "md5": "0118075d598df37da0d16c999f0f482a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-8_L008_R1.recovered.cleaned.matched.fastq.gz", "size": "347310401", "date": "2024-02-27 00:33:43", "md5": "43de745f297e8b906cb1a35ae790fbd2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-8_L008_R2.recovered.cleaned.matched.fastq.gz", "size": "367734111", "date": "2024-02-27 00:33:45", "md5": "4aaf1b5dac50e9d483a2023fb5756d28", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR28106357", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR28106357/SRR28106357", "size": "2146422118", "date": "2024-02-27 00:34:04", "md5": "c8a1bf04d9b7d8dd7ec7877c8d584bb7", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR28106357.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR028/28106/SRR28106357/SRR28106357.lite.1", "size": "1397082362", "date": "2024-02-27 02:08:36", "md5": "ba3716400aa62c27078afac0a9560f71", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]