EXPERIMENT_TITLE: Hi-C for LMNB1-LMNB2_treated24hrs_withdraw_rep8
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time points assessed for RNA-seq are 0-hour auxin, 12-hour auxin, 48-hour auxin, and 48-hour auxin with 6 days of auxin withdrawn. For Hi-C, the conditions tested are 0-hour auxin, 24-hour auxin, and 24-hour auxin with 6 days of auxin withdrawn.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-LMNB2_treated24hrs_withdraw_rep8
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "isolate", "VALUE": "LMNB1+B2 withdraw 8"}, {"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&B2)-AID"}, {"TAG": "cell_type", "VALUE": "epithelial"}, {"TAG": "disease", "VALUE": "Carcinoma; Colorectal"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
Pool_Member_@attributes_sample_title: LMNB1-LMNB2_treated24hrs_withdraw_rep8
RUN_SET_RUN_Pool_Member_@attributes_sample_title: LMNB1-LMNB2_treated24hrs_withdraw_rep8
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR28106334.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR028/28106/SRR28106334/SRR28106334.lite.1", "size": "2486819806", "date": "2024-02-27 02:08:50", "md5": "2b56ba95079a7f1c7b9a18cb3578d210", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR28106334", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR28106334/SRR28106334", "size": "3966195506", "date": "2024-02-27 00:40:21", "md5": "e5b785ff9f79f968969442526b87647a", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-14_L008_R2.recovered.cleaned.matched.fastq.gz", "size": "1276831710", "date": "2024-02-27 00:39:40", "md5": "bf7c9824ca509644c16f3585e4157199", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-14_L007_R2.recovered.cleaned.matched.fastq.gz", "size": "1265970022", "date": "2024-02-27 00:39:48", "md5": "ac1e9ea08aba4888bb599a1706fadabd", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180406_HLMV5_SRLaminPool2-14_L006_R2.recovered.cleaned.matched.fastq.gz", "size": "1268355830", "date": "2024-02-27 00:39:43", "md5": "598066008f9c93dcad46f7c306d78e55", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "180330_HKN7M_SRLaminPool2-14_L002_R2.fastq.gz", "size": "1656063933", "date": "2024-02-27 00:39:52", "md5": "219e0992625be36e88ed1aa92b521937", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]