EXPERIMENT_TITLE: GSM4272417: A375_Bottom5_R1_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Briefly, 5 million of A375 cells subpopulations were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing. Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We investigated the effect of constricted migration (using transwell assays with 5-µm or 12-µm in diameter) on the organization of the 3D genome in melanoma and breast cancer cells. Overall design: Hi-C was performed to investigate changes in 3D genome organization after constricted migration. This experiment was performed on all sub-populations of A375 with two biological replicates per condition.
SAMPLE_TITLE: A375_Bottom5_R1_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Skin epithelium"}, {"TAG": "condition", "VALUE": "Bottom-5"}, {"TAG": "media", "VALUE": "DMEM,10%FBS,1% Pen-Strep, 1% L-Glut"}]
Pool_Member_@attributes_sample_title: A375_Bottom5_R1_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: A375_Bottom5_R1_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR10894094.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR010/894/SRR10894094.sralite.1", "size": "9894768486", "date": "2020-06-20 06:40:57", "md5": "da8b6870b5f8cb53b683e904a03e357e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR10894094", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10894094/SRR10894094", "size": "11733557870", "date": "2020-01-14 23:51:24", "md5": "464da1ed1fbe33f0f63d93a3cfd33bb5", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SequentialMig-A375-Bottom5-R1_S5_L001_R2_001.fastq.gz", "size": "10559289901", "date": "2020-01-14 23:40:46", "md5": "6000b8d5d6c7480ab0aee39e36b43e91", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SequentialMig-A375-Bottom5-R1_S5_L001_R1_001.fastq.gz", "size": "10141429538", "date": "2020-01-14 23:34:52", "md5": "66bd23b3d3970fc740acd7823db7aa66", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]