EXPERIMENT_TITLE: GSM4436417: WT_T47D_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For the in situ Hi-C, adherent cells were crosslinked with 1% formaldehyde in PBS for 10 min at room temperature. Glycine 0.125M was added for 5 min at room temperature and for 15 min at 4ºC to stop the crosslink reaction. Before permeabilization, cells were treated for 5 min with trypsin. Nuclei digestion was performed with 400 units of MboI restriction enzyme. The ends of the restriction fragments were labeled using biotinylated nucleotides and ligated with T4 DNA ligase. After reversal of crosslinks, DNA was purifed and sheared (Diagenode BioruptorPico) to obtain fragments of around 300-500 bp and ligation junctions were pull-down with streptavidin beads. Hi-C libraries were finally amplified, controlled for quality and prepared for sequencing using standard Illumina protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The topology of the genome in untreated T47D-MTVL cells expressing a Dox-inducible shRNA against multiple H1 variants was analyzed by performing a Hi-C experiment. The data allowed the obtention of Hi-C chromosome interaction maps, which were used to define TADs and A/B compartments, and to study the relationship between the 3D genome in breast cancer cells and other genomic properties as well as the histone H1 variants genome-wide distribution. Overall design: Stable breast cancer-derived cells expressing an shRNA against different histone H1 isoforms in response to doxycycline (Dox) were grown for six days in the absence of Dox. An in situ Hi-C library was subsequently prepared and high-throughput sequenced to study the 3D genome.
SAMPLE_TITLE: WT_T47D_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Breast cancer cell line"}, {"TAG": "tissue", "VALUE": "Breast cancer ductal carcinoma"}, {"TAG": "cell line", "VALUE": "T47D-MTVL"}, {"TAG": "dox treatment", "VALUE": "Untreated"}]
Pool_Member_@attributes_sample_title: WT_T47D_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: WT_T47D_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR11433769.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR011/11433/SRR11433769/SRR11433769.lite.1", "size": "9103098875", "date": "2022-07-16 04:12:35", "md5": "9b7a3fb5e17961da104fb1e0f20b26a5", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR11433769", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR11433769/SRR11433769", "size": "17379427243", "date": "2020-03-27 15:07:48", "md5": "98289f755b47c7caeb6c09052e92ed57", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "AJ_F01_33026_read2.fastq.gz", "size": "14495178423", "date": "2020-03-27 12:56:48", "md5": "6febee1fc16dfb07571ce8b0e2d3f16d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "AJ_F01_33026_read1.fastq.gz", "size": "14145501286", "date": "2020-03-27 13:13:26", "md5": "921a2ff4146c60c9e13eb8762c46e0c9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]