EXPERIMENT_TITLE: GSM5840593: HiC_TRP_15min_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In situ Hi-C was essentially performed as described  (Rao, S.S. et al, Cell 159, 1665-80 , 2014), using the restriction enzymes  MboI for Hexanediol Hi-C, or DpnII for flavopiridol and triptolide Hi-C. Hi-C DNA was purified on Dynabeads MyOne Streptavidin T1 beads (Thermo Fisher), and sequencing libraries were prepared using the KAPA HTP/LTP Library Preparation Kits.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Chromatin is partitioned into distinct topological domains in an activity-dependent manner, with  topological boundaries limiting the interaction between adjacent domains. Recent studies support the concept that several well-established nuclear compartments are assembled as ribonucleoprotein condensates. Here we ask whether the physical processes driving the assembly of the nuclear condensates play any role in three-dimensional chromatin architecture. We report that the insulation of approximately 20% of topological boundaries in human embryonic stem cells is substantially weakened following brief treatment with 1,6-hexanediol, a chemical known to disrupt several nuclear condensates. The disrupted boundaries are characterized by a high level of transcription, striking spatial clustering, and the augmented presence of transcription units widely expressed in diverse cell types. These topological boundary regions tend to be spatially associated, even inter-chromosomally,  and segregate with nuclear speckles. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring widely-expressed transcription units and associated transcriptional condensates. Overall design: Human RUES1 cells were treated with  either 7% 2,5-Hexanediol or 7% 1,6-Hexanediol for 5 minutes, washed with media, and  incubate with fresh media for additoinal time points at 37 deg C as indicated. Cells were subsuqently prccesed for in situ Hi-C, ChIp-seq, GRO-seq and PRO-seq. For transcription inhibition experiments, RUES1 cells were treated with either 5uM flavopiridol hydrochloride (F3055 Sigma) or 1uM triptolide (T3652 Sigma), for 15 minutes, 1 hour and 3 hours. Cells were then washed with PBS, cross-linked with 1% formaldehyde in PBS at room temperature for 10 min and neutralized with 0.125M glycine, and further proccessed for in situ Hi-C.
SAMPLE_TITLE: HiC_TRP_15min_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "human embryonic stem cells"}, {"TAG": "cell line", "VALUE": "RUES1"}, {"TAG": "treatment", "VALUE": "Triptolide 15 minutes"}]
Pool_Member_@attributes_sample_title: HiC_TRP_15min_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC_TRP_15min_rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "AG608_isHiC_RUES_TRP_15min_rep2_S56_L003_R1_001.fastq.gz", "size": "6521491450", "date": "2022-01-27 16:13:00", "md5": "2a49bbe9aa1711f10eda614612c60936", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "AG608_isHiC_RUES_TRP_15min_rep2_S56_L003_R2_001.fastq.gz", "size": "7066759136", "date": "2022-01-27 16:09:55", "md5": "653f0fa3a4271cd9facc927f41ffdd3d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR17786753", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR17786753/SRR17786753", "size": "8217165793", "date": "2022-01-27 16:15:35", "md5": "7e2e560745e3482eb43126b4c658d55f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR17786753.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR017/17786/SRR17786753/SRR17786753.lite.1", "size": "6151755749", "date": "2022-09-15 13:34:30", "md5": "b4b9404356f7c888353549941d8b44de", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]