EXPERIMENT_TITLE: GSM5354335: HeLa_Hi-C_rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: RNA was harvested using Trizol reagent. Cells were croseelinked with 1% formaldehyde for 10 minutes at room temperature. For Hi-C, we followed in-situ Hi-C protocol, the cells were lysed. Then the lysed cells were digested by MboI overnight at 37℃. DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature for 4 hours. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. For NicE-seq, the cells were lysed and then digested by Nt.CviPII and DNA polemerase I (Ecoli)  with dGTP, dTTP, biotin-dATP, biotin-dCTP and 5-methyl-dCTP for 20 min at 37℃. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. For NicE-C,  the cells were lysed and then digested by Nt.CviPII and DNA polemerase I (Ecoli)  with dGTP, dTTP, dATP and 5-methyl-dCTP for 20 min at 37℃. DNA fragment ends were filled with dNTP and dA-tailing was performed. Proximity ligation by bridge-linker was performed at room temperature for 4 hours. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. Hi-C, NicE-C and NicE-seq DNA were sonicated and binding to M280 beads, then end-repair, dA-tailing and adapter ligation on beads. After PCR amplification and DNA purification, the libraries were sequenced on Illumina NovaSeq 6000 using 150bp paired-end reads. RNA libraries were prepared for sequencing using standard Illumina protocols
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Enhancer-promoter communication is known to regulate spatiotemporal gene expression. Here, we present NicE-C, a method that leverages nicking enzyme mediated open chromatin profiling and chromosome conformation capture to enable robust and cost-effective detection of chromatin interactions among open chromatin regions (e.g., between enhancers and promoters). Demonstrating its application utility, NicE-C revealed dynamic enhancer-promoter interactions associated with gene expression changes after TNF? stimulation in HeLa cells and during aging process in mice kidney. Overall design: NicE-C  are generated for HeLa cells, HeLaS3 cells with or without TNFa stimulation, IMR90 cells, Mice kidney of young and old mice. RNA-seq are generated for HeLa cells, HeLaS3 cells with or without TNFa stimulation and kidney of young and old mice. HiC and  NicE-seq are generated for HeLa cells.
SAMPLE_TITLE: HeLa_Hi-C_rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HeLa cells"}, {"TAG": "cell line", "VALUE": "HeLa"}]
Pool_Member_@attributes_sample_title: HeLa_Hi-C_rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HeLa_Hi-C_rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14714486.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/SRR014/14714/SRR14714486/SRR14714486.lite.1", "size": "14776844317", "date": "2022-07-28 06:52:58", "md5": "af93b90aef6b4c031ea12d0a788640ab", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14714486", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14714486/SRR14714486", "size": "18758260009", "date": "2021-06-04 11:44:18", "md5": "dae05601bb0af9f8a5d73b573032da32", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HeLa_Hi-C_rep2_R2.fastq.gz", "size": "16570824430", "date": "2021-06-04 11:32:26", "md5": "b9563747c964e2032600d79bd546723e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HeLa_Hi-C_rep2_R1.fastq.gz", "size": "15888174818", "date": "2021-06-04 11:23:32", "md5": "5924c82cb9817c402350b95addbdfd56", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]