EXPERIMENT_TITLE: GSM4287673: K562-HiCoP1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For mouse CoP, thymus, spleen and kidney were removed,cells were filtered through nylon mech. Red cells were lysed in AcK buffer.Cells were crosslinked,lysates of CoP sample were clarified from sonicated nuclei and open chromatin were isolated with DNA purification column. For K562 CoP, cells were crosslinked,open chromatin were isolated with DNA purification column from sonicated nuclei. For K562 Hi-CoP, cells were crosslinked,digested and ligated. After sonication, open chromatin were isolated with DNA purification column. For mouse ATAC, thymus was removed,cells were filtered through nylon mech. Red cells were lysed in AcK buffer.Cells were perforated and dealed with Tn5, open chromatin were isolated with DNA purification column. The CoP libraries were prepared by either Tn5 tagmentation or linker ligation. Tagmentation was done with TransNGS Tn5 DNA Library Prep kit for Illumina following the manufacturer's recommendations. The reaction was incubated 5 min at 55 ºC followed by adding 30μl of 2x Tn5 Digestion Mix and incubated 5min at 55ºC, then purified with MagicPure Size Selection DNA Beads and elution in21 μL of water. After that, library (20 μL)was amplified by using TransNGS Library Amplification SuperMix. Alternatively, end repair and dA tailing were done with VAHTSTM Universal End preparation Module for Illumina. DNA was purified with VAHTS DNA Clean beads. Added adapter by Quick ligase, then library was amplified with PCR amplification kit. After 5 cycles of amplification, qPCR was done to determine additional cycle number. After library amplification, purification and size selection, library concentration was detected by Qubit. The libraries were sequenced by HiseqXten-PE150 Illumina sequencing platform in Novogene Corporation Inc. Hi-CoP libraries were prepared using in-situ HiC protocol. Dynabeads MyOne Streptavidin C1 beads was washed once with 1×Tween Washing Buffer. The beads were added to HiCoP DNA and incubated at RT for 15 min with rotation. The beads were washed by adding 200μl of 1×TWB. Heat the tubes on a Thermomixer at 55°C for 2 min with mixing. The beads were reclaimed using a magnet, supernatant was discarded. Repeat washing. End-repair and dA tailing following the in situ Hi-C protocol, adapters were added to DNA fragments. PCR amplification was performed with thirteen to nineteen cycles using Illumina primers. ATAC library was prepared according to Vazyme's instructions accompanying the TruePrep DNA Library Prep Kit V2 for Illumina (#TD501).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: First we developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of accessible regions by directly purifying fragmentized crosslinked chromatin with DNA purification column. The CoP chromatin regions by CoP-seq are consistent with the accessible regions detected by ATAC-seq and FARIE-seq. Then we integrated CoP-seq and Hi-C technique (Hi-CoP) for interactions of accessible chromatin regions which represent active cis-regulatory elements in cells. Our data showed that Hi-CoP assay can robustly detect interactions of regulatory regions. Overall design: Open chromatin were isolated with DNA purification column in K562 cell line and 4-12 weeks C57BL/6 WT mice thymocytes integrated Hi-C technique (Hi-CoP)or not.
SAMPLE_TITLE: K562-HiCoP1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "K562"}, {"TAG": "strain", "VALUE": "Cell line"}, {"TAG": "genotype", "VALUE": "wild type"}]
Pool_Member_@attributes_sample_title: K562-HiCoP1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: K562-HiCoP1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "K562-Hicop-Rep1_R1.fq.gz", "size": "12660693262", "date": "2020-01-28 20:13:19", "md5": "1bdaad2c76644e1eeb093eb0ebeed75c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "K562-Hicop-Rep1_R2.fq.gz", "size": "13429082973", "date": "2020-01-28 20:21:50", "md5": "c37e36b88d26b3c54c63a43f8681d8cd", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR10982078", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10982078/SRR10982078", "size": "14992848826", "date": "2020-01-28 20:36:03", "md5": "66db253a5257f932968cbdbda5b42920", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR10982078.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR010/10982/SRR10982078/SRR10982078.lite.1", "size": "11372768354", "date": "2022-06-23 14:34:34", "md5": "c5f6c51b1200f00257fc0348160ead77", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]