EXPERIMENT_TITLE: GSM4782075: CTR2_HiC_Lib3; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: About one million monocytes were crosslinked by 40 ml 1% formaldehyde solution at room temperature for 10 min and 2.5 M Glycine was added to quench the crosslinking reaction. Supernatant was removed and the cells were washed three times by 1 X PBS. Crosslinked cells were resuspended in 500 µL of ice-cold Hi-C lysis buffer and rotated at 4 °C for 30 min. in situ MboI Hi-C were assembled based on Illumina-compatible protocols.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Although the Hi-C maps in cultured immune cell has been reported, there still lacks 3D landscape of human primary monocytes. The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison. We firstly presented the 3D genome structure heterogeneity in human primary monocytes. Significantly diversity of chromatin interaction in HLA complex region might regulates many immunologic processes. The chromatin loop regulation around CD16 and its relevant expression pattern indicated the CD16 associated monocyte functions are dominated regulated by this variable TAD boundary. Overall design: The peripheral blood from two health people and two SLE patients was collected and CD14+ monocytes were selected to perform Hi-C, RNA-seq, ATAC-seq and ChIP-seq. The raw data of THP1 cell Hi-C library was also used in comparison.
SAMPLE_TITLE: CTR2_HiC_Lib3
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "primary monocyte"}, {"TAG": "tissue", "VALUE": "peripheral blood"}, {"TAG": "cell type", "VALUE": "CD14+ monocytes"}, {"TAG": "disease state", "VALUE": "healthy"}, {"TAG": "age", "VALUE": "adult"}, {"TAG": "gender", "VALUE": "female"}]
Pool_Member_@attributes_sample_title: CTR2_HiC_Lib3
RUN_SET_RUN_Pool_Member_@attributes_sample_title: CTR2_HiC_Lib3
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CTR2_HiC_Lib3_R1.fastq.gz", "size": "77509321417", "date": "2020-09-16 00:44:38", "md5": "869c962021e6f35ad317453a733b0903", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CTR2_HiC_Lib3_R2.fastq.gz", "size": "85311378457", "date": "2020-09-16 01:29:03", "md5": "ca0270dea159bd3177fae22fee1a3987", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR12643327", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR12643327/SRR12643327", "size": "111547837702", "date": "2020-09-16 03:09:38", "md5": "0c664cd9102dafbda09b0e2cbb22e1be", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR12643327.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/SRR012/12643/SRR12643327/SRR12643327.lite.1", "size": "77272651102", "date": "2022-07-23 11:22:06", "md5": "bc7bf12ccba6270aa3c7dfa4f408e605", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]