EXPERIMENT_TITLE: GSM4280810: In_Situ_HiC_ in EPZ6438 treated CD34+; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were fixed by 1% formaldehyde, then isolated nucleus were cutted by MboI for 4hours, then isolated nuclear were end-filled with bio-dATP. Liagation was then performed overnight. Biotin enrichment was then performed with strepvadin beads. After washes, beads were tagmented by Tn5 enzyme for 10min at 55 degree. Libraries are amplified off the beads by PCR for 5 cycles, additional PCR is then applified with libraries under BioRad CF96 qPCR machine.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The overall goal is to understand how does the DNA methylation Canyon interactions in CD34+ HSPCs can be impacted by the inhibition of EZH2 Overall design: We has thus treat the CD34+ HSPCs in the ex vivo culture condition with DMSO and EZH2 inhibitor, we then utilzed the in situ HiC to detect the interactions of chromosomal loops, DNA methylation Canyons.We also use H3K27me3 ChIP-seq to detect the H3K27me3 in the EZH2 inhibitor treatment setting and use RNA-seq to test if the DNA methylation Canyon associated genes will be altered in the gene expresion
SAMPLE_TITLE: In_Situ_HiC_ in EPZ6438 treated CD34+
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "hematopietic progenitor and stem cells"}, {"TAG": "treatment", "VALUE": "EZH2 inhibitor EPZ6438"}]
Pool_Member_@attributes_sample_title: In_Situ_HiC_ in EPZ6438 treated CD34+
RUN_SET_RUN_Pool_Member_@attributes_sample_title: In_Situ_HiC_ in EPZ6438 treated CD34+
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CD34+_EPZ6438_HiC_R1_001.fastq.gz", "size": "28818807868", "date": "2020-01-23 19:31:09", "md5": "7fcf8bc1c5fd47de0abbbb5c84b86fab", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "CD34+_EPZ6438_HiC_R2_001.fastq.gz", "size": "29298112144", "date": "2020-01-23 18:50:41", "md5": "b66dc4a16054a94d72baae45e817d9d2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR10957040", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10957040/SRR10957040", "size": "39991243637", "date": "2020-01-23 20:24:58", "md5": "18ffb33f2046dc41f2d9463cb6e04a6d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR10957040.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR010/10957/SRR10957040/SRR10957040.lite.1", "size": "22354714821", "date": "2022-07-05 14:51:01", "md5": "591f1e989f35920112670e6b32f7703e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]