EXPERIMENT_TITLE: GSM2627273: CD4_stimulated_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were cross-linked with 1% formaldehyde for 10 minutes at RT. 10 X 106 cells were lysed in 10 ml lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP40; 10 μl protease inhibitors (Sigma)) with rotation at 4°C for 60 minutes. The cells were then treated with 400 μl 1X NEB cutsmart buffer with 0.1% SDS at 65°C for 10 minutes, followed by addition of 44 μl 10% Triton X-100 to quench SDS. Chromatin was subsequently digested with 20 Units 4 cutters (NEB). The reaction was stopped by washing the cells twice with 600 ml wash buffer. After reversing crosslink, the purified DNA were ready for the library preparation. The libraries were processed same as Hi-C protocol (Lieberman-Aiden et al., 2009, Science. 2009 Oct 9;326(5950):289-93)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Interaction between different chromatin regions plays critical roles in genome organization and regulation of transcription. Existing technologies of analyzing genome-wide chromatin interactions rely on in vitro proximity-based ligation of interacting chromatin fragments and thus are prone to potential artifacts. We now report a novel technique, Transposase-mediated Analysis of Chromatin loops (TrAC-loop), for detection of genome-wide chromatin interactions between regulatory regions. With this technique, a bivalent oligonucleotide linker is inserted between two interacting chromatin regions such that the distant interacting chromatin regions can be directly amplified by PCR and thus avoids the prior chromatin fragmentation and subsequent error-prone re-ligation steps. TrAC-loop selectively targets accessible regions, which effectively reduces the sequencing cost for detecting promoter-enhancer interactions at high resolution. Application of TrAC-loop to human CD4+ T cells reveals a substantial reorganization of enhancer-promoter interaction associated with changes in gene expression upon TCR stimulation. Overall design: Examination of enhancer-promoter interaction associated with changes in gene expression upon TCR stimulation.
SAMPLE_TITLE: CD4_stimulated_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "blood"}, {"TAG": "tissue", "VALUE": "blood"}, {"TAG": "cell type", "VALUE": "CD4+ T cells"}, {"TAG": "treatment", "VALUE": "stimulated"}, {"TAG": "fixation", "VALUE": "fixed"}]
Pool_Member_@attributes_sample_title: CD4_stimulated_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: CD4_stimulated_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5558587", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5558587/SRR5558587", "size": "3921781538", "date": "2017-05-15 08:57:34", "md5": "5ba2cb255f553088fa890c7aa21b99cc", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5558587.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/558/SRR5558587.sralite.1", "size": "2448459810", "date": "2020-06-22 11:41:13", "md5": "c800811466a59ea55989c2a1db616002", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "KZ1242_GA9078_S15_L007_R2_001.fastq.gz", "size": "3568744951", "date": "2020-03-27 13:52:27", "md5": "7ea371854ce087912e596ebc42b68b73", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "KZ1242_GA9078_S15_L007_R1_001.fastq.gz", "size": "3050250707", "date": "2020-03-27 14:28:43", "md5": "65e719d720e1d78994c09b665715f1af", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]