EXPERIMENT_TITLE: GSM6402443: PDS5A-dTAG, dTAG, rep1_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were crosslinked using 1% formaldehyde, followed by quenching with 125 mM glycine for 5 min.Cells were penetrated and nuclei restriction reaction was performed overnight using DpnI digested DNA fragments were filled with biotin at 37°C for 1hr, and proximally ligated at RT for 4hr. Then DNA was de-crosslinked and purified with ethanol precipitation. After shearing to 300-700bp fragments,the biotin tagged DNA was captured by streptavidin T1 beads. Hi-C libraries were prepared on streptavidin T1 beads using VAHTSTM Universal DNA Library Prep Kit for Illumina.After final PCR amplification, DNA could detach from beads.Size selection were perfromed with Agencourt AMPure XP beads from Beckman Coulter
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Cohesin regulates sister chromatids cohesion but also contributes to chromosome folding by promoting the formation of chromatin loops, a process proposed to be mediated by loop extrusion. PDS5 plays a crucial role in regulating the cohesin dynamic on chromatin, mainly through WAPL-mediated release activity and the opponent ESCO1/2-sororin dependent pathway. However, the exact function of PDS5 on cohesin-mediated chromatin looping remains ambiguous. Two versions of PDS5 exist in vertebrates, PDS5A and PDS5B. Here, we construct cells for rapid PDS5A or PDS5B degradation in PLC/PRF/5 cell line with the FKBP12F36V-dTAG degron system to perform loss of function studies. Combining Hi-C, ChIP-seq for cohesin regulators, and RNA-seq data, we describe the redundant and discrete roles of PDS5A and PDS5B in three-dimensional genome organization and gene expression. Overall design: In situ Hi-C experiments performed in PDS5A/B-dTAG cells with DMSO or dTAG treatment
SAMPLE_TITLE: PDS5A-dTAG, dTAG, rep1_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "PLC/PRF/5"}, {"TAG": "cell line", "VALUE": "PLC/PRF/5"}, {"TAG": "cell type", "VALUE": "Hepatocarcinoma cells"}, {"TAG": "genotype", "VALUE": "PDS5A-dTAG"}, {"TAG": "treatment", "VALUE": "dTAG"}]
Pool_Member_@attributes_sample_title: PDS5A-dTAG, dTAG, rep1_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: PDS5A-dTAG, dTAG, rep1_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "PDS5A-dTAG_dTAG_rep1_R1.fq.gz", "size": "29130073169", "date": "2022-07-27 15:21:02", "md5": "c5dc37116259278fd313f5932de0bf25", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "PDS5A-dTAG_dTAG_rep1_R2.fq.gz", "size": "32244881976", "date": "2022-07-27 15:22:50", "md5": "6f2ad5f331a4fb271da4348760cbad9c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR20665238", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR20665238/SRR20665238", "size": "43865844888", "date": "2022-07-27 15:28:36", "md5": "57e700d4e46b852bad03e7ae207b3ef3", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR20665238.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR020/20665/SRR20665238/SRR20665238.lite.1", "size": "29968303448", "date": "2022-10-09 09:59:38", "md5": "a686106007e97c45e77b35ad4708ed88", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]