EXPERIMENT_TITLE: GSM8254283: DLD-1 cells, sgGATA6, HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In situ Hi-C experiments were performed following the previously described protocol (Rao et al., 2014) with modifications. Briefly, chromatin extracted from crosslinked cells was digested with restriction enzymes, followed by biotin labeling, ligation, and biotin pull down. HiChIP experiments were performed using Arima HiC+ kit following manufacture's protocol with modifications. Briefly, 10 million cells were crosslinked with 2% formaldehyde (Millipore Sigma, 252549), followed by cell lysis, restriction enzyme digestion, end repair and biotin labeling, ligation, and shearing following Arima Hi-C procedure. Chromatin was then subjected to immunoprecipitation with H3K27ac antibody (active motif, 39133) ChIA-PET data was generated following the previously described ChIA-PET protocol 3, 4. Antibody against GATA6 (CST, 5851) was used. The final library was sequenced as 150 PE reads on Illumina Novaseq 6000 platform. The final library was prepared using the KAPA HyperPrep kit (KAPA, 7962363001). The final library was sequenced as 150 PE reads on Illumina Novaseq 6000 platform.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Colorectal cancer (CRC) is one of the most lethal and prevalent malignancies with elusive molecular causes. While the abnormal activity of transcription factors has been reported as a vital component of cancer progression, the mechanism through which they function remains unclear. Here, through the analysis of primary human CRC tissue data, we identified GATA6 as a CRC specific regulator, whose expression upregulation is potentially associated with promoter hypomethylation. In the human genome, GATA6 showed preferential binding at tumor specific active enhancers. Through both auxin-inducible degron (AID) and CRISPR knockout, we showed that GATA6 depletion severely impaired clonogenicity and proliferation. GATA6 depletion caused the loss of CRC specific open chromatin, suggesting a specific regulatory role of GATA6 in CRC pathogenesis. Interestingly, we also discovered the co-occupancy of GATA6 with CTCF and its direct involvement in promoter enhancer loops, suggesting the possibility that GATA6 mediate transcriptional regulation through 3D genome. The loss of GATA6 led to alterations in E-P chromatin interactions of a panel of oncogenes, accompanied by the oncogene downregulation. Finally, we showed that GATA6 loss is detrimental to the xenograft tumor growth and thereby rescued mice survival. Taken together, we unrevealed a novel mechanism by which GATA6 contributes to CRC. Overall design: DLD1-GATA6-AID-IAA7 cell lines were established using the auxin-inducible degron(AID) system, in which target gene GATA6 has been degraded. DLD-1 cells were also engineered to knockout target gene GATA6 using CRISPR/cas9 system.
SAMPLE_TITLE: DLD-1 cells, sgGATA6, HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "DLD-1"}, {"TAG": "cell line", "VALUE": "DLD-1"}, {"TAG": "cell type", "VALUE": "colorectal adenocarcinoma"}, {"TAG": "genotype", "VALUE": "GATA6-KO"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: DLD-1 cells, sgGATA6, HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: DLD-1 cells, sgGATA6, HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR28919478.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos7/sra-pub-zq-41/SRR028/28919/SRR28919478/SRR28919478.lite.1", "size": "37498058654", "date": "2024-05-07 02:29:30", "md5": "04fd996dc0e699e3bc933523321e1779", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR28919478", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR28919478/SRR28919478", "size": "50276344134", "date": "2024-05-06 23:16:41", "md5": "b5d09c520710ab7c5f91bbf42e355fd6", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DLD1-GATA6-KO-HiC_R2.fastq.gz", "size": "36080653194", "date": "2024-05-06 22:40:37", "md5": "32f3c119ca503cd0fd91d8770e8d2fc0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DLD1-GATA6-KO-HiC_R1.fastq.gz", "size": "33031707120", "date": "2024-05-06 22:48:42", "md5": "fc58c244096188270ed3daf89932a43e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]