EXPERIMENT_TITLE: GSM6552754: ATRX+/+ TERT-/- clone 26; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Micro-C assay was performed following Dovetail Micro-C kit protocol on 1x106 XXX  cells. Briefily, frozen cells were resuspended in 1X PBS and crosslinked with 3mM DSG and 1% formaldehyde. Washed cells were digested with 0.5 uL MNase in 100 uL of Nuclease digest buffer with MgCl2. Digestion was stop by addition of 5 µl of EDTA 0.5M. Chromatin was solubilize by addition of 3µl of 20% SDS and capture on chromatin capture beads. Chromatin bound DNA ends were repaired and A-tailed using the End Polishing enzyme mix and buffer. Dovetail bridge was then ligated to the chromatin bound DNA free ends following the Micro-C kit protocol then subjected to intra-aggregate ligation to create chromatin-chromatin long range interaction. Finally, the DNA bound to chromatin was recovered by proteinase K treatment and crosslink reversal and purify using SPRIselect beads (Beckman Coulter). NEB NEBNext Ultra II DNA Library Prep Kit for Illumina
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Alternative Lengthening of Telomeres (ALT) is an aberrant DNA recombination pathway which grants replicative immortality to approximately 10% of all cancers. Despite this high prevalence of ALT in cancer, the mechanism and genetics by which cells activate this pathway remain incompletely understood. A major challenge in dissecting the events that initiate ALT is the extremely low frequency of ALT induction in human cell systems. Guided by the genetic lesions that have been associated with ALT from cancer sequencing studies, we genetically engineered primary human pluripotent stem cells to deterministically induce ALT upon differentiation. Using this genetically defined system, we demonstrate that disruption of the p53 and Rb pathways in combination with ATRX loss-of-function is sufficient to induce all hallmarks of ALT and results in functional immortalization in a cell type-specific manner. We further demonstrate that ALT can be induced in the presence of telomerase, is neither dependent on telomere shortening nor crisis, but is rather driven by continuous telomere instability triggered by the induction of differentiation in ATRX-deficient stem cells. Overall design: Micro-C analysis in human fibroblasts derived from ATRX+/+ or ATRX-/- hESCs.
SAMPLE_TITLE: ATRX+/+ TERT-/- clone 26
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "WIBR3"}, {"TAG": "cell line", "VALUE": "WIBR3"}, {"TAG": "cell type", "VALUE": "fibroblasts"}, {"TAG": "genotype", "VALUE": "ATRX+/+"}, {"TAG": "treatment", "VALUE": "E7 differentiation"}]
Pool_Member_@attributes_sample_title: ATRX+/+ TERT-/- clone 26
RUN_SET_RUN_Pool_Member_@attributes_sample_title: ATRX+/+ TERT-/- clone 26
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR21461214.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/SRR021/21461/SRR21461214/SRR21461214.lite.1", "size": "7050038930", "date": "2022-10-26 15:34:05", "md5": "ab04f721792845825801bfedcf431697", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR21461214", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR21461214/SRR21461214", "size": "9601004774", "date": "2022-09-09 09:30:40", "md5": "cad1fc17b9f1c5b124ced5c672b04094", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DHAM001-L_S12_L004_R2_001.fastq.gz", "size": "6645894040", "date": "2022-09-09 09:20:43", "md5": "e010731e1e3d59a0e2f0f6144d18c61b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DHAM001-L_S12_L004_R1_001.fastq.gz", "size": "6445238243", "date": "2022-09-09 09:15:34", "md5": "7adc38de026756ee1f1863321c636485", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]