EXPERIMENT_TITLE: GSM8264912: Mononuclear cells, diagnosis, TMD, 273; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: We have employed the Omni-C kit from Dovetail Genomics for DNase-based Hi-C. 1 x 10^6 MNCs were fixed in DSG, followed by formaldehyde and fixed cells were treated with DNaseI. Next, the chromatin ends were polished and biotin-tagged bridges were used to create chimeric molecules. The library preparation kit used in the Dovetail Omni-C protocol is called the  "Dovetail Library Kit." This kit is specifically designed to prepare sequencing libraries from the DNA fragments generated during the Hi-C experiment using the Dovetail Omni-C technology. It includes steps such as end repair, adapter ligation, and PCR amplification to generate libraries.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Relapse remains a determinant of treatment failure and contributes significantly to mortality in acute myeloid leukemia (AML) patients. Despite efforts to understand AML progression and relapse mechanisms, findings on acquired gene mutations in relapse vary, suggesting inherent genetic heterogeneity and emphasizing the role of epigenetic modifications. Herein, we characterized genetic and epigenetic changes in AML progression using multi-omics approaches to elucidate the underlying mechanisms of relapse. Differential interaction analysis showed significant 3D chromatin landscape reorganization between relapse and diagnosis samples. Comparing global open chromatin profiles revealed that relapse samples had significantly fewer accessible chromatin regions than diagnosis samples. In addition, we discovered that relapse-related upregulation was achieved either by forming new active enhancer contacts or by losing interactions with poised enhancers/potential silencers. Altogether, our study highlights the impact of genetic and epigenetic changes on AML progression, underlining the importance of multi-omics approaches in understanding disease relapse mechanisms and guiding potential therapeutic interventions. Overall design: We conducted a multi-omics analysis using Omni-C, ATAC-seq, and RNA-seq on longitudinal samples from two adult AML patients at diagnosis and relapse.
SAMPLE_TITLE: Mononuclear cells, diagnosis, TMD, 273
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Diagnosis"}, {"TAG": "tissue", "VALUE": "Diagnosis"}, {"TAG": "disease", "VALUE": "AML"}, {"TAG": "cell type", "VALUE": "Mononuclear cells"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: Mononuclear cells, diagnosis, TMD, 273
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Mononuclear cells, diagnosis, TMD, 273
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TMD-273_R1.fastq.gz", "size": "15580054571", "date": "2024-05-14 08:49:53", "md5": "c8e64f7fbe91260f3fe1c77c0954e311", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "TMD-273_R2.fastq.gz", "size": "16362149940", "date": "2024-05-14 08:46:11", "md5": "c6d00539db7a63979c777f0e4a94281a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR29015929", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR29015929/SRR29015929", "size": "22191651547", "date": "2024-05-14 09:02:54", "md5": "4b63955515ce4ad7187b45d993e24e25", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR29015929.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR029/29015/SRR29015929/SRR29015929.lite.1", "size": "14562254959", "date": "2024-05-14 09:39:06", "md5": "ec98faa94ea8b06d0ecfa6d1d7937692", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]