EXPERIMENT_TITLE: Illumina NovaSeq X paired end sequencing of SAMD00759998
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Myelodysplastic syndrome (MDS) is a poor prognosis cancer that predominantly affects the elderly, arising from hematopoietic stem cell (HSC), resulting in hematopoietic failure, and partly transforming into acute myelogenous leukemia (AML). It has long been known that numerical chromosome anomalies such as Trisomy 8 (+8) is an important criterion for diagnosis for MDS, but also is closely associated with clinical outcome of patients with MDS. Next generation sequencing (NGS) studies revealed that trisomy 8 MDS cells highly mutated RUNX1 transcriptional factor and ASXL1, an epigenetic modifier, both of which regulate HSC function and the differentiation, relative to MDS cells without trisomy 8, suggesting that those mutations may help trisomy 8 to drive the development of MDS. However, the underlying pathogenetic mechanism of +8 MDS is still unclear at levels of gene, chromosome, and cell in patients. Based on those findings, we attempted to generate a new trisomy 8 mouse model to prove our hypothesis which trisomy 8 initiates the transformation by multiple malfunctions of epigenetic and transcriptional regulators in HSC other than a gene dosage effect due to the extra chromosome 8. These NGS data were used in this project for the multi-omics analyses.
SAMPLE_TITLE: THP1_rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "sample_name", "VALUE": "THP1_rep1"}, {"TAG": "age", "VALUE": "1"}, {"TAG": "biomaterial_provider", "VALUE": "RIKEN BRC"}, {"TAG": "cell_line", "VALUE": "RCB3686"}, {"TAG": "collection_date", "VALUE": "2023-10-20"}, {"TAG": "geo_loc_name", "VALUE": "Japan:Kumamoto"}, {"TAG": "isolate", "VALUE": "RCB3686"}, {"TAG": "sex", "VALUE": "male"}, {"TAG": "tissue", "VALUE": "Peripheral blood"}, {"TAG": "BioSampleModel", "VALUE": "Human"}]
Pool_Member_@attributes_sample_title: THP1_rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: THP1_rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "DRR541703.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/DRR000/541/DRR541703/DRR541703.lite.1", "size": "44015434611", "date": "2024-04-08 20:02:30", "md5": "e3d582c86337ea605ae262f1ed34eb18", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DRR541703", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/DRR541703/DRR541703", "size": "51380149943", "date": "2024-04-08 19:22:37", "md5": "8c9b2b95096e51918c5e5c2c0fcf188e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]