run_metadata: 76980
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| 76980 | SRR25411166 | SRX21146779 | SRS18409872 | SRP451262 | PRJNA998264 | Depletion of tet2 results in age dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome [RNAseq] | GSE238175 | Transcriptome Analysis | Myelodysplastic Syndrome MDS is a heterogenous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis cytopenias and dysplasia. The gene encoding Ten ele¬ven translocation 2 TET2 a dioxygenase enzyme that catalyzes the conversion of 5 methylcytosine 5mC to 5 hydroxymethylcytosine is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously we reported a stable zebrafish line with a loss of function mutation in the tet2 gene. The tet2m/m mutant zebrafish developed a pre MDS state with kidney marrow dysplasia but normal circulating blood counts by 11 month of age and accompanying anemia signifying the onset of MDS by 24 month of age. In the current study we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 month and 15 month of age and performed enhanced reduced representation of bisulphite sequencing ERRBS and bulk RNA seq to measure changes in DNA methylation and gene expression of HSPCs. A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Further hypermethylated genes were significantly enriched for targets of SUZ12 and MTF2 involved in polycomb repressive complex 2 PRC2. However between 4 month and 15 month of age however we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analysis identified upregulation of genes associated mTORC1 signaling and interferon gamma and alpha response in tet2m/m HSPCs at 4 month of age when compared to the wildtype. Downregulated genes in HSPCs of tet2 mutant fish at 4 month of age were enriched for cell cycle regulation heme metabolism and IL2/STAT5 signaling possibly related to increased self renewal and clonal advantage in HSPCs with tet2 loss of function. Finally there was an overall inverse correlation between overall increased promoter methylation and gene expression. Overall design: To understand the effect of tet2 loss on the CpG methylation state of the genome and gene expression patterns to identify potential molecular mechanisms that associate with clonal expansion of the progenitor cells and disease progression in myelodysplastic syndrome | parent bioproject:PRJNA998260 | pubmed:37937078 | RNAseq 4month tet2 mut rep1 | GSM7659928 | source name:Kidney|tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant|geo loc name:missing|collection date:missing | RNAseq 4month tet2 mut rep1 | Fastq files were checked for quality using FASTQC v 0.10.1. Reads were then aligned using STAR aligner v 2.3.0 in single end mode. post sorting and indexing the aligned files were used with bedtools v 2.16.1 and Ensembl zebrafish transcriptome Zv9 to generate read counts for genes for all samples. Assembly: Zv9 Ensemble Supplementary files format and content: text file containing read counts per gene | Kidney | RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations | tissue:Kidney|cell type:marrow cells|genotype:TET2 mutant | GSM7659928 | GSM7659928: RNAseq 4month tet2 mut rep1; Danio rerio; RNA Seq | GSM7659928 r1 | GSM7659928 | 1 | RNA was extracted from marrow cells using Qiagen's allprep extraction kit per manufacturer's recommendation RNA seq libraries were prepared using TruSeq RNA Seq by polyA enrichment Illumina and sequenced on HiSeq2000 Illumina using a 50 bp single end approach per the manufacturer's recommendations | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP451262 | RNAseq_4month_tet2_mut_rep1_AGTCAA_L002_R1_003.fastq.gz | fastq | 192468441.0 | 3773891.0 | GSM7659928 r6 | 0:51 | A:51989979;C:45058442;G:43960412;T:51339541;N:120067 | 51 | 51989979 | 45058442 | 43960412 | 51339541 | 120067 | SRX21146779 | SRS18409872 | SRA1679257 | Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia | Garrett-Bakelman Lab, Department of Biochemistry and Molecular Genetics, University of Virginia | 1 | 0.94177 | 0.06438 | 0.76751 | 0.50837 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2023-07-25 | Adult | Adult | Kidney | Renal System |