{"database": "metadata", "table": "run_metadata", "rows": [[76331, "SRR24835117", "SRX20599522", "SRS17899569", "SRP441312", "PRJNA980571", "Targeting TNF/IL 17/MAPK Pathway in hE2A PBX1 Leukemia: effects of OUL35  KJ Pyr 9  and CID44216842", "GSE234222", "Transcriptome Analysis", "t1;19q23;p13 is one of the most common translocation genes in childhood acute lymphoblastic leukemia ALL and is also present in acute myeloid leukemia AML and mixed phenotype acute leukemia MPAL. This translocation results in the formation of the oncogenic E2A PBX1 fusion protein  which contains a trans activating domain from E2A and a DNA binding homologous domain from PBX1. Despite its clear oncogenic potential  the pathogenesis of E2A PBX1 fusion protein is not fully understood especially in leukemias other than ALL  and effective targeted clinical therapies have not been developed. To address this  we established a stable and heritable zebrafish line expressing human E2A PBX1 hE2A PBX1 for high throughput drug screening. Blood phenotype analysis showed that hE2A PBX1 expression induced myeloid hyperplasia by increasing myeloid differentiation propensity of hematopoietic stem cells HSPCs and myeloid proliferation in larvae  and progressed to AML in adults. Mechanistic studies revealed that hE2A PBX1 activated the TNF/IL 17/MAPK signaling pathway in blood cells and induced myeloid hyperplasia by up regulating the expression of the runx1. Interestingly  through high throughput drug screening  three small molecules targeting the TNF/IL 17/MAPK signaling pathway were identified  including OUL35  KJ Pyr 9  and CID44216842  which not only alleviated the hE2A PBX1 induced myeloid hyperplasia in zebrafish but also inhibited the growth and oncogenicity of human pre B ALL cells with E2A PBX1. Overall  this study provides a novel hE2A PBX1 transgenic zebrafish leukemia model and identifies potential targeted therapeutic drugs  which may offer new insights into the treatment of E2A PBX1 leukemia and improve the quality of life of leukemia patients. Overall design: Kidney marrow of the wild type  Tghsp70:E2A PBX1 EGFP zebrafish post 3 month heat shock were isolated separately. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.", null, "pubmed:38385270", null, "E2A PBX1 KM 2", "GSM7457555", null, "source name:kidney marrow|development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:Tghsp70:E2A PBX1 EGFP|geo loc name:missing|collection date:missing", "E2A PBX1 KM 2", "To get high quality clean reads  reads were further filtered by fastp version 0.18.0. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1  the better the repeatability between two parallel experiments. Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables gene expression into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas. RNA differential expression analysis was performed by DESeq2  software between two different groups and by edgeR between two samples. The genes/transcripts with the parameter of false discovery rate FDR below 0.05 and absolute fold change\u22652 were considered differentially expressed genes/transcripts. We performed gene set enrichment analysis using software GSEA and MSigDB to identify whether a set of genes in specific GO terms\\KEGG pathways\\Reactome pathways\\DO terms shows significant differences in the two groups. Briefly  we input the gene expression matrix and rank genes by the SignaltoNoise normalization method. Enrichment scores and p value were calculated in default parameters. Assembly: GRCz11 Ensembl release 108 Supplementary files format and content: gene exppression.txt", "kidney marrow", null, "Kidney marrows were isolated from 6 mpf fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen  Carlsbad  CA  USA according to the manufacturer\u2019s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted  eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The purified double stranded cDNA fragments were end repaired  A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:Tghsp70:E2A PBX1 EGFP", "GSM7457555", "GSM7457555: E2A PBX1 KM 2; Danio rerio; RNA Seq", "GSM7457555 r1", "GSM7457555", "1", "Kidney marrows were isolated from 6 mpf fish  placed in PBS with 5% fetal bovine serum  triturated by pipet  and filtered through a 40 \u03bcm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen  Carlsbad  CA  USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted  eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The purified double stranded cDNA fragments were end repaired  A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP441312", null, "loader:fastq load.py", "E2A-PBX1-KM-2_2.fq.gz E2A-PBX1-KM-2_1.fq.gz", "fastq fastq", 6481440000.0, 21604800.0, "GSM7457555 r1", "0:150 1:150", "A:1773856613;C:1460702707;G:1475415238;T:1771402610;N:62832", 150, 150, null, null, 1773856613, 1460702707, 1475415238, 1771402610, 62832, "SRX20599522", "SRS17899569", "SRA1650345", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", "Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology", 2, 0.93286, 0.9293, 0.11326, 0.11315, 0.7274, 0.7292, 0.49505, 0.48961, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "nebnext", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "China", "2023-06-06", "Adult", "Adult", "Kidney", "Renal System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["76331"], "units": {}, "query_ms": 9.944174002157524}