{"database": "metadata", "table": "run_metadata", "rows": [[74899, "SRR24112510", "SRX19911927", "SRS17265414", "SRP431649", "PRJNA953763", "Low input RNA seq of endothelial cells sorted from tail of zebrafish larvae", "GSE229261", "Transcriptome Analysis", "To characterize the mechanism by which AML derived  extracellular vesiclesEV impaired the vascular architecture and function  EV or PBS injected flk:GFP zebrafish larvae were used for sorting endothelial cells and performing RNA Seq. Vascular niches sustain hematopoietic stem and progenitor cells HSPC and are drastically remodeled in myeloid leukemia to support pathological progression. By utilizing the leukemia xenografted zebrafish model  we identified that myeloid leukemia secreted extracellular vesicles EVs to impair HSPC proliferation  survival and differentiation towards lymphoid/erythroid lineages. The leukemia EVs delivered arginase 1 into venous vasculature to deplete L arginine and cause NOS uncoupling  which catalyzes production of ROS instead of NO. The oxidative stress caused endothelial cell loss  vascular constriction and failure of secreting niche factors and supporting hematopoiesis. Our findings indicate that myeloid leukemia impaired the vascular function of supporting hematopoiesis by delivering arginase in EVs and arginase inhibition has the potential to improve normal hematopoiesis in myeloid leukemia. Overall design: Comparative gene expression profiling analysis of RNA seq data for endothelial cells sorted from tails of  MV4 11 derived EV or PBS injected flk:GFP zebrafish larvae.", null, null, null, "flk:GFP injected with MV4 11 derived Evs 3", "GSM7157754", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:WT|treatment:injected with MV4 11 derived EVs sorting|geo loc name:missing|collection date:missing", "flk:GFP injected with MV4 11 derived Evs 3", "post removing low quality reads and trimming the adaptor sequences by Trim Galore v0.5.0  Babraham Bioinformatics  RNA Seq reads were aligned to zebrafish genome GRCz11 by Salmon v0.03.1  COMBINE lab with ENCODE options and genes were annotated by Ensembl database. For expression quantification  the uniquely mapped reads were transformed to counts by Salmon and normalized to counts per million CPM or log2CPM+1 by edgeR v3.40.1  Bioconductor. The batch effect was removed by sva v3.46.0  Bioconductor. Three replicates of PBS or EV treated ECs were aligned by Principal ComponentAnalysis PCA  and one replicate that was diverged from the other two was removed for the following analysis. Assembly: GRCz11 Supplementary files format and content: Zebrafish  Raw Counts.tar with raw counts matrices", "endothelial cells", null, "Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 \u03bcL pipette tip for 20 min. The dissociated cells were then filtered with a 70 \u03bcm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 \u03bcg/mL  BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP  Beckman and total RNA was extracted with Trizol 15596  Invitrogen according to the manufacturer\u2019s instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly  mRNAs were purified by VAHTS RNA Clean Beads N412  Vayzme in RNase free H2O with reverse transcription mix  amplified for 15 cycles  and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411  Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285  Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503  Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411  Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.", null, "cell type:endothelial cells|genotype:WT|treatment:injected with MV4 11 derived EVs sorting", "GSM7157754", "GSM7157754: flk:GFP injected with MV4 11 derived Evs 3; Danio rerio; RNA Seq", "GSM7157754 r1", "GSM7157754", "1", "Five hundred of Tgflk:GFP larvae were injected with PBS control or EVs and three replicates were prepared for each treatment. The larvae were then anesthetized at 24 h post injection hpi before cutting tails on ice. The tails were collected and gently triturated in 1.5 mL cold trypsin solution 0.5 g/L; T3924; Sigma with 1 000 \u03bcL pipette tip for 20 min. The dissociated cells were then filtered with a 70 \u03bcm filter BD Transduction Laboratories to remove the undissociated tissue and washed twice with cold PBS. Cells were then resuspended in 2.5 mL PBS and stained with 7 AAD 5 \u03bcg/mL  BD Transduction Laboratories on ice for 30 min. About 1X10^5 GFP+ cells were sorted by FACS MoFlo XDP  Beckman and total RNA was extracted with Trizol 15596  Invitrogen according to the manufacturer's instructions. Low input RNA Seq was performed according to the published protocol with modifications . Briefly  mRNAs were purified by VAHTS RNA Clean Beads N412  Vayzme in RNase free H2O with reverse transcription mix  amplified for 15 cycles  and reverse transcribed for cDNAs before purifying with VAHTS DNA Clean Beads N411  Vazyme. Enriched cDNA was quantified using Qubit dsDNA HS Assay Kit Q3285  Guangzhou IGE biotechnology ltd and verified by DNA gel electrophoresis 1.5 2 kb. Libraries were prepared by using TruePrep DNA library Prep Kit V2 for Illumina TD503  Vazyme and adaptor ligated DNAs 400 bp were selected by VAHTS DNA Clean Beads N411  Vazyme. Libraries were sequenced by using NovaSeq PE150 as 150 bp paired end.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP431649", null, "loader:fastq load.py", "EC-EVs-3_L4_Q803602.R1.fastq.gz EC-EVs-3_L4_Q803602.R2.fastq.gz", "fastq fastq", 6010992300.0, 20036641.0, "GSM7157754 r1", "0:150 1:150", "A:1551150109;C:1411943134;G:1418582790;T:1629299477;N:16790", 150, 150, null, null, 1551150109, 1411943134, 1418582790, 1629299477, 16790, "SRX19911927", "SRS17265414", "SRA1622779", "Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL", "Jianglinjia Lab, SUN YAT-SEN MEMORIAL HOSPITAL", 2, 0.91791, 0.92553, 0.05853, 0.05906, 0.82609, 0.82509, 0.59566, 0.59001, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-04-09", "Larval", "Larval", "Endothelium", "Cardiovascular 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": ["74899"], "units": {}, "query_ms": 15.834186997381039}