{"database": "metadata", "table": "run_metadata", "rows": [[52139, "SRR8945527", "SRX5725657", "SRS4663725", "SRP193485", "PRJNA534270", "Genome wide strategies reveal downstream target genes of Npas4l associated with cardiovascular development in zebrafish [RNA Seq 2]", "GSE130200", "Transcriptome Analysis", "The development of a vascular network is essential to nourish tissues and sustain organ function throughout life.  Endothelial cells ECs are the building blocks of blood vessels  yet our understanding of EC specification in vertebrates remains incomplete.  cloche/npas4l mutants have broadly been used as an avascular model in zebrafish  but little is known about the molecular mechanism of action of Npas4l.  Here  to identify the direct and indirect target genes of this transcription factor  we combined complementary genome wide approaches  including transcriptome analyses and chromatin immunoprecipitation ChIP.  The cross analysis of these datasets indicate that Npas4l functions as a master regulator by directly inducing a wave of transcription factor genes crucial for hematoendothelial specification in vertebrates  including etv2  tal1  and lmo2.  We identified additional target genes acting downstream of npas4l and investigated the function of a subset of them using CRISPR/Cas9 technology.  Phenotypic characterization of tspan18b mutants reveals a novel role for tspan18b in developmental angiogenesis  confirming the reliability of the datasets generated.  Collectively  these data represent a useful resource for future studies aimed to investigate novel genes with a potential role in vascular development and EC fate determination in vertebrates. Overall design: RNA seq examination of Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 zebrafish embryos at 6 somite stage  in duplicates.", "parent bioproject:PRJNA534269", "pubmed:31097478", null, "Cre Injected 2", "GSM3733699", null, "tissue:Embryo|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "Cre Injected 2", "The resulting raw reads were assessed for quality  adapter content and duplication rates with FastQC 0.11.8 Andrews S. 2010  FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Trimmomatic version 0.36 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Only reads longer than 15 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11 using STAR 2.6.0c with the parameter \u201c  outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al.  STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.14.1 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. The Ensemble annotation was enriched with UniProt data release 12.04.2018 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: danrer11 / GRCz11 Supplementary files format and content: The tab delimited matrix with DESeq normalized counts.", "Embryo", "Fish embryos raised at 28 \u030aC were subject to a 37 \u030aC heat shock for 1 hr by replacing the egg water with pre warmed 37 \u030aC egg water starting at different time points  and then keeping them in a 37 \u030aC incubator.", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with cre at the one cell stage and uninjected  were grown in E3 medium at xxx\u00b0C until tailbud stage.", "genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298 injected with Cre to induce recombinase", "GSM3733699", "GSM3733699: Cre Injected 2; Danio rerio; RNA Seq", "GSM3733699", null, "1", "For RNAseq  total RNA was isolated from zebrafish embryos at 6 somite stage using the miRNeasy micro Kit Qiagen. For exclusion of genomic DNA contamination  the samples were treated by on column DNase digestion DNase Free DNase Set  Qiagen. Total RNA and library integrity were verified with LabChip Gx Touch 24 Perkin Elmer. 10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit   Pico Input Mammalian Takara Clontech following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry  resulting in average of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3733699", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP193485", null, null, "Marass_RNA_lib_inj_2.fastq.gz", "fastq", 1318624367.0, 17749685.0, "GSM3733699 r1", "0:74.29 1:0", "A:320435609;C:333825364;G:380093353;T:284207932;N:62109", 74, 0, null, null, 320435609, 333825364, 380093353, 284207932, 62109, "SRX5725657", "SRS4663725", "SRA878585", "GEO", "Bioinformatics, Max Planck Institute for Heart and Lung Research", 1, 0.93022, null, 0.12203, null, 0.75935, null, 0.65366, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "bulk", "bulk", null, "Germany", "2019-04-23", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "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": ["52139"], "units": {}, "query_ms": 8.225151992519386}