run_metadata: 52141

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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
52141	SRR8945525	SRX5725655	SRS4663726	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		Uninjected 2	GSM3733697		tissue:Embryo\|genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298	Uninjected 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 “ outFilterMismatchNoverLmax 0.1” 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 ̊C were subject to a 37 ̊C heat shock for 1 hr by replacing the egg water with pre warmed 37 ̊C egg water starting at different time points and then keeping them in a 37 ̊C 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°C until tailbud stage.	genotype:Tghsp70l:loxP STOP loxP npas4l GGGGGLSRS P2A mCherrybns298	GSM3733697	GSM3733697: Uninjected 2; Danio rerio; RNA Seq	GSM3733697		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:GSM3733697	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP193485			Marass_RNA_lib_Ab_2.fastq.gz	fastq	1403915686.0	18892344.0	GSM3733697 r1	0:74.31 1:0	A:317311926;C:374434129;G:413852871;T:298232684;N:84076	74	0			317311926	374434129	413852871	298232684	84076	SRX5725655	SRS4663726	SRA878585	GEO	Bioinformatics, Max Planck Institute for Heart and Lung Research	1	0.92665		0.1128		0.75929		0.67981		74		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	smarter	bulk	bulk	bulk		Germany	2019-04-23	Multi-stage	Embryo	Embryo Imprecise	All anatomical structures