run_metadata: 66760

This data as json

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
66760	SRR16573983	SRX12775941	SRS10721245	SRP343153	PRJNA774550	Single cell RNA sequencing of zebrafish hematopoietic stem cells and endothelial cells	GSE186565	Transcriptome Analysis	Assessing gene changes in endothelial to hematopoietic transition in control zebrafish embryos and comparing gene changes to those seen in vegfc knock down embryos. Overall design: 52 hpf embryos were dissociated for FACs sorting to isolate GFP+ HSPCs mCherry+ ECs and double positive cells undergoing EHT. Following the sort cells underwent standard 10x encapsulation.		pubmed:34919128		Vegfc MO	GSM5655701		tissue:Endothelial Cells HSPCs\|treatment:Vegfc MO\|strain:flk:mCherry; cd41:gfp\|age:52 hpf	Vegfc MO	Demultiplexing of raw base call files was done using cellranger mkfastq; version 4.0.0 Alignment filtering barcode counting and UMI counting was done using cellranger count; version 4.0.0 Samples were aggregated and normalized using cellranger aggr; version 4.0.0 Genome build: custom GRCz11 reporters Supplementary files format and content: Filtered feature barcode matrix	Endothelial Cells HSPCs	Control samples were not injected uninjected and treated samples were injected with 4 ng of vegfc MO at the one cell stage	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell 3’ v3.1 Reagents under standard conditions scRNA seq	Embryos were maintained in E3 embryo medium until 52 hpf	treatment:Vegfc MO\|strain:flk:mCherry;cd41:gfp\|age:52 hpf	GSM5655701	GSM5655701: Vegfc MO; Danio rerio; RNA Seq	GSM5655701 r1	GSM5655701	1	Embryos were treated with a dissociation mix consisting of 480 ml 0.25% trypsin EDTA + 20 ml Collagenase 100 mg/ml for 15 mins at 30C. Once embryos were fully homogenized dissociation was stopped with addition of 800 ml of DMEM 10%FBS. The homogenate was run though a 70 uM strainer before centrifugation for 5 min at 700 g at room temperature. The pellet was resuspended in 1mL PBS and centrifuged again for 5 min at 700 g at room temperature. The pellet was resuspended in 500uL PBS + 2% FBS and run through a 70uM cell strainer the strainer was then washed with 500uL of PBS + 2% FBS giving a total volume of 1mL. Libraries were prepared for sequencing using Illumina Single Cell three prime v3.1 Reagents under standard conditions scRNA seq		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP343153			VegfcMo_S3_L001_R1_001.fastq.gz VegfcMo_S3_L001_R2_001.fastq.gz	fastq fastq	13667302233.0	116814549.0	GSM5655701 r1	0:28 1:89	A:3845447410;C:3000770206;G:3051184574;T:3769610622;N:289421	28	89			3845447410	3000770206	3051184574	3769610622	289421	SRX12775941	SRS10721245	SRA1317383	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	Tamplin, Cell and Regenerative Biology, University of Wisconsin-Madison	2	0.00828	0.92236	0.00351	0.1852	0.99036	0.75982	0.37956	0.50465	28	89	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc_generic	single_cell_generic	generic-scrnaseq-only		United States	2021-10-26	Hatching	Embryo	Endothelium	Cardiovascular System