run_metadata: 63888

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
63888	SRR14202113	SRX10569026	SRS8675161	SRP314271	PRJNA720970	Single cell transcriptional profiles of islet1 derived ECs and the other ECs in the tail of 48 hpf zebrafish embryos	GSE171822	Transcriptome Analysis	We report transcriptional heterogeneity of venous endothelial cells ECs in the tail of zebrafish embryos which consist of HSPC niche constituting ECs and caudal vessel CV constituting ECs. To characterize isl1 derived ECs which derive from the endoderm and mainly constitute the HSPC niche in the caudal hematopoietic tissue CHT we performed single cell RNA sequencing scRNA seq of isl1 derived ECs and the other ECs separately isolated from the tails of zebrafish embryos. Our analyses revealed that tail venous ECs were split into 5 distinct sub clusters where isl1 derived ECs and the other ECs were similarly distributed to all venous EC clusters and further revealed that genes whose expression levels are different between isl1 derived ECs and the other ECs tend to show similar changes across all of the clusters even post their diversification. Overall design: We isolated live TagRFP+/EGFP+ cells for isl1 derived ECs and TagRFP /EGFP+ cells for the other ECs separately by FACS sorting from the tails of TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf. Then barcoded single cell cDNA libraries were prepared using the Chromium Single Cell three prime Reagents Kits v3.1 and were then sequenced using Illumina NovaSeq6000.		pubmed:36693371		RNA seq isl1 derived ECs	GSM5235245		source name:resected tails posterior to the yolk end\|strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:isl1 derived ECs TagRFP+/EGFP+	RNA seq isl1 derived ECs	The 10x Genomics Cell Ranger pipeline version 5.0.0 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 and reporter sequences EGFP and RFP with the gene annotation file Danio rerio.GRCz11.99.chr.gtf.gz barcode/UMI processing and gene counting for each cell. Genome build: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI counts for each sample.	resected tails posterior to the yolk end		Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco’s modified Eagle’s medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.		strain:AB\|genotype:TgBACisl1:TagRFP;Tgdab2:EGFP\|developmental stage:48 hpf\|tissue:Tail\|cell type:isl1 derived ECs TagRFP+/EGFP+	GSM5235245	GSM5235245: RNA seq isl1 derived ECs; Danio rerio; RNA Seq	GSM5235245		1	Tails resected from TgBACisl1:TagRFP;Tgdab2:EGFP embryos at 48 hpf were subjected to mechanical and enzymatic dissociation by pipetting every 5 minutes in 1 ml of protease solution TrypLE Express with 2.7 mg/ml Collagenase P and incubated at 28 °C until full dissociation 15 min. Cells were pelleted 3000 rpm 5 minutes at 4 °C and resuspended in suspension medium phenol red free Dulbecco's modified Eagle's medium with 1% FBS and 0.8 mM calcium chloride twice. Resuspended cells were passed through a cell strainer and subjected to cell sorting using a FACS Aria III cell sorter to isolate live TagRFP+/EGFP+ cells and TagRFP /EGFP+ cells separately. For scRNA seq single cell suspensions were resuspended with the suspension medium and barcoded with a 10x Chromium Controller 10x Genomics. RNA from the barcoded cells for each sample was subsequently reverse transcribed and sequencing libraries were constructed with reagents from a Chromium Single Cell v3.1 reagent kit 10x Genomics. Sequencing was performed with Illumina NovaSeq6000.	GEO Accession:GSM5235245	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP314271		loader:fastq load.py\|options: platform=Illumina readTypes=TTTB read1PairFiles=ZebEmb GFP I1.fastq.gz read2PairFiles=ZebEmb GFP I2.fastq.gz read3PairFiles=ZebEmb GFP R1.fastq.gz read4PairFiles=ZebEmb GFP R2.fastq.gz	ZebEmb_GFP_I1.fastq.gz ZebEmb_GFP_I2.fastq.gz ZebEmb_GFP_R1.fastq.gz ZebEmb_GFP_R2.fastq.gz	fastq fastq fastq fastq	53036547366.0	384322807.0	GSM5235245 r1	0:10 1:10 2:28 3:90	A:14610188978;C:12169986421;G:12283689207;T:13969658178;N:3024582	10	10	28	90	14610188978	12169986421	12283689207	13969658178	3024582	SRX10569026	SRS8675161	SRA1217192	GEO	Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute	1	0.94469		0.10454		0.79133		0.51214		90		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Japan	2021-04-09	Hatching	Embryo	Tail	Multi-system