run_metadata: 75394

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
75394	SRR24492134	SRX20277377	SRS17604630	SRP436855	PRJNA971152	scRNAseq datasets supporting a common precursor expression program leading to brain pericyte differentiation from neural crest and mesoderm	GSE232163	Transcriptome Analysis	Brain pericytes are critical for regulating endothelial barrier function and activity thus ensuring adequate blood flow to the brain. How the developmental acquisition of pericytes to naked endothelium is regulated is largely unknown but is relevant to disorders where vessels are poorly stabilized. Although pericytes are derived from neural crest and mesoderm brain pericytes from both origins are currently indistinguishable; the genetic pathways leading to a convergent pericyte phenotype are unknown. We show here that a precursor population expressing the transcription factor nkx3.1 with origins in both NCC and mesoderm develops into brain pericytes. We identify the gene signature of these precursors and show that an nkx3.1 foxf2a and cxcl12b expressing pericyte precursor population is present around the cxcr4 expressing basilar artery and that these cells later spread throughout the brain. Cxcl12b Cxcr4 signaling is required for pericyte attachment and differentiation but not for later pericyte development. Further both nkx3.1 and cxcl12b are necessary and sufficient in regulating pericyte number. Thus we have defined an undescribed population of pericyte precursors and identified genes critical for their differentiation. Overall design: Embryos expressing the nkx3.1NTR mcherry transgene were dissociated from wildtype 30 hpf zebrafish embryos and mCherry positive FACs sorted cells were subjected to single cell RNA sequencing. Two replicate libraries were generated from FACS sorted nkx3.1 expressing cells . To examine molecular changes within specific cell compartments we isolated single cells from both biopsies and processed according to 10X Genomics Chromium Single Cell three prime Reagent Guidelines v3 Chemistry as per the manufacturer's protocol. In brief single cells were sorted based on forward versus side scatter gating into 0.1% BSA–PBS and partitioned into Gel Bead In EMulsions GEMs using 10x GemCodeTM Technology. Next Generation Sequencing was performed using the Illumina NovaSeq S2 Flow cells. All raw FASTQs were aligned to the human reference genome generated using cellranger mkref pipeline. The resulting gene barcode matrix was processed using Seurat R toolkit.	parent bioproject:PRJNA973709	pubmed:38683849		Wildtype 30 hpf Zebrafish Embryo Replicate 2	GSM7316667		source name:Embryo 2\|tissue:embryo\|age:30 hpf\|transgenic strain:nkx3.1NTR mCherry\|background:TL background\|facs strategy:nkx3.1 transgene expressing cells. Dead cells excluded using the forward/side scatter gating and viability dye Fixable Viability Dye eFluor™ 780\|library preparation:10X Genomics Single Cell RNAseq v3\|geo loc name:missing\|collection date:missing	Wildtype 30 hpf Zebrafish Embryo Replicate 2	All raw FASTQs reads were aligned to Danio rerio zebrafish GRCz11 genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v.6.1.2 single cell pipeline with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis. Assembly: Samples aligned to a custom Zebrafish Genome Assembly GRCz11 version 4.3.2 Lawson et al eLife 2020 which is included in the GEO submission. Supplementary files format and content: Filtered gene barcode matrix output from CellRanger	Embryo 2		Wildtype zebrafish embryos expressing the Tgnkx3.1:Gal4;UAS:NTR mCherryca101 transgene were dissociated assessed for viability processed resuspended in a designated solution and subsequently sorted via fluorescence activated cell sorting to isolate red fluorescent nkx3.1 transgene expressing cells. The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead In EMulsions GEMs using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA generating full length cDNA from poly adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. Pfive primers P7 primers i7 sample index and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.		tissue:embryo\|age:30 hpf\|transgenic strain:nkx3.1NTR mCherry\|background:TL background\|facs strategy:nkx3.1 transgene expressing cells. Dead cells excluded using the forward/side scatter gating and viability dye Fixable Viability Dye eFluor™ 780\|library preparation:10X Genomics Single Cell RNAseq v3	GSM7316667	GSM7316667: Wildtype 30 hpf Zebrafish Embryo Replicate 2; Danio rerio; RNA Seq	GSM7316667 r1	GSM7316667	1	Wildtype zebrafish embryos expressing the Tgnkx3.1:Gal4;UAS:NTR mCherryca101 transgene were dissociated assessed for viability processed resuspended in a designated solution and subsequently sorted via fluorescence activated cell sorting to isolate red fluorescent nkx3.1 transgene expressing cells. The sample was prepared according to 10X Genomics ChromiumTM Single Cell three prime Reagent Guidelines v3 Chemistry. Briefly single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead In EMulsions GEMs using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA generating full length cDNA from poly adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. Pfive primers P7 primers i7 sample index and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP436855		dangling references:treat as unmapped\|assembly:GRCz11\|intentional duplicate	S_2_count_possorted_genome_bam.bam	10X Genomics bam file	5745139764.0	63133404.0	GSM7316667 r1	0:91	A:1647050159;C:1282617598;G:1470594174;T:1344666383;N:211450	91				1647050159	1282617598	1470594174	1344666383	211450	SRX20277377	SRS17604630	SRA1656031	Biernaskie Lab, Comparative Biology and Experimental Medicine, University of Calgary	Biernaskie Lab, Comparative Biology and Experimental Medicine, University of Calgary	1	0.90392		0.1262		0.81032		0.46145		91		B		usable mapping rate	illumina	novaseq_era	full_length	poly_a	unknown	sc	single_cell_droplet	10x		Canada	2023-05-10	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures