{"database": "metadata", "table": "run_metadata", "rows": [[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\u2013PBS 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", null, "Wildtype 30 hpf Zebrafish Embryo   Replicate 2", "GSM7316667", null, "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\u2122 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", null, "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\u2019 Reagent Guidelines v3 Chemistry. Briefly  single cells were sorted into 0.1% BSA\u2013HBSS 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\u00ae 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.", null, "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\u2122 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\u2013HBSS 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\u00ae 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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP436855", null, "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, null, null, null, 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, null, 0.1262, null, 0.81032, null, 0.46145, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Canada", "2023-05-10", "Pharyngula", "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": ["75394"], "units": {}, "query_ms": 12.680907995672897}