{"database": "metadata", "table": "run_metadata", "rows": [[51191, "SRR8592251", "SRX5392462", "SRS4380285", "SRP186305", "PRJNA522917", "Pbx4 limits vertebrate heart size and promotes pharyngeal arch artery development through partitioning progenitor fates within the second heart field and restricting proliferation", "GSE126647", "Transcriptome Analysis", "Development of the vertebrate heart requires the appropriate integration of temporally distinct differentiating progenitor populations. While factors that promote accrual of later differentiating second heart field SHF derived cells to the outflow tract OFT have been intensively investigated  few signals are understood that specifically restrict the size of the vertebrate OFT. Here  we show that improper specification and proliferation of SHF progenitors in zebrafish lazarus lzr mutants  which lack the transcription factor Pbx4  produces enlarged hearts with a specific increase in ventricular cardiomyocytes and smooth muscle cells within the OFT. Specifically  optogenetic lineage tracing demonstrates Pbx4 initially promotes the proper partitioning of the SHF into anterior progenitors  which contribute to the OFT  and adjacent endothelial cell progenitors  which contribute to posterior pharyngeal arch arteries. Subsequently  Pbx4 also limits the size of the SHF through repressing SHF progenitor proliferation. Single cell RNA sequencing of nkx2.5+ cells revealed that the enlarged SHF progenitor population within Pbx4 deficient embryos assimilates characteristics of normally distinct proliferative and more anterior  differentiated cardiomyocyte populations. Therefore  the generation of proper OFT size and great arteries in vertebrates requires Pbx dependent stratification of unique progenitor differentiation states to facilitate homeotic like transformations and limit progenitor production within the SHF. Overall design: To determine the effects of Pbx4 loss on cardiac progenitors and differentiated cardiomyocytes  we utilized  single cell RNA Seq scRNA Seq data sets collected from  control and Pbx4 depleted embryos nkx2.5:ZsYellow+ cells at 28 hours post ferlilization. The 10x Genomics platform was used for these studies version 2 library chemistry.", null, "pubmed:32094112", null, "Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq", "GSM3610371", null, "source name:Pbx4 depleted nkx2.5:ZsYellow+ cells|strain background:AB/TU|age:28 hpf depleted|tissue:cardiac progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells", "Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq", "Illumina HiSeq2500 used for basecalling CellRanger software package used for alignment  filtering  barcode reading prior to post processing with ICGS in AltAnalyze. Genome build: GRCz10/danRer10 Supplementary files format and content: 10X Genomics Chromium Raw Gene BC Cellular Barcodes barcode.tsv  Genes genes.tsv  and Matrix matrix.mtx", "Pbx4 depleted nkx2.5:ZsYellow+ cells", null, "Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver  2016 with the following modifications  approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank\u2019s Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 \u00b5l HBSS and dissociation was initiated by adding 60 \u00b5l Liberase Roche. Embryos were deyolked by pipetting up and down  first with a p1000 tip and subsequently with a p100 tip  as described by Samsa et al.  2016. Following yolk removal  embryos were incubated at 32.5\u00b0C. To facilitate dissociation  embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5\u00b0C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation  cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4\u00b0C. The supernatant was discarded and the resulting pellets were resuspended in 500 \u00b5l of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 \u00b5m strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 \u00b5m nozzle and a gating strategy as described by Samsa et al.  2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer.\u00a0Using this library  we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry", null, "strain background:AB/TU|age:28 hpf depleted|tissue:cardiac progenitors and cardiomyocytes|cell type:nkx2.5:ZsYellow+ cells", "GSM3610371", "GSM3610371: Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq; Danio rerio; RNA Seq", "GSM3610371", null, "1", "Nkx2.5:ZsYellow+ cells from control and Pbx4 depleted embryos were isolated via FACS at 28 hpf. Dissociation of embryos was performed as described by Stachura and Traver  2016 with the following modifications  approximately 180 embryos per condition were manually dechorionated and rinsed in ice cold Hank's Balance Salt Solution HBSS containing Ca2+ and Mg2+. Embryos were subsequently transferred to 1.5ml tubes in 500 \u00b5l HBSS and dissociation was initiated by adding 60 \u00b5l Liberase Roche. Embryos were deyolked by pipetting up and down  first with a p1000 tip and subsequently with a p100 tip  as described by Samsa et al.  2016. Following yolk removal  embryos were incubated at 32.5\u00b0C. To facilitate dissociation  embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5\u00b0C. This process was repeated until complete dissociation was achieved which took approximately 15 minutes. Dissociation of embryos was monitored using a dissecting microscope. Following dissociation  cell suspensions were centrifuged for 5 minutes at 13 000 rpm at 4\u00b0C. The supernatant was discarded and the resulting pellets were resuspended in 500 \u00b5l of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 \u00b5m strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 \u00b5m nozzle and a gating strategy as described by Samsa et al.  2016. The 10X Genomics Chromium Instrument and cDNA synthesis kit 10x Genomics was used by the CCHMC Genomics core to generate a barcoded cDNA library for single cell RNA sequencing from approximately 4 000 cells. cDNA library quality was determined using an Agilent Bioanalyzer.\u00a0Using this library  we performed one full lane sequence on two paired end 75bp Flow Cells using on an Illumina HiSeq2500. 10X Genomics Chromium v2 chemistry", "GEO Accession:GSM3610371", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP186305", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=10X PBX4 mo injected 3zf S2 L002 I1 001.fastq.gz   read2PairFiles=10X PBX4 mo injected 3zf S2 L002 R1 001.fastq.gz   read3PairFiles=10X PBX4 mo injected 3zf S2 L002 R2 001.fastq.gz", "10X_PBX4_mo_injected_3zf_S2_L002_I1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L002_R1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L002_R2_001.fastq.gz", "fastq fastq fastq", 13960104704.0, 76703872.0, "GSM3610371 r2", "0:8 1:27 2:147", "A:3921736827;C:3045954411;G:3216708567;T:3758217760;N:17487139", 8, 27, 147, null, 3921736827, 3045954411, 3216708567, 3758217760, 17487139, "SRX5392462", "SRS4380285", "SRA850447", "GEO", "Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital", 1, 0.91469, null, 0.06915, null, 0.82747, null, 0.49959, null, 147, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-02-15", "Pharyngula", "Embryo", "Heart", "Cardiovascular System"]], "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": ["51191"], "units": {}, "query_ms": 6.61550099903252}