run_metadata: 51190

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
51190	SRR8592250	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.		pubmed:32094112		Pbx4 depleted nkx2.5:ZsYellow+ cells 10X Genomics single cell RNA Seq	GSM3610371		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		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 µl HBSS and dissociation was initiated by adding 60 µl 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°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. 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°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm 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. Using 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		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		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 µl HBSS and dissociation was initiated by adding 60 µl 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°C. To facilitate dissociation embryos were gently homogenized using a handheld pestle homogenizer 5 10 seconds and returned to 32.5°C. 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°C. The supernatant was discarded and the resulting pellets were resuspended in 500 µl of FACS medium consisting of 0.9X PBS and 2% fetal bovine serum FBS. Samples were filtered twice through a 40 µm strainer and collected in a FACs tube. FACS sorting was performed by the CCHMC Research Flow Cytometry Core using a 70 µm 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. Using 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		SRP186305		loader:fastq load.py\|options: platform=Illumina readTypes=TTB read1PairFiles=10X PBX4 mo injected 3zf S2 L001 I1 001.fastq.gz read2PairFiles=10X PBX4 mo injected 3zf S2 L001 R1 001.fastq.gz read3PairFiles=10X PBX4 mo injected 3zf S2 L001 R2 001.fastq.gz	10X_PBX4_mo_injected_3zf_S2_L001_I1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L001_R1_001.fastq.gz 10X_PBX4_mo_injected_3zf_S2_L001_R2_001.fastq.gz	fastq fastq fastq	13771731610.0	75668855.0	GSM3610371 r1	0:8 1:27 2:147	A:3868981340;C:3004344480;G:3173242889;T:3705905113;N:19257788	8	27	147		3868981340	3004344480	3173242889	3705905113	19257788	SRX5392462	SRS4380285	SRA850447	GEO	Nathan Salomonis, Biomedical Informatics, Cincinnati Children's Hospital	1	0.91532		0.07049		0.82722		0.50962		147		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2019-02-15	Pharyngula	Embryo	Heart	Cardiovascular System