run_metadata: 32609

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
32609	SRR29325925	SRX24842084	SRS21553259	SRP512516	PRJNA1121299	Gene expression profile of single endocardial cells in 48 hpf and 72 hpf zebrafish embryos/larvae. In the study "The heart is a niche for hematopoietic stem and progenitor cells in zebrafish."	GSE269378	Transcriptome Analysis	We used single cell RNA expression to uncover the cellular and molecular heterogeneity of isolated endocardial cells in the heart. From this study we uncovered the presence of an endocardial hematopoietic cluster along with other significant clusters including valve endocardial and interstitial cells and non valve cells. Overall design: Endocardial cells were isolated using FACS from physically extracted Tgkdrl:nls mCherry and Tgcd41:GFP hearts according to presence of mCherry positive cells and further analyzed using scRNAseq.		pubmed:39217144		EC 2d	GSM8314110		source name:Heart\|tissue:Heart\|cell type:Endocardial cells\|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP\|developmental stage:48 hpf loc name:missing\|collection date:missing	EC 2d	Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 5 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 5%. Furthermore we filtered 24259 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA retaining 50 principal components. Subsequent steps like low dimensional UMAP embedding McInnes & Healy https://arxiv.org/abs/1802.03426 and cell clustering via community detection were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs	Heart		Embryos were raised in a solution composed of 0.33 Danieau's medium containing the following concentrations: 17.4 mM NaCl 0.21 mM KCl 0.12 mM MgSO4·H2O and 0.18 mM CaNO32 while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment hearts from 48 and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS. Hearts were then centrifuged for 60 seconds at 3000 rpm washed with 1 mL Hanks’ Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit Thermo Fisher Scientific Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79. The samples were centrifuged for 5 minutes at 3000 rpm the supernatant was discarded and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes. Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates. Cells were sorted using the BD FACSAria™ III BD Biosciences instrument. Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter. The software used for sorting and analysis is BD FACSDiva v8.0.1. Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS. Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing. mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 4.000 2d HC and 8.000 3d 10.497 EC 1.569 HC single cell data points per sample respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Library preparation was conducted according to the manufacturer indications.	Embryos/larvae were grown in 28 degree incubator until extraction at 48 or 72 hpf	tissue:Heart\|cell type:Endocardial cells\|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP\|developmental stage:48 hpf	GSM8314110	GSM8314110: EC 2d; Danio rerio; RNA Seq	GSM8314110 r1	GSM8314110	1	Embryos were raised in a solution composed of 0.33 Danieau's medium containing the following concentrations: 17.4 mM NaCl 0.21 mM KCl 0.12 mM MgSO4·H2O and 0.18 mM CaNO32 while being maintained at a stable temperature of 28°C. To isolate EdCs for the single cell RNA sequencing experiment hearts from 48 and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS. Hearts were then centrifuged for 60 seconds at 3000 rpm washed with 1 mL Hanks' Balanced Salt Solution and dissociated into single cells by incubating in 100 μl Enzyme 1 and 5 μl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit Thermo Fisher Scientific Cat#88281 for 20 minutes at 300 rpm in a 30°C shaker 79. The samples were centrifuged for 5 minutes at 3000 rpm the supernatant was discarded and fresh medium was added to the dissociated cells and passed through 40 μM filter polystyrene 5ml tubes. Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates. Cells were sorted using the BD FACSAria™ III BD Biosciences instrument. Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter. The software used for sorting and analysis is BD FACSDiva v8.0.1. Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS. Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing. mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 4.000 2d HC and 8.000 3d 10.497 EC 1.569 HC single cell data points per sample respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 10xGenomics. Library preparation was conducted according to the manufacturer indications.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 2000		SRP512516			Felix_10x_Lib_EC-2d_R1.fastq.gz Felix_10x_Lib_EC-2d_R2.fastq.gz	fastq fastq	37849382027.0	476135961.0	GSM8314110 r1	0:28 1:51.49	A:10212120425;C:8162504214;G:8573129268;T:10704929378;N:196698742	28	51			10212120425	8162504214	8573129268	10704929378	196698742	SRX24842084	SRS21553259	SRA1892449	MPI for heart and lung research	MPI for heart and lung research												T	B	mate1 technical by mapping diff	illumina	nextseq_v2	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Germany	2024-06-07	Hatching	Embryo	Heart	Cardiovascular System