run_metadata: 49914

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
49914	SRR8883765	SRX5669566	SRS4612435	SRP166782	PRJNA498309	Functional heterogeneity within the developing zebrafish epicardium	GSE121750	Transcriptome Analysis	The epicardium is essential during cardiac development homeostasis and repair and yet fundamental insights into its underlying cell biology notably epicardium formation lineage heterogeneity and functional cross talk with other cell types in the heart is currently lacking. In this study we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion migration and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells		pubmed:32084358		133 2 D09 KOtgm2b ctr 3	GSM3718993		tissue:Heart\|transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	133 2 D09 KOtgm2b ctr 3	Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin 1 1 1 1 outSJfilterCountTotalMin 30 10 10 10 outSAMstrandField intronMotif outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1 p B a t exon g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC Column 1 = Ensembl gene ID column 2 = gene length in basepairs column 3 = gene name columns 4 151 = counts for each cell colnames = gene id gene length gene name cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC	Heart		Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT		transgenic reporter:tbx18:myr Citrine\|cell fluorescence:myr Citrine\|age:5 dpf	GSM3718993	GSM3718993: 133 2 D09 KOtgm2b ctr 3; Danio rerio; RNA Seq	GSM3718993		1	Larvae were physically disrupted hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2 Illumina Nextera XT	GEO Accession:GSM3718993	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP166782			133-2-D09-KOtgm2b-ctr-3_all_lanes_R1.fastq.gz 133-2-D09-KOtgm2b-ctr-3_all_lanes_R2.fastq.gz	fastq fastq	48591328.0	327743.0	GSM3718993 r1	0:74.13 1:74.13	A:12088250;C:12179083;G:12474240;T:11798218;N:51537	74	74			12088250	12179083	12474240	11798218	51537	SRX5669566	SRS4612435	SRA798477	GEO	University of Oxford	2	0.9338	0.93207	0.21936	0.22034	0.76359	0.76948	0.60676	0.59959	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq		United Kingdom	2019-04-11	Larval	Larval	Heart	Cardiovascular System