run_metadata: 43756

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
43756	SRR6054092	SRX3201031	SRS2528003	SRP118319	PRJNA408129	Spatially resolved RNA sequencing of the embryonic zebrafish heart	GSE104057	Transcriptome Analysis	Development of specialized cell types and structures in the vertebrate heart is regulated by spatially restricted molecular pathways. Disruptions in these pathways can cause severe congenital cardiac malformations or functional defects. To better understand these pathways and how they regulate cardiac development and function we used tomo seq combining high throughput RNA sequencing with tissue sectioning to establish a genome wide expression dataset with high spatial resolution for the developing zebrafish heart. Analysis of the dataset revealed over 1100 genes differentially expressed in sub compartments. Pacemaker cells in the sinoatrial region induce heart contractions but little is known about the mechanisms underlying their development and function. Using our transcriptome map we identified spatially restricted Wnt/ß catenin signaling activity in pacemaker cells which was controlled by Islet 1 activity. Moreover Wnt/ß catenin signaling at a specific developmental stage in the myocardium controls heart rate by regulating pacemaker cellular response to parasympathetic stimuli. Thus this high resolution transcriptome map incorporating all cell types in the embryonic heart can expose spatially restricted molecular pathways critical for specific cardiac functions. Overall design: To generate spatially resolved RNA seq data for the developing zebrafish hearts 2 dpf we cryosectioned 3 hearts extracted RNA from the individual sections amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al. Cell Reports 2012 with a few modifications. Libraries were sequenced on Illumina NextSeq using 75bp paired end sequencing. Sample Heart #1 is the primary sample. Heart #2 and #3 are biological replicates used for comparison.		pubmed:29400650		heart2 2dpf wt	GSM2788519		source name:isolated embryonic heart\|tissue:embryonic heart\|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #49 #96\|section thickness:10µm sections	heart2 2dpf wt	Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al. Cell Reports 2012 processed data files contain transcript read counts normalized against spike in read count and total read count per section Genome build: zv9 with improved three prime annotation see Junker et al 2014 Cell Supplementary files format and content: csv file containing transcript counts per gene rows and section columns	isolated embryonic heart	Unfixed embryonic hearts were dissected and embedded in tissue freezing medium. Blocks were cryosectioned and individual sections were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.	Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell		tissue:embryonic heart\|developmental stage:48 hpf direction:posterior/inflow tract to anterior/outflow tract; located in sections #49 #96\|section thickness:10µm sections	GSM2788519	GSM2788519: heart2 2dpf wt; Danio rerio; RNA Seq	GSM2788519		1	Total RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al. Cell Reports 2012 see also: Junker et al. 2014 Cell CEL seq protocol Hashimshony et al. Cell Reports 2012; also see: Junker et al. 2014 Cell	GEO Accession:GSM2788519	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP118319			heart_02_SB-150707_R1.fastq.gz heart_02_SB-150707_R2.fastq.gz	fastq fastq	5482437730.0	36337096.0	GSM2788519 r1	0:75.41 1:75.47	A:1859596349;C:686627791;G:950285046;T:1980208127;N:5720417	75	75			1859596349	686627791	950285046	1980208127	5720417	SRX3201031	SRS2528003	SRA610777	GEO	Jeroen Bakkers lab, Cardiac Development and Genetics, Hubrecht Institute	2	0.14301	0.55835	0.12504	0.16935	0.99285	0.86334	0.46837	0.58661	76	74	T	B	mate1 technical by mapping diff	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	celseq		Netherlands	2017-09-20	Hatching	Embryo	Heart	Cardiovascular System