run_metadata: 43658

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
43658	SRR5984238	SRX3140234	SRS2472998	SRP116311	PRJNA400391	Multiple roles for Wwtr1 in cardiac wall maturation	GSE103169	Transcriptome Analysis	Cardiac trabeculation is a highly regulated process that starts with the delamination of cardiomyocytes from the compact wall to form stereotypical muscular ridges in the developing ventricle. The Hippo signaling pathway has been implicated in cardiac development but many questions remain. We investigated the role of Wwtr1 a nuclear effector of the Hippo pathway in zebrafish and find that its loss results in hearts with reduced trabeculation. However in mosaic animals wwtr1 / cardiomyocytes contribute more frequently than wwtr1+/ cardiomyocytes to the trabecular layer of wild type hearts. To investigate this paradox we examined the myocardial wall at early stages and find that loss of Wwtr1 leads to disruption of the compact wall architecture as evidenced by the disorganized cortical actin structure and abnormal cell cell junctions. The mutant compact wall is not able to support trabeculation as in mosaic animals wild type cardiomyocytes are more frequently in the compact layer of mutant than heterozygous hearts. Therefore we propose that Wwtr1 establishes the compact wall architecture necessary for trabeculation and that it also modulates a cardiomyocyte's decision to enter the trabecular layer. Overall design: larval hearts from mutants and WT siblings were manuall dissected out at 57 hpf 59 hpf. A total of 23 hearts per biological replicate was collected. RNA sequencing was performed on three biological replicates for each genotype.		pubmed:29773645		WT2	GSM2756545		source name:larval hearts\|developmental stage:57 hpf 59 hpf\|tissue:whole hearts	WT2	Basecalls with RTA v2 Illumina Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Mapping: alignment versus the Ensembl Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1" The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers. Genome build: DanRer10 Supplementary files format and content: library size normalized counts per sample	larval hearts		RNA extraction was performed with Qiagen miRNeasy kit Clontech Pico Input Mammalian Takara Clontech. Briefly 6.5ng of total RNA was used as input for Pico Input Mammalian Takara Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.		developmental stage:57 hpf 59 hpf\|tissue:whole hearts	GSM2756545	GSM2756545: WT2; Danio rerio; RNA Seq	GSM2756545		1	RNA extraction was performed with Qiagen miRNeasy kit Clontech Pico Input Mammalian Takara Clontech. Briefly 6.5ng of total RNA was used as input for Pico Input Mammalian Takara Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.	GEO Accession:GSM2756545	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP116311			jason_heart_WT2_R1.fastq.gz	fastq	2428761873.0	34256225.0	GSM2756545 r1	0:70.90 1:0	A:548982414;C:680177405;G:725438417;T:473983208;N:180429	70	0			548982414	680177405	725438417	473983208	180429	SRX3140234	SRS2472998	SRA603246	GEO	MPI for heart and lung research	1	0.92891		0.26633		0.81742		0.68958		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Germany	2017-08-28	Hatching	Embryo	Heart	Cardiovascular System