run_metadata: 28777

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
28777	SRR26639104	SRX22339475	SRS19389124	SRP469857	PRJNA1034995	Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.	GSE246850	Transcriptome Analysis	Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis differentiation and stress survival which is particularly important to the pathophysiology of the cardiovascular system. What is more both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis and in particular valve development. However it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required. Here we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development including abnormal endocardial organization impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates each consisting of four pools50 hearts were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and dual indexed using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina 20028319 on an Illumina NovaSeq 6000.		pubmed:39720516		spns mutant replicate 1 snRNAseq	GSM7880032		source name:heart\|tissue:heart\|age:3dpf\|genotype:spns mutant\|geo loc name:missing\|collection date:missing	spns mutant replicate 1 snRNAseq	The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0 or demultiplexing barcode processing gene count processing. For alignment we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes tab seprated values Supplementary files format and content: feature counts tab seprated values Supplementary files format and content: matrix matrix	heart		Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and 3’ gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and dual indexed using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina 20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles i7 index: 10 cycles i5: 10 cycles and read 2: 89 91 cycles. snRNA seq		tissue:heart\|age:3dpf\|genotype:spns mutant	GSM7880032	GSM7880032: spns mutant replicate 1 snRNAseq; Danio rerio; RNA Seq	GSM7880032 r1	GSM7880032	1	Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described65. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific supplemented with 10% fetal bovine serum Sigma Aldrich F7524 centrifuged for 4 minutes at 300 g snap frozen and preserved in liquid nitrogen. Two replicates each consisting of four pools were obtained for each experimental group sibling mutant. Single nuclei suspensions containing 3800 4000 nuclei/ µL were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics PN 1000494 following the samples Prep User Guide 10 x Genomics CG000505 Rev A. The Transposition GEM generation & barcoding reverse transcription and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at 80° C. When samples were retrieved from storage they were cleaned up as stipulated in step 3.0 of the user guide. Therepost a pre amplification step was performed with 6 PCR cycles followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent DNF 473 respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM asymmetric paired end and dual indexed using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina 20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles i7 index: 10 cycles i5: 10 cycles and read 2: 89 91 cycles. snRNA seq		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP469857		loader:fastq load.py	mut_1_S1_L001_R1_001.fastq.gz mut_1_S1_L001_R2_001.fastq.gz	fastq fastq	30027997254.0	254474553.0	GSM7880032 r1	0:29 1:89	A:9128230353;C:6473885422;G:6895366272;T:7530354635;N:160572	29	89			9128230353	6473885422	6895366272	7530354635	160572	SRX22339475	SRS19389124	SRA1744308	University of Bern	University of Bern	2	0.03908	0.86231	0.0274	0.38263	0.98701	0.87113	0.48114	0.78783	29	89	T	B	sc-like readlen	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Switzerland	2023-11-02	Larval	Larval	Heart	Cardiovascular System