{"database": "metadata", "table": "run_metadata", "rows": [[28772, "SRR26639099", "SRX22339478", "SRS19389127", "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/ \u00b5L 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.", null, "pubmed:39720516", null, "sibling  replicate 2  snRNAseq", "GSM7880035", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 2  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", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. 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/ \u00b5L 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\u00b0 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\u2019 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", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880035", "GSM7880035: sibling  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880035 r1", "GSM7880035", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. 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/ \u00b5L 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\u00b0 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_2_S1_L002_R1_001.fastq.gz sib_2_S1_L002_R2_001.fastq.gz", "fastq fastq", 29238445684.0, 247783438.0, "GSM7880035 r2", "0:29 1:89", "A:8764474921;C:6441070570;G:6601843083;T:7430828352;N:228758", 29, 89, null, null, 8764474921, 6441070570, 6601843083, 7430828352, 228758, "SRX22339478", "SRS19389127", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03758, 0.89628, 0.02664, 0.33912, 0.98711, 0.87442, 0.4887, 0.42456, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["28772"], "units": {}, "query_ms": 11.247240996453911}