{"database": "metadata", "table": "run_metadata", "rows": [[25085, "SRR25557918", "SRX21286754", "SRS18536867", "SRP453890", "PRJNA1003061", "dact1/2 modifies noncanonical Wnt signaling and calpain 8 expression to regulate convergent extension and craniofacial development", "GSE240264", "Transcriptome Analysis", "Wnt signaling plays a fundamental role in the initial patterning and development of the embryo  including in the regulation of convergent extension during gastrulation and the establishment of the dorsal axis. Further  Wnt signaling is a crucial regulator of craniofacial morphogenesis. The relationship between early embryo patterning and craniofacial outcomes warrants further study. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled  however  the distinct roles of Dact1 and Dact2 during embryogenesis remain to be fully elucidated. In this study  we investigated the spatiotemporal gene expression patterns of dact1 and dact2 during zebrafish embryogenesis  revealing both shared and unique domains of expression. We found that both dact1 and dact2 contribute to axis extension  with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the wnt11f2/slb mutant. Utilizing single cell RNAseq and gpc4 /  zebrafish  a convergent extension mutant with an opposite craniofacial phenotype  we identified dact1/2 specific roles during early development. Using this subtractive approach  we discovered a novel role for dact1/2 in regulating the mRNA expression of the classical calpain  capn8  suggesting a previously unappreciated role of calcium dependent proteolysis during embryogenesis. Taken together  our findings highlight the distinct and overlapping roles of dact1 and dact2 in embryonic craniofacial development  providing new insights into the multifaceted regulation of Wnt signaling. Overall design: Single cell RNA sequencing scRNA seq analyses were performed on 10 zebrafish embryos 4 WT  3 dact1 / ;dact2 /  compound mutant  and 3 gpc4 /  mutant embryos harvested at the 3 somite stage  to assess transcriptomic perturbations during development induced by deletion of dact1/2.", null, "pubmed:37986847", null, "Zebrafish  3 somite stage embryo  dact1 / ;dact2 /  compound mutant  replicate 1", "GSM7689208", null, "source name:whole embryo|tissue:whole embryo|strain:Tubingen|developmental stage:3 somite stage|genotype:dact1 / ;dact2 / |geo loc name:missing|collection date:missing", "Zebrafish  3 somite stage embryo  dact1 / ;dact2 /  compound mutant  replicate 1", "FASTQ files were demultiplexed and aligned to the GRCz11 build of the zebrafish genome using Cellranger version 6.1.0.", "whole embryo", null, "Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase  washed 3x in embryo medium  and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation  cells were passed through a 70 um cell strainer  and cell counts and viability were measured. post droplet encapsulation  barcoding  and library preparation using the 10X Genomics Chromium Single Cell 3\u2019 kit version 3  data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation  barcoding  and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell 3\u2019 kit version 3", "Zebrafish Danio rerio embryos were raised at 28.5C in E3 medium  and staged visually and according to standardized developmental timepoints. Embryos were collected at the 3 stomite stage; mutants were identified by their truncated body axis.", "tissue:whole embryo|strain:Tubingen|developmental stage:3 somite stage|genotype:dact1 / ;dact2 / ", "GSM7689208", "GSM7689208: Zebrafish  3 somite stage embryo  dact1 / ;dact2 /  compound mutant  replicate 1; Danio rerio; RNA Seq", "GSM7689208 r1", "GSM7689208", "1", "Embryos were dechorionated with a 10 min incubation in 1 mg/mL Pronase  washed 3x in embryo medium  and dissociated on ice in 200 uL DPBS without xxx+ and Mg2+ with 0.1% BSA. Embryos were disrupted by pipetting 10x with a P200 pipette tip. 500 uL of DPBS + 0.1% BSA was added and cells were centrifuged at 300g for 1 min. Cell pellets were resuspended in 200 ul DPBS + 0.1% BSA and kept on ice. Prior to encapsulation  cells were passed through a 70 um cell strainer  and cell counts and viability were measured. post droplet encapsulation  barcoding  and library preparation using the 10X Genomics Chromium Single Cell three prime kit version 3  data were sequenced on an Illumina NovaSeq 6000 sequencer. Droplet encapsulation  barcoding  and library preparation were performed per the manufacturer protocol using the 10X Genomics Chromium Single Cell three prime kit version 3", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP453890", null, "loader:fastq load.py", "SCa3_S2_L001_I1_001.fastq.gz SCa3_S2_L001_R1_001.fastq.gz SCa3_S2_L001_R2_001.fastq.gz", "fastq fastq fastq", 7236003222.0, 57428597.0, "GSM7689208 r1", "0:8 1:28 2:90", "A:1419674513;C:1150647971;G:1309649875;T:1282359791;N:6241580", 8, 28, 90, null, 1419674513, 1150647971, 1309649875, 1282359791, 6241580, "SRX21286754", "SRS18536867", "SRA1688444", "Harvard Chan Bioinformatics Core, Biostatistics, The Harvard T. H. Chan School of Public Health", "Computational and Single Cell Genomics Group, Kennedy Institute of Rheumatology (KIR)", 1, 0.94312, null, 0.22026, null, 0.78859, null, 0.52624, null, 90, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-07", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"]], "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": ["25085"], "units": {}, "query_ms": 10.48701599938795}