{"database": "metadata", "table": "run_metadata", "rows": [[61606, "SRR12874637", "SRX9340661", "SRS7562470", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 56 hpf Rep1 [1 56 O]", "GSM4848060", null, "source name:optic fissure retina 56 hpf|hpf:56|tissue:optic fissure retina", "OF 56 hpf Rep1 [1 56 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:optic fissure retina", "GSM4848060", "GSM4848060: OF 56 hpf Rep1 [1 56 O]; Danio rerio; RNA Seq", "GSM4848060", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848060", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "1-56-O_R1.fastq.gz 1-56-O_R2.fastq.gz", "fastq fastq", 2610698400.0, 13053492.0, "GSM4848060 r1", "0:100 1:100", "A:747164488;C:558793373;G:578023357;T:723973829;N:2743353", 100, 100, null, null, 747164488, 558793373, 578023357, 723973829, 2743353, "SRX9340661", "SRS7562470", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.92606, 0.92637, 0.20702, 0.20634, 0.72056, 0.72121, 0.50668, 0.50793, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory 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": ["61606"], "units": {}, "query_ms": 7.484343994292431}