{"database": "metadata", "table": "run_metadata", "rows": [[65001, "SRR14883457", "SRX11200537", "SRS9255516", "SRP325167", "PRJNA740056", "Transcriptome RNA seq analysis of the retina of crumbs 2a crb2a m289/m289 zebrafish model of Leber congenital amaurosis and retinitis pigmentosa.", "GSE178709", "Transcriptome Analysis", "The crumbs cell polarity complex plays a crucial role in apical basal epithelial polarity. When human CRB1 is mutated  it results in autosomal recessive Leber congenital amaurosis and retinitis pigmentosa  with no established genotype phenotype correlation. Using the oko meduzym289/m289 crb2a /  zebrafish model  we performed integrative transcriptomic and methylomic analysis to identify dysregulated genes and pathways. We reveal delayed retinal cell type specification confirmed in patient derived retinal organoids  with disruption to cell cycle modulation and epigenetic transcriptional control. Hence  using reduced representation bisulphite sequencing RRBS we explored differential DNA methylation  identifying hypermethylated pathways involving biological adhesion  Hippo and transforming growth factor beta TGFbeta signalling. Functional epigenetic modules FEM were highlighted through the integration of RNA seq and RRBS  confirming cell cycle involvement and disturbance of TGFbeta  BMP  Hippo and SMAD protein signal transduction. Taken together our work provides insights for epigenetic regulation in early retinal development and considerations for future therapeutic development. Overall design: We used RNA seq to identify differentially expressed genes between the zebrafish model of CRB  crb2a m289. Samples were isolated retinal regions of the dorsal retina at 56 hpf; crb2a /  and control wildtype. Biological replicates were taken.", null, "pubmed:36656098", null, "crb2a m289/m289 retina rep 1 [R56 crb01]", "GSM5396378", null, "source name:crb2a m289/m289 retina|genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina", "crb2a m289/m289 retina rep 1 [R56 crb01]", "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 HISAT2 v2.2.1 using using standard paired end based parameters. Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using featurecounts v2 and modelled using DESeq2 v1.30.1 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include raw count values for each sample", "crb2a m289/m289 retina", 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", "genotype:crb2a m289/m289|hpf:56|tissue:dorsal retina", "GSM5396378", "GSM5396378: crb2a m289/m289 retina rep 1 [R56 crb01]; Danio rerio; RNA Seq", "GSM5396378", 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:GSM5396378", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP325167", null, null, "R56-crb01_R1.fastq.gz R56-crb01_R2.fastq.gz", "fastq fastq", 2947225600.0, 14736128.0, "GSM5396378 r1", "0:100 1:100", "A:906619457;C:624314744;G:678281106;T:735161202;N:2849091", 100, 100, null, null, 906619457, 624314744, 678281106, 735161202, 2849091, "SRX11200537", "SRS9255516", "SRA1249569", "GEO", "Institute of Ophthalmology, UCL", 2, 0.90444, 0.90345, 0.15985, 0.15916, 0.81049, 0.81067, 0.51786, 0.52746, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2021-06-22", "Undetermined", "Undetermined", "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": ["65001"], "units": {}, "query_ms": 6.723454993334599}