{"database": "metadata", "table": "run_metadata", "rows": [[36381, "SRR514031", "SRX155011", "SRS346297", "SRP013815", "PRJNA168635", "Id2a knockdown in zebrafish retina", "GSE38786", "Transcriptome Analysis", "During vertebrate retinogenesis the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways. Moreover there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor Id2a in regulating retinoblast proliferation and differentiation with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia. Here we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis. Id2a deficient retinae possess elevated levels of Notch pathway component gene expression while retinae overexpressing id2a possess reduced expression of Notch pathway component genes. Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity through an RNA Seq and differential gene expression analysis of Id2a deficient retinae we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a. These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples", null, "pubmed:22981606", null, "Zebrafish retina with id2a morpholino treatment replicate 2", "GSM949497", null, "source name:Zebrafish retina with id2a morpholino treatment replicate 2|tissue:retina|genotype/variation:id2a knockdown", "Zebrafish retina with id2a morpholino treatment replicate 2", "Filter out all reads with no call \u2018N\u2019 and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample DESeq output for differentially expressed genes.", "Zebrafish retina with id2a morpholino treatment replicate 2", null, "Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.", null, "tissue:retina|genotype/variation:id2a knockdown", "GSM949497", "GSM949497: Zebrafish retina with id2a morpholino treatment replicate 2; Danio rerio; RNA Seq", "GSM949497 2", "GSM949497: Zebrafish retina with id2a morpholino treatment replicate 2", "1", null, "GEO Accession:GSM949497", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2020Application ReadForward11Application ReadReverse102", "SRP013815", null, null, "Uribe201204_id2aKD2.untie_2.fastq.gz", "fastq", 12244707932.0, 60617366.0, "GSM949497 r1", "0:101 1:101", "A:3345422426;C:2833723441;G:2860980232;T:3204581833;N:0", 101, 101, null, null, 3345422426, 2833723441, 2860980232, 3204581833, 0, "SRX155011", "SRS346297", "SRA054377", "GEO", "Department of Biomedical Engineering, Ulsan National Institute of Science and Technology", 2, 0.8674, 0.87016, 0.09985, 0.10059, 0.75442, 0.75187, 0.47467, 0.47364, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2012-06-18", "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": ["36381"], "units": {}, "query_ms": 8.178780000889674}