{"database": "metadata", "table": "run_metadata", "rows": [[75429, "SRR24526052", "SRX20310269", "SRS17634744", "SRP437444", "PRJNA971920", "Foxj1 controls olfactory ciliogenesis and differentiation program of the olfactory sensory neurons", "GSE232397", "Transcriptome Analysis", "Olfaction plays important roles in food and mate choice  and also in the avoidance of predators  making it a vital sensory modality for preservation and reproduction. In the vertebrates  olfactory receptors are thought to localise on multiple cilia elaborated on the dendritic knobs of olfactory sensory neurons OSNs. Although olfactory cilia dysfunction can cause loss of the sense of smell  how their differentiation is programmed at the transcriptional level has remained largely unexplored. We discovered in zebrafish and mice that Foxj1  a fork head domain containing transcription factor traditionally linked with motile cilia biogenesis  is expressed in OSNs and required for olfactory epithelium formation. In keeping with the immotile nature of the olfactory cilia  we observed that ciliary motility genes that are the targets of Foxj1 in motile ciliated cells  are repressed in the OSNs. Strikingly  we also found that besides ciliogenesis  Foxj1 controls the differentiation of the OSNs by regulating their cell type specific gene expression  such as that of olfactory marker protein omp involved in odour evoked signal transduction. In line with these requirements  response to bile acid  an odour detected by OMP positive OSNs  was significantly diminished in the foxj1 mutant zebrafish. Taken together  our findings establish how the canonical Foxj1 mediated motile ciliogenic transcriptional program has been repurposed for the biogenesis of the immotile olfactory cilia and for the development of the OSNs themselves. Overall design: to investigate the role of Foxj1 genes in zebrafish  foxj1a and foxj1b knock out fish used for RNA isolation at 4 dpf.", null, "pubmed:38271330", null, "Foxj1a Control R2", "GSM7329925", null, "source name:whole embryo|tissue:whole embryo|genotype:Wild Type|geo loc name:missing|collection date:missing", "Foxj1a Control R2", "In order to analyze the RNA Sequencing data  the paired end sequencing reads were aligned to the Zebrafish genome GRCz11 using and read counts per gene were determined by using featureCounts using GTF file from Ensembl version 106. The raw read counts were used as input for DESeq2 for Differentially expressed genes. Genes with abslog2 fold change > 2 and p adj < 0.1 were assumed as significantly expressed genes. Assembly: GRCz11/ensembl 106 Supplementary files format and content: tab delimited raw read counts", "whole embryo", null, "To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI\u2019s DNBSEQTM Technology.", "Embryonic  larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 \u00b0C  14/10 light/dark cycle.", "tissue:whole embryo|genotype:Wild Type", "GSM7329925", "GSM7329925: Foxj1a Control R2; Danio rerio; RNA Seq", "GSM7329925 r1", "GSM7329925", "1", "To isolate RNA for sequencing  4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5mins at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2mins at room temperature and then centrifuged for 15mins at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30secs at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30secs at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10\u03bcL DNase+ 70\u03bcL RDD buffer per tube for 45mins at room temperature. post incubation 350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30secs. This step was repeated twice  and the tubes were then centrifuged for 1min at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2mins. The tubes were then centrifuged for 1min at 8000rpm to elute the RNA. The library construction and sequencing was done by BGI's DNBSEQTM Technology.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP437444", null, null, "5-Foxj1aControl-2-30th-June_1.fq.gz 5-Foxj1aControl-2-30th-June_2.fq.gz", "fastq fastq", 4958039400.0, 24790197.0, "GSM7329925 r1", "0:100 1:100", "A:1388012642;C:1078189151;G:1080159974;T:1411677633;N:0", 100, 100, null, null, 1388012642, 1078189151, 1080159974, 1411677633, 0, "SRX20310269", "SRS17634744", "SRA1637502", "NTNU", "NTNU", 2, 0.92573, 0.92653, 0.16139, 0.16191, 0.65512, 0.65541, 0.4936, 0.49512, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-05-12", "Multi-stage", "Multi-stage", "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": ["75429"], "units": {}, "query_ms": 16.041390001191758}