run_metadata: 75426

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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
75426	SRR24526049	SRX20310272	SRS17634746	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.		pubmed:38271330		Foxj1b Mutant R2	GSM7329928		source name:whole embryo\|tissue:whole embryo\|genotype:Foxj1b Knockout\|geo loc name:missing\|collection date:missing	Foxj1b Mutant 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		To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL 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°C. 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 700μL 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 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL 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 30μL 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.	Embryonic larval and adult zebrafish were reared according to standard procedures of husbandry at 28.5 °C 14/10 light/dark cycle.	tissue:whole embryo\|genotype:Foxj1b Knockout	GSM7329928	GSM7329928: Foxj1b Mutant R2; Danio rerio; RNA Seq	GSM7329928 r1	GSM7329928	1	To isolate RNA for sequencing 4dpf larvae were collected in a 1.5ml tube and placed on ice. To lyse the samples 500μL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500μL trizol the samples were incubated for 5mins at room temperature. The larvae were then treated with 200μL 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°C. 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 700μL 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 350μL of RW1 buffer followed by DNase enzyme Qiagen in RDD buffer 10μL DNase+ 70μL RDD buffer per tube for 45mins at room temperature. post incubation 350μL of RW1 buffer was added to the tubes and centrifuged for 15secs at 8000rpm. The tubes were then treated with 500μL 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 30μL 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.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7		SRP437444			8-Foxj1bmutant-2-30th-June_1.fq.gz 8-Foxj1bmutant-2-30th-June_2.fq.gz	fastq fastq	4886103400.0	24430517.0	GSM7329928 r1	0:100 1:100	A:1331170839;C:1099736133;G:1102504200;T:1352692228;N:0	100	100			1331170839	1099736133	1102504200	1352692228	0	SRX20310272	SRS17634746	SRA1637502	NTNU	NTNU	2	0.93144	0.93303	0.1297	0.13001	0.65729	0.6579	0.48133	0.48014	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		Unknown	2023-05-12	Multi-stage	Multi-stage	Whole Organism	All anatomical structures