run_metadata: 33668

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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
33668	SRR30502669	SRX25926473	SRS22513924	SRP529840	PRJNA1154960	Deletion of ddx4 ovary specific transcript causes downregulation of sycp1 and derepression of DNA transposons in zebrafish ovaries	GSE276129	Transcriptome Analysis	Ddx4 DEAD box helicase 4 is a well established marker gene for early stage germlines and is required for the development of germ cells. Alternative splicing of ddx4 produces a long transcript that is exclusively expressed in zebrafish ovaries. The function of this ovary specific transcript ddx4 L remains unclear. In this study using the ddx4 L knockout zebrafish model we found that elimination of ddx4 L results in a decrease in fertilization rate and in the number of mature eggs laid by the female mutants. Transcriptome analysis was performed to identify the underlying changes of gene expression between WT and ddx4 L knockout ovaries. A total of 1134 differentially expressed genes were identified of which 524 were upregulated and 610 were downregulated. Functional enrichment analysis showed that the terms of negative regulation of fertilization sperm egg recognition process and oocyte meiosis might be affected by elimination of ddx4 L. Furthermore we found that Sycp1 a synaptonemal complex protein involved in meiosis and fertility was dramatically decreased in the ddx4 L knockout ovaries at both mRNA and protein levels. Moreover the activities of transposable elements were analyzed based on the RNA seq data. The result showed that elimination of ddx4 L causes the derepression of DNA transposons a subclass of transposable elements in zebrafish ovaries. In conclusion the aforementioned findings indicate that the ovary specific transcript of ddx4 plays an important role in oocyte development and egg quality possibly by maintaining sycp1 expression and repressing DNA transposons. Our work provide novel insights into the functions and regulatory mechanisms of ddx4 in zebrafish oogenesis. Overall design: Ovaries were dissected from three WT and three ddx4 E4? zebrafish at 6 mpf respectively. Six total RNA samples were extracted and subjected to RNA sequencing. Differentially expressed genes DEGs and transposable elements TEs between WT and ddx4 E4? zebrafish ovaries were analyzed.		pubmed:39765722		WT ovary rep1	GSM8491756		source name:Ovary\|tissue:Ovary\|genotype:WT\|geo loc name:missing\|collection date:missing	WT ovary rep1	The raw paired end reads were trimmed and quality controlled by SeqPrep https://github.com/jstjohn/SeqPrep and Sickle https://github.com/najoshi/sickle with default parameters. Then clean reads were separately aligned to zebrafish reference genome GRCz11 with orientation mode using HISAT2 http://ccb.jhu.edu/software/hisat2/index.shtml software. The mapped reads of each sample were assembled by StringTie https://ccb.jhu.edu/software/stringtie/index.shtml in a reference based approach. To identify DEGs differential expression genes between the ovaries of WT and ddx4 E4Δ zebrafish the expression level of each transcript was calculated according to the transcripts per million reads TPM method. RSEM http://deweylab.biostat.wisc.edu/rsem/ was used to quantify gene abundances. Essentially differential expression analysis was performed using the DESeq2 software. DEGs with \|log2FC\|>1 and Q value <= 0.05 were considered to be significantly different expressed genes. Functional enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni corrected P value ≤0.05 compared with the whole transcriptome background. Assembly: GRCz11 Supplementary files format and content: read count.txt is a tab delimited text file for read count numbers of each gene in all six samples.	Ovary		Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer’s protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.		tissue:Ovary\|genotype:WT	GSM8491756	GSM8491756: WT ovary rep1; Danio rerio; RNA Seq	GSM8491756 r1	GSM8491756	1	Ovaries were dissected from WT and ddx4 E4Δ zebrafish at 6 mpf. Total RNA was extracted using the Trizol reagent according to the manufacturer's protocol. RNA quality was determined by 2100 Bioanalyser Agilent and quantified using the ND 2000 spectrophotometer NanoDrop Technologies. RNA seq libraries were constructed using the TruSeqTM RNA sample preparation Kit Illumina San Diego CA. About 1μg of high quality total RNA samples OD260/280=1.82.2 RIN≥6.5 was used for each RNA seq library. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. The final sequencing libraries were quantified by TBS 380 Mini Fluorometer Promega.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP529840			W1_R1.fastq.gz W1_R2.fastq.gz	fastq fastq	8347159200.0	27639600.0	GSM8491756 r1	0:151 1:151	A:2109928092;C:2033967699;G:2079802211;T:2123438464;N:22734	151	151			2109928092	2033967699	2079802211	2123438464	22734	SRX25926473	SRS22513924	SRA1960397	Institute of Hydrobiology, Chinese Academy of Sciences	Institute of Hydrobiology, Chinese Academy of Sciences												B	B	biological fallback assumption	illumina	novaseq_era	full_length	random_priming	unknown	bulk	unknown	unknown		China	2024-08-31	Adult	Adult	Gonad	Reproductive System