run_metadata: 34909

This data as json

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
34909	SRR32321887	SRX27657146	SRS24062613	SRP563479	PRJNA1222877	Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage	GSE289416	Transcriptome Analysis	Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation and link this to intracellular calcium release via the protease receptor Par2a. This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls				Severe par2a mutant B3	GSM8790741		source name:1hpf\|tissue:1hpf\|genotype:par2a mutant Severe\|batch:biol rep 1\|geo loc name:missing\|collection date:missing	Severe par2a mutant B3	In order to remove technical sequences including adapters polymerase chain reaction PCR primers or fragments thereof and quality of bases lower than 20 pass filter data of fastq format were processed by Cutadapt V1.9.1 phred cutoff: 20 error rate: 0.1 adapter overlap: 1bp min. length: 75 proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls Excel file with all samples raw counts and FPKM in alternating columns	1hpf		RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.	Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted	tissue:1hpf\|genotype:par2a mutant Severe\|batch:biol rep 1	GSM8790741	GSM8790741: Severe par2a mutant B3; Danio rerio; RNA Seq	GSM8790741 r1	GSM8790741	1	RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP563479			B3_R1.fq.gz B3_R2.fq.gz	fastq fastq	10602259500.0	35340865.0	GSM8790741 r1	0:150 1:150	A:2890092630;C:2407378053;G:2504194258;T:2799754016;N:840543	150	150			2890092630	2407378053	2504194258	2799754016	840543	SRX27657146	SRS24062613	SRA2077074	Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine	Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		Singapore	2025-02-12	Multi-stage	Embryo	Oocyte	Reproductive System