metadata: run_metadata: 29 rows where devstage_curation = "Multi-stage" and tissue

29 rows where devstage_curation = "Multi-stage" and tissue_curation = "Oocyte"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
30755	30755	SRR28348921	SRX23954975	SRS20755396	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832		Zebrafish Oocyte Stage IV rep2	GSM8147872	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage IV rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF	GSM8147872	GSM8147872: Zebrafish Oocyte Stage IV rep2; Danio rerio; RNA Seq	GSM8147872 r1	GSM8147872	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_4_2_Pa.fastq	fastq	2456514332.0	32322557.0	GSM8147872 r1	0:76	A:588246161;C:609187233;G:593122683;T:665837765;N:120490	76		588246161	609187233	593122683	665837765	120490	SRX23954975	SRS20755396	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30756	30756	SRR28348922	SRX23954974	SRS20755395	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832		Zebrafish Oocyte Stage IV rep1	GSM8147871	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage IV rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		tissue:Oocyte\|developmental stage:Stage IV\|genotype:AB TF and TLF	GSM8147871	GSM8147871: Zebrafish Oocyte Stage IV rep1; Danio rerio; RNA Seq	GSM8147871 r1	GSM8147871	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_4_1_Pa.fastq	fastq	2650784696.0	34878746.0	GSM8147871 r1	0:76	A:649971632;C:640667370;G:632570967;T:727447552;N:127175	76		649971632	640667370	632570967	727447552	127175	SRX23954974	SRS20755395	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30757	30757	SRR28348923	SRX23954973	SRS20755394	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832		Zebrafish Oocyte Stage III rep2	GSM8147870	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage III rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF	GSM8147870	GSM8147870: Zebrafish Oocyte Stage III rep2; Danio rerio; RNA Seq	GSM8147870 r1	GSM8147870	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_3_2_Pa.fastq	fastq	2809957956.0	36973131.0	GSM8147870 r1	0:76	A:679041537;C:690924547;G:702857353;T:736996218;N:138301	76		679041537	690924547	702857353	736996218	138301	SRX23954973	SRS20755394	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30758	30758	SRR28348924	SRX23954972	SRS20755393	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832		Zebrafish Oocyte Stage III rep1	GSM8147869	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage III rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		tissue:Oocyte\|developmental stage:Stage III\|genotype:AB TF and TLF	GSM8147869	GSM8147869: Zebrafish Oocyte Stage III rep1; Danio rerio; RNA Seq	GSM8147869 r1	GSM8147869	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_3_1_Pa.fastq	fastq	2828372376.0	37215426.0	GSM8147869 r1	0:76	A:701751055;C:680571938;G:664212213;T:781698241;N:138929	76		701751055	680571938	664212213	781698241	138929	SRX23954972	SRS20755393	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30759	30759	SRR28348925	SRX23954971	SRS20755392	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832		Zebrafish Oocyte Stage II rep2	GSM8147868	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage II rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF	GSM8147868	GSM8147868: Zebrafish Oocyte Stage II rep2; Danio rerio; RNA Seq	GSM8147868 r1	GSM8147868	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_2_2_Pa.fastq	fastq	2837652432.0	37337532.0	GSM8147868 r1	0:76	A:698931608;C:681467909;G:683751172;T:773364392;N:137351	76		698931608	681467909	683751172	773364392	137351	SRX23954971	SRS20755392	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30760	30760	SRR28348926	SRX23954970	SRS20755391	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832		Zebrafish Oocyte Stage II rep1	GSM8147867	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage II rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		tissue:Oocyte\|developmental stage:Stage II\|genotype:AB TF and TLF	GSM8147867	GSM8147867: Zebrafish Oocyte Stage II rep1; Danio rerio; RNA Seq	GSM8147867 r1	GSM8147867	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_2_1_Pa.fastq	fastq	3360126820.0	44212195.0	GSM8147867 r1	0:76	A:829333798;C:802089215;G:804982077;T:923557236;N:164494	76		829333798	802089215	804982077	923557236	164494	SRX23954970	SRS20755391	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30761	30761	SRR28348927	SRX23954969	SRS20755390	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832		Zebrafish Oocyte Stage I rep2	GSM8147866	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage I rep2	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF	GSM8147866	GSM8147866: Zebrafish Oocyte Stage I rep2; Danio rerio; RNA Seq	GSM8147866 r1	GSM8147866	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_1_2_Pa.fastq	fastq	2739674220.0	36048345.0	GSM8147866 r1	0:76	A:653441701;C:681445567;G:663740568;T:740918288;N:128096	76		653441701	681445567	663740568	740918288	128096	SRX23954969	SRS20755390	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
30762	30762	SRR28348928	SRX23954968	SRS20755389	SRP495323	PRJNA1088158	Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis.	GSE261646	Transcriptome Analysis	The maternal to zygotic transition is crucial in embryonic development marked by the degradation of maternally provided mRNAs and initiation of zygotic gene expression. However the changes occurring at the protein level during this transition remain unclear. Here we conducted protein profiling throughout zebrafish embryogenesis using quantitative mass spectrometry integrating transcriptomics and translatomics datasets. Our data shows that unlike RNA changes protein changes are less dynamic. Further increases in protein levels correlate with mRNA translation whereas declines in protein levels do not suggesting active protein degradation processes. Interestingly proteins from pure zygotic genes are present at fertilization challenging existing mRNA based gene classifications. As a proof of concept we utilized CRISPR Cas13d to target znf281b mRNA a gene whose protein significantly accumulates within the first two hpf demonstrating its crucial role in development. Consequently our protein profiling coupled with CRISPR Cas13d offers a new approach to unravel maternal mRNAs function during embryonic development. Overall design: Two biological replicate samples containing 50 zebrafish oocytes per stage were collected by pairing females in natural matings to ''purge'' mature eggs and used to establish an oogenesis time line. Fish were euthanized and ovaries harvested within 1–11 days post purging dpp. Stage I and II oocytes were collected at 1–2 dpp stage III oocytes germinal vesicle in central position at 4–7 dpp and stage IV oocytes germinal vesicle asymmetrically located at 8–10 dpp. Oocyte isolations were based on73 and conducted in isolation medium Leibovitz L 15 Sigma Aldrich #L5520 plus Collagenase I and II depending on the stages as follows. Stages I and II were isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130 and 3 mg/mL Collagenase II Gibco 17101015. Stage III was isolated with 3 mg/mL Collagenase I Sigma Aldrich C0130. Stage IV was isolated by mechanical stripping with forceps and nee…	pubmed:39302832		Zebrafish Oocyte Stage I rep1	GSM8147865	source name:Oocyte\|tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF\|geo loc name:missing\|collection date:missing	Zebrafish Oocyte Stage I rep1	Raw reads from zebrafish oocytes stages I IV and embryos 0 2 4 and 6 hpf were demultiplexed into FASTQ format allowing up to one mismatch using Illumina bcl convert 3.10.5. Reads were aligned to UCSC genome danRer11 with STAR aligner version 2.7.3a using Ensembl 106 gene models. Counts were converted to TPM values using RSEM version v1.3.0 and all subsequent analysis was done using TPM. Assembly: danRer11 Ensembl 106 gene models Supplementary files format and content: comma separated files with TPMs from all replicates	Oocyte		Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer’s protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer’s protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer’s directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer’s instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		tissue:Oocyte\|developmental stage:Stage I\|genotype:AB TF and TLF	GSM8147865	GSM8147865: Zebrafish Oocyte Stage I rep1; Danio rerio; RNA Seq	GSM8147865 r1	GSM8147865	1	Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. 0 2 4 and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols. Ribo dep Stranded RNA Seq Zebrafish embryos 0 2 4 and 6 hpf total RNA sequencing libraries were generated from 500ng of high quality total RNA as assessed using Bioanalyzer Agilent. Libraries were made according to the manufacturer's directions for the TruSeq Stranded Total RNA Library Prep Gold Illumina #20020598 and TruSeq RNA Single Indexes Sets A and B Illumina #20020492 and #20020493. Resulting short fragment libraries were checked for quality and quantity using the Bioanalyzer Agilent Technologies and Qubit Fluorometer Life Technologies. Libraries were pooled quantified and sequenced as 75bp single reads on a high output flow cell using the Illumina NextSeq500 instrument. Following sequencing Illumina Primary Analysis version RTA 2.11.3.0 and bcl convert 3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files. Zebrafish oocytes stages I IV total RNA Seq libraries were generated from 100 ng of high quality total RNA as assessed by a Bioanalyzer Agilent Technologies. Libraries were prepared according to manufacturer's instructions using the TruSeq Stranded Total RNA Library Prep Gold Illumina Cat. No. 20020598 and TruSeq RNA Single Indexes; Sets A and B Illumina Cat. No. 20020492 and 20020493. Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer and a Qubit Fluorometer Life Technologies. Libraries were normalized pooled and sequenced on a NextSeq 500 instrument Illumina as 75 bp single end reads on a high output flowcell using NextSeq Control Software 2.2.0.4. Following sequencing Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP495323	Z_oocyte_stage_1_1_Pa.fastq	fastq	3348831852.0	44063577.0	GSM8147865 r1	0:76	A:815134657;C:817210346;G:809175239;T:907149915;N:161695	76		815134657	817210346	809175239	907149915	161695	SRX23954968	SRS20755389	SRA1824599	Computational Biology, Stowers Institute for Medical Research	Computational Biology, Stowers Institute for Medical Research												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	bulk	bulk	United States	2024-03-14	Multi-stage	Embryo	Oocyte	Reproductive System
34904	34904	SRR32321882	SRX27657151	SRS24062618	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			Mild par2a mutant Enew	GSM8790746	source name:1hpf\|tissue:1hpf\|genotype:par2a mutant Mild\|batch:biol rep 3\|geo loc name:missing\|collection date:missing	Mild par2a mutant Enew	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 Mild\|batch:biol rep 3	GSM8790746	GSM8790746: Mild par2a mutant Enew; Danio rerio; RNA Seq	GSM8790746 r1	GSM8790746	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	ENew_R1.fq.gz ENew_R2.fq.gz	fastq fastq	10329910500.0	34433035.0	GSM8790746 r1	0:150 1:150	A:2799891916;C:2357268078;G:2464224845;T:2708331200;N:194461	150	150	2799891916	2357268078	2464224845	2708331200	194461	SRX27657151	SRS24062618	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
34905	34905	SRR32321883	SRX27657150	SRS24062617	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			Mild par2a mutant Dnew	GSM8790745	source name:1hpf\|tissue:1hpf\|genotype:par2a mutant Mild\|batch:biol rep 2\|geo loc name:missing\|collection date:missing	Mild par2a mutant Dnew	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 Mild\|batch:biol rep 2	GSM8790745	GSM8790745: Mild par2a mutant Dnew; Danio rerio; RNA Seq	GSM8790745 r1	GSM8790745	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	DNew_R1.fq.gz DNew_R2.fq.gz	fastq fastq	10248079200.0	34160264.0	GSM8790745 r1	0:150 1:150	A:2793260638;C:2326676658;G:2420206143;T:2707745384;N:190377	150	150	2793260638	2326676658	2420206143	2707745384	190377	SRX27657150	SRS24062617	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
34906	34906	SRR32321884	SRX27657149	SRS24062616	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			Mild par2a mutant D2	GSM8790744	source name:1hpf\|tissue:1hpf\|genotype:par2a mutant Mild\|batch:biol rep 1\|geo loc name:missing\|collection date:missing	Mild par2a mutant D2	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 Mild\|batch:biol rep 1	GSM8790744	GSM8790744: Mild par2a mutant D2; Danio rerio; RNA Seq	GSM8790744 r1	GSM8790744	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	D2_R1.fq.gz D2_R2.fq.gz	fastq fastq	11762172300.0	39207241.0	GSM8790744 r1	0:150 1:150	A:3175985473;C:2693452522;G:2817123539;T:3074667110;N:943656	150	150	3175985473	2693452522	2817123539	3074667110	943656	SRX27657149	SRS24062616	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
34907	34907	SRR32321885	SRX27657148	SRS24062615	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 Cnew	GSM8790743	source name:1hpf\|tissue:1hpf\|genotype:par2a mutant Severe\|batch:biol rep 3\|geo loc name:missing\|collection date:missing	Severe par2a mutant Cnew	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 3	GSM8790743	GSM8790743: Severe par2a mutant Cnew; Danio rerio; RNA Seq	GSM8790743 r1	GSM8790743	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	CNew_R1.fq.gz CNew_R2.fq.gz	fastq fastq	10738375500.0	35794585.0	GSM8790743 r1	0:150 1:150	A:2913601251;C:2451840201;G:2552925604;T:2819808486;N:199958	150	150	2913601251	2451840201	2552925604	2819808486	199958	SRX27657148	SRS24062615	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
34908	34908	SRR32321886	SRX27657147	SRS24062614	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 Bnew	GSM8790742	source name:1hpf\|tissue:1hpf\|genotype:par2a mutant Severe\|batch:biol rep 2\|geo loc name:missing\|collection date:missing	Severe par2a mutant Bnew	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 2	GSM8790742	GSM8790742: Severe par2a mutant Bnew; Danio rerio; RNA Seq	GSM8790742 r1	GSM8790742	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	BNew_R1.fq.gz BNew_R2.fq.gz	fastq fastq	10032138000.0	33440460.0	GSM8790742 r1	0:150 1:150	A:2725263740;C:2280983708;G:2404101885;T:2621602178;N:186489	150	150	2725263740	2280983708	2404101885	2621602178	186489	SRX27657147	SRS24062614	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
34909	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
34910	34910	SRR32321888	SRX27657145	SRS24062612	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			Sibling3 S3 New	GSM8790740	source name:1hpf\|tissue:1hpf\|genotype:Sibling\|batch:biol rep 3\|geo loc name:missing\|collection date:missing	Sibling3 S3 New	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:Sibling\|batch:biol rep 3	GSM8790740	GSM8790740: Sibling3 S3 New; Danio rerio; RNA Seq	GSM8790740 r1	GSM8790740	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	S3New_R1.fq.gz S3New_R2.fq.gz	fastq fastq	10090266900.0	33634223.0	GSM8790740 r1	0:150 1:150	A:2751527796;C:2286318705;G:2376241359;T:2675989647;N:189393	150	150	2751527796	2286318705	2376241359	2675989647	189393	SRX27657145	SRS24062612	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
34911	34911	SRR32321889	SRX27657144	SRS24062611	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			Sibling2 S2 New	GSM8790739	source name:1hpf\|tissue:1hpf\|genotype:Sibling\|batch:biol rep 2\|geo loc name:missing\|collection date:missing	Sibling2 S2 New	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:Sibling\|batch:biol rep 2	GSM8790739	GSM8790739: Sibling2 S2 New; Danio rerio; RNA Seq	GSM8790739 r1	GSM8790739	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	S2New_R1.fq.gz S2New_R2.fq.gz	fastq fastq	10203807000.0	34012690.0	GSM8790739 r1	0:150 1:150	A:2771950983;C:2329534166;G:2415425258;T:2686709429;N:187164	150	150	2771950983	2329534166	2415425258	2686709429	187164	SRX27657144	SRS24062611	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
34912	34912	SRR32321890	SRX27657143	SRS24062610	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			Sibling1 S1 New	GSM8790738	source name:1hpf\|tissue:1hpf\|genotype:Sibling\|batch:biol rep 1\|geo loc name:missing\|collection date:missing	Sibling1 S1 New	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:Sibling\|batch:biol rep 1	GSM8790738	GSM8790738: Sibling1 S1 New; Danio rerio; RNA Seq	GSM8790738 r1	GSM8790738	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	S1New_R1.fq.gz S1New_R2.fq.gz	fastq fastq	10109834700.0	33699449.0	GSM8790738 r1	0:150 1:150	A:2734326027;C:2315919523;G:2410121939;T:2649275286;N:191925	150	150	2734326027	2315919523	2410121939	2649275286	191925	SRX27657143	SRS24062610	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
40962	40962	SRR3470786	SRX1738401	SRS1418771	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.	pubmed:27870856		60mg arm 3	GSM2140605	source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	60mg arm 3	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	GSM2140605	GSM2140605: 60mg arm 3; Danio rerio; RNA Seq	GSM2140605		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140605	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP074244	60mg-arm-3.fastq.gz	fastq	2353067800.0	23530678.0	GSM2140605 r1	0:100	A:550921675;C:559384489;G:553530174;T:689218350;N:13112	100		550921675	559384489	553530174	689218350	13112	SRX1738401	SRS1418771	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.95538		0.04454		0.7512		0.62731		100		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40963	40963	SRR3470785	SRX1738399	SRS1418770	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.	pubmed:27870856		60mg arm 2	GSM2140604	source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	60mg arm 2	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	GSM2140604	GSM2140604: 60mg arm 2; Danio rerio; RNA Seq	GSM2140604		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140604	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP074244	60mg-arm-2.fastq.gz	fastq	2552419200.0	25524192.0	GSM2140604 r1	0:100	A:598028827;C:604381782;G:600136410;T:749858137;N:14044	100		598028827	604381782	600136410	749858137	14044	SRX1738399	SRS1418770	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.95953		0.04033		0.75408		0.63549		100		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40964	40964	SRR3470784	SRX1738397	SRS1418769	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.	pubmed:27870856		60mg arm 1	GSM2140603	source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	60mg arm 1	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:60 mg	GSM2140603	GSM2140603: 60mg arm 1; Danio rerio; RNA Seq	GSM2140603		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140603	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP074244	60mg-arm-1.fastq.gz	fastq	2471843300.0	24718433.0	GSM2140603 r1	0:100	A:578536744;C:593318438;G:586674975;T:713299111;N:14032	100		578536744	593318438	586674975	713299111	14032	SRX1738397	SRS1418769	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.95474		0.04276		0.75625		0.61194		100		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40965	40965	SRR3470783	SRX1738395	SRS1418767	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.	pubmed:27870856		5mg arm 3	GSM2140602	source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	5mg arm 3	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	GSM2140602	GSM2140602: 5mg arm 3; Danio rerio; RNA Seq	GSM2140602		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140602	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP074244	5mg-arm-3.fastq.gz	fastq	2562336500.0	25623365.0	GSM2140602 r1	0:100	A:599122965;C:614407524;G:605967391;T:742824547;N:14073	100		599122965	614407524	605967391	742824547	14073	SRX1738395	SRS1418767	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.95071		0.0461		0.74483		0.61788		100		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40966	40966	SRR3470782	SRX1738393	SRS1418765	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.	pubmed:27870856		5mg arm 2	GSM2140601	source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	5mg arm 2	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	GSM2140601	GSM2140601: 5mg arm 2; Danio rerio; RNA Seq	GSM2140601		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140601	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP074244	5mg-arm-2.fastq.gz	fastq	2841710700.0	28417107.0	GSM2140601 r1	0:100	A:663485391;C:679416584;G:665850494;T:832942768;N:15463	100		663485391	679416584	665850494	832942768	15463	SRX1738393	SRS1418765	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.94998		0.04837		0.75442		0.63571		100		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
40967	40967	SRR3470781	SRX1738391	SRS1418764	SRP074244	PRJNA320266	Dietary intake influences fertility and offspring development in zebrafish.	GSE81007	Transcriptome Analysis	We report that increased nutrient availability increases breeding success and egg production. RNA seq analysis revealed that parental diet altered the expression of metabolic genes in the unfertilized eggs. Offspring from the differentially fed parents showed altered survival and energy expenditure as adults. Overall design: RNA from unfertilized eggs post two parental diets.	pubmed:27870856		5mg arm 1	GSM2140600	source name:Unfertilized eggs\|strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	5mg arm 1	Sequence reads were filtered for quality using trimgalore. Reads were then mapped to the zebrafish genome using tophat v2.0.9 then assembled and merged with cufflinks v2.2.0 and cuffmerge respectively. Differentially expressed transcripts were determined using cuffdiff v2.2.0. Gene ontology was assessed using BinGO 3.0.3 a plugin for cytoscape v3.3.0. Genome build: Zv9	Unfertilized eggs	Zebrafish were fed either 5 mg or 60 mg Artemia each day for eight weeks.	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were maintained under standard conditions	strain:In house AB/Pet shop\|tissue:Unfertilized eggs\|FISH age:9 mpf\|treatment arm:5 mg	GSM2140600	GSM2140600: 5mg arm 1; Danio rerio; RNA Seq	GSM2140600		1	The eggs were transferred to tube containing RA1 buffer Macherey Nagel cat. 740955.250 with b mercaptoethanol and stored at 80 °C until RNA extraction. The RNA was filtered with the NucleoSpin RNA kit Macherey Nagel cat. 740955.250 and bound and eluted with columns 17 23 000 nt size range from the RNA clean and concentrator kit Zymo cat. no. R1017. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM2140600	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP074244	5mg-arm-1.fastq.gz	fastq	2409548800.0	24095488.0	GSM2140600 r1	0:100	A:519836883;C:638777587;G:641445656;T:609475335;N:13339	100		519836883	638777587	641445656	609475335	13339	SRX1738391	SRS1418764	SRA422860	GEO	Chromosome Structure and Development Group, Department of Pathology, University of Otago	1	0.88003		0.04264		0.76138		0.66721		100		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2016-05-02	Multi-stage	Multi-stage	Oocyte	Reproductive System
49742	49742	SRR8197481	SRX5016863	SRS4049994	SRP169068	PRJNA495892	Danio rerio Genome sequencing	PRJNA495892	Whole Genome Sequencing	Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.		three samples of zebrafish unfertilized eggs and three samples zebrafish fries at the stage of prim5.	Model organism or animal sample from Danio rerio	The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.	isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage\|dev stage:2 stages of unfertilized egg and prim 5\|sex:pooled male and female\|tissue:zebrafish in 2 stages of unfertilized egg and prim 5\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: prim5 stage	Z2 3 F	Z2 3 F	The unfertilized eggs of zebrafish were taken as three samples Z1 1 Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1 Z2 2 and Z2 3 in the prim5 stage.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP169068	Z2_3_1.fq.gz Z2_3_2.fq.gz	fastq fastq	6979181500.0	27916726.0	Z2 3 1.fq.gz	0:125 1:125	A:1822429760;C:1670132153;G:1694226275;T:1791552753;N:840559	125	125	1822429760	1670132153	1694226275	1791552753	840559	SRX5016863	SRS4049994	SRA810793	Institute of Hydrobiology, Chinese Academy of Sciences\|State Key Laboratory of Freshwater Ecology and Bio	Institute of Hydrobiology, Chinese Academy of Sciences	2	0.9586	0.9518	0.02217	0.02129	0.81022	0.80921	0.50342	0.51319	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-11-16	Multi-stage	Embryo	Oocyte	Reproductive System
49743	49743	SRR8197482	SRX5016862	SRS4049994	SRP169068	PRJNA495892	Danio rerio Genome sequencing	PRJNA495892	Whole Genome Sequencing	Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.		three samples of zebrafish unfertilized eggs and three samples zebrafish fries at the stage of prim5.	Model organism or animal sample from Danio rerio	The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.	isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage\|dev stage:2 stages of unfertilized egg and prim 5\|sex:pooled male and female\|tissue:zebrafish in 2 stages of unfertilized egg and prim 5\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: prim5 stage	Z2 1 F	Z2 1 F	The unfertilized eggs of zebrafish were taken as three samples Z1 1 Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1 Z2 2 and Z2 3 in the prim5 stage.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP169068	Z2_1_2.fq.gz Z2_1_1.fq.gz	fastq fastq	6728695750.0	26914783.0	Z2 1 1.fq.gz	0:125 1:125	A:1732100690;C:1624557456;G:1649046037;T:1722193010;N:798557	125	125	1732100690	1624557456	1649046037	1722193010	798557	SRX5016862	SRS4049994	SRA810793	Institute of Hydrobiology, Chinese Academy of Sciences\|State Key Laboratory of Freshwater Ecology and Bio	Institute of Hydrobiology, Chinese Academy of Sciences	2	0.9585	0.95335	0.01902	0.01833	0.8131	0.81014	0.48431	0.493	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-11-16	Multi-stage	Embryo	Oocyte	Reproductive System
49744	49744	SRR8197483	SRX5016861	SRS4049994	SRP169068	PRJNA495892	Danio rerio Genome sequencing	PRJNA495892	Whole Genome Sequencing	Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.		three samples of zebrafish unfertilized eggs and three samples zebrafish fries at the stage of prim5.	Model organism or animal sample from Danio rerio	The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.	isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage\|dev stage:2 stages of unfertilized egg and prim 5\|sex:pooled male and female\|tissue:zebrafish in 2 stages of unfertilized egg and prim 5\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: unfertilized egg	Z1 3 F	Z1 3 F	The unfertilized eggs of zebrafish were taken as three samples Z1 1 Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1 Z2 2 and Z2 3 in the prim5 stage.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP169068	Z1_3_1.fq.gz Z1_3_2.fq.gz	fastq fastq	6657035500.0	26628142.0	Z1 3 1.fq.gz	0:125 1:125	A:1796541492;C:1535300915;G:1557971133;T:1766443902;N:778058	125	125	1796541492	1535300915	1557971133	1766443902	778058	SRX5016861	SRS4049994	SRA810793	Institute of Hydrobiology, Chinese Academy of Sciences\|State Key Laboratory of Freshwater Ecology and Bio	Institute of Hydrobiology, Chinese Academy of Sciences	2	0.95543	0.94989	0.02312	0.02201	0.79689	0.79421	0.51212	0.51203	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-11-16	Multi-stage	Embryo	Oocyte	Reproductive System
49745	49745	SRR8197484	SRX5016860	SRS4049994	SRP169068	PRJNA495892	Danio rerio Genome sequencing	PRJNA495892	Whole Genome Sequencing	Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.		three samples of zebrafish unfertilized eggs and three samples zebrafish fries at the stage of prim5.	Model organism or animal sample from Danio rerio	The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.	isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage\|dev stage:2 stages of unfertilized egg and prim 5\|sex:pooled male and female\|tissue:zebrafish in 2 stages of unfertilized egg and prim 5\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: unfertilized egg	Z1 2 F	Z1 2 F	The unfertilized eggs of zebrafish were taken as three samples Z1 1 Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1 Z2 2 and Z2 3 in the prim5 stage.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP169068	Z1_2_1.fq.gz Z1_2_2.fq.gz	fastq fastq	8869328500.0	35477314.0	Z1 2 1.fq.gz	0:125 1:125	A:2367358711;C:2085652811;G:2116692954;T:2298597848;N:1026176	125	125	2367358711	2085652811	2116692954	2298597848	1026176	SRX5016860	SRS4049994	SRA810793	Institute of Hydrobiology, Chinese Academy of Sciences\|State Key Laboratory of Freshwater Ecology and Bio	Institute of Hydrobiology, Chinese Academy of Sciences	2	0.95776	0.95084	0.01896	0.01811	0.79823	0.79608	0.49565	0.49345	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-11-18	Multi-stage	Embryo	Oocyte	Reproductive System
49746	49746	SRR8197485	SRX5016859	SRS4049994	SRP169068	PRJNA495892	Danio rerio Genome sequencing	PRJNA495892	Whole Genome Sequencing	Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.		three samples of zebrafish unfertilized eggs and three samples zebrafish fries at the stage of prim5.	Model organism or animal sample from Danio rerio	The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.	isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage\|dev stage:2 stages of unfertilized egg and prim 5\|sex:pooled male and female\|tissue:zebrafish in 2 stages of unfertilized egg and prim 5\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: unfertilized egg	Z1 1 F	Z1 1 F	The unfertilized eggs of zebrafish were taken as three samples Z1 1 Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1 Z2 2 and Z2 3 in the prim5 stage.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP169068	Z1_1_1.fq.gz Z1_1_2.fq.gz	fastq fastq	7205390500.0	28821562.0	Z1 1 1.fq.gz	0:125 1:125	A:1900562357;C:1700185416;G:1728383049;T:1875415232;N:844446	125	125	1900562357	1700185416	1728383049	1875415232	844446	SRX5016859	SRS4049994	SRA810793	Institute of Hydrobiology, Chinese Academy of Sciences\|State Key Laboratory of Freshwater Ecology and Bio	Institute of Hydrobiology, Chinese Academy of Sciences	2	0.95593	0.95003	0.01844	0.01778	0.80064	0.80008	0.4858	0.48331	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-11-18	Multi-stage	Embryo	Oocyte	Reproductive System
49747	49747	SRR8197486	SRX5016858	SRS4049994	SRP169068	PRJNA495892	Danio rerio Genome sequencing	PRJNA495892	Whole Genome Sequencing	Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.		three samples of zebrafish unfertilized eggs and three samples zebrafish fries at the stage of prim5.	Model organism or animal sample from Danio rerio	The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.	isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage\|dev stage:2 stages of unfertilized egg and prim 5\|sex:pooled male and female\|tissue:zebrafish in 2 stages of unfertilized egg and prim 5\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio: prim5 stage	Z2 2 F	Z2 2 F	The unfertilized eggs of zebrafish were taken as three samples Z1 1 Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1 Z2 2 and Z2 3 in the prim5 stage.			RNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP169068	Z2_2_2.fq.gz Z2_2_1.fq.gz	fastq fastq	7724266250.0	30897065.0	Z2 2 1.fq.gz	0:125 1:125	A:1986625683;C:1864133349;G:1894026843;T:1978566785;N:913590	125	125	1986625683	1864133349	1894026843	1978566785	913590	SRX5016858	SRS4049994	SRA810793	Institute of Hydrobiology, Chinese Academy of Sciences\|State Key Laboratory of Freshwater Ecology and Bio	Institute of Hydrobiology, Chinese Academy of Sciences	2	0.95577	0.94831	0.01968	0.01899	0.80793	0.80667	0.48789	0.48551	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2018-11-16	Multi-stage	Embryo	Oocyte	Reproductive System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;