metadata: run_metadata: 75 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" and tissue

75 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "cDNA" 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.attributes	study.PMIDs	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
15550	15550	ERR647595	ERX604031	ERS557915	ERP007147	PRJEB7420	Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq	ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622	Other	There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.			Egg	SAMEA2796300	UNIVERSITY OF AMSTERDAM	Alias:Egg\|ENA checklist:ERC000011\|INSDC center alias:UNIVERSITY OF AMSTERDAM\|INSDC center name:UNIVERSITY OF AMSTERDAM\|INSDC first public:2014 11 29T17:02:28Z\|INSDC last update:2014 10 01T14:29:23Z\|INSDC status:public\|SRA accession:ERS557915\|Sample Name:ERS557915\|Title:Zebrafish Egg samples\|dev stage:Oocytes									Ion Torrent Proton sequencing	ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1	RID0024	1			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		ERP007147	Ion Torrent Proton sequencing	ENA FIRST PUBLIC:2014 11 29\|ENA LAST UPDATE:2018 11 16	RID0024_016.fastq.gz	fastq	6684767188.0	89052017.0	ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:25:29:391 1	0:75.07	A:1523328157;C:1795624453;G:1849675240;T:1516139338;N:0	75		1523328157	1795624453	1849675240	1516139338	0	ERX604031	ERS557915	ERA363845	UNIVERSITY OF AMSTERDAM	UNIVERSITY OF AMSTERDAM	1	0.89536	0.15322	0.91421	0.69019	73	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2014-10-01	Zygote	Embryo	Oocyte	Reproductive System
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
36260	36260	SRR062657	SRX025025	SRS085804	SRP003165	PRJNA127881	High throughput sequencing of mRNA from oocyte 1 cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf zebrafish embryos Wild type; AB line	GSE22830	Transcriptome Analysis	mRNA seq based approach to determine the transcriptome dynamics during early development To study the mechanisms regulating this developmental event in zebrafish we applied RNA deep sequencing technology and generated comprehensive transcriptome profiles of 6 developmental stages from oocyte to early gastrulation. We determined the expression levels of maternal and zygotic transcripts and clustered them based on expression pattern. We identified a large number of novel transcribed regions in un annotated regions of the genome as well as splice variants with an estimated frequency of 40 75% during early zebrafish embryogenesis. Our data constitute a useful resource for developmental studies gene discovery and genome annotation. Overall design: RNA was extracted from pooled embryos of desired stages and one RNA seq library was generated for each sample. Totally 6 stages were selected: Maternal 1cell 16/32 cells 128/256 cells 3.5hpf and 5.3hpf		pubmed:21555364;pubmed:24586560;pubmed:23676078	Maternal	GSM564427		tissue:Unfertilized egg\|background:AB; wild type\|developmental stage:unfertilized eggs	Maternal	ABI pipeline BioScope v1.0.1 Data analysis: The SOLiD generated RNA Seq reads was in 50bp length and an initial filtering process was taken to remove any non desirable contamination sequences such as rRNA tRNA and repeats etc. A seed and extension mapping approach was developed to map the 50bp reads into reference genome zv7 and also into the respective zv7 refGene annotation separately. During mapping of the reads to the refGene annotation a splice junction database fasta file is generated to which the reads are mapped to. This database contains known and putative junction sequences created by taking 46bp from the joining ends of adjacent and non adjacent exons for each gene and putting them together simulating the genomic sequences of known and putative junctions respectively. The first 25bp of the 50bp read was used as the seed for alignment for each read. When an alignment cannot be found using these 25bp seed the seed window is shifted and the next 25bp seed is taken from the 21st to the 45th base of the read. An extension step follows when the seed is able to map and a score generated for each extended base to determine best alignment. A merging step is performed on the genome mapping and splice junction mapping to determine a set of alignments for each read from which a unique alignment is found based on the score generated for these alignments. Mapping parameters: Mapping was done using Applied Biosystems’ SOLiD BioScope alignment for whole transcriptome analysis pipeline. Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location. A score is computed for each mapping location and any location that scored <22 were filtered. Generation of gff and bedgraph files: GFF files were produced by parsing the output BAM format and extracted for unique alignments with score >22. The bedgraph files are then produced with the resulting gff file.	Unfertilized egg	Embryos were frozen at the desired developmental stages and RNAs was extracted for sequencing.	mRNA seq was performed by Mission Biotech Taiwan. SOLiD sequencing libraries were prepared using the Whole Transcriptome Library Preparation for SOLiD™ Sequencing kit ABI according to manufacturer’s instructions. About 200 280 µg of total RNAs were used as starting materials which were subjected to polyA selection using Applied Biosystems PolyA Purist Kit AM1916 fragmentation and library construction using distinct adapters for each library SOLiD Barcoding. From each library equal volumes were pooled together and sequenced in SOLiD3 ABI platform generating 50bp tags.	Zebrafish embryos AB background collected just post fertilization were reared and harvested at desired time points. Unfertilized oocytes were collected by squeezing the abdomen of spawning females. Harvested embryos were snap frozen in liquid nitrogen and stored in −80°C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer’s instructions. RNA concentrations were determined using NanoDrop 2000 Thermo Scientific. Integrity of RNA samples were determined using Agilent RNA 6000 Nano chip and size separated using Agilent 2100 Bioanalyzer. Total RNA obtained per 100 embryos at each developmental stage was calculated for data normalization purposes.	background:AB; wild type\|developmental stage:unfertilized eggs	GSM564427	GSM564427: Maternal	GSM564427: Maternal	GSM564427: Maternal	1		GEO Accession:GSM564427	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP003165					1566199300.0	31323986.0	GSM564427 1	0:50		50							SRX025025	SRS085804	SRA022850	GEO	Computational and Systems Biology, Genome Institute of Singapore	1	0.72688	0.05657	0.876	0.51223	50	B	usable mapping rate	legacy	early	full_length	poly_a	unknown	bulk	unknown	unknown	Singapore	2010-07-08	Zygote	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
41847	41847	SRR5892569	SRX3058262	SRS2404198	SRP100178	PRJNA375788	'Placeholder' nucleosomes underlie germline to embryo DNA methylation reprogramming [RNA Seq]	GSE95031	Transcriptome Analysis	The function and retention/reprogramming of epigenetic marks during the germline to embryo transition is a key issue in developmental and cellular biology with relevance to stem cell programming and trans generational inheritance. In zebrafish DNAme patterns are programmed in transcriptionally quiescent early cleavage embryos; paternally inherited patterns are maintained whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a 'placeholder' nucleosome containing the histone H2A variant H2A.ZFV and H3K4me1 occupies virtually all regions lacking DNAme in both sperm and cleavage embryos – residing at promoters encoding housekeeping and early embryonic transcription factors. Upon genome wide transcriptional onset genes with the Placeholder become either active H3K4me3 marked or silent H3K4me3/K27me3 marked bivalent. Importantly functional perturbation causing Placeholder loss confers DNAme acquisition whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation. Thus during transcriptionally quiescent stages gamete zygote cleavage an H2A.ZFV/H3K4me1 containing Placeholder nucleosome deters DNAme poising parental genes for either gene specific activation or facultative repression. Overall design: Transcript abundance was analyzed for zebrafish sperm and cleavage stage embryos that were either wild type or mutant for the anp32e gene.	parent bioproject:PRJNA375781	pubmed:29456083	Anp32e Null Sperm RNA Seq Rep2	GSM2730572		tissue:Sperm Stage\|developmental stage:Sperm Stage\|strain:NA\|injection:NA\|mutation:Anp32e Null	Anp32e Null Sperm RNA Seq Rep2	Reads were aligned to the Zv10 genome using Novoalign v2.8 Novocraft using the following options: o SAM r All 50 Sam files were then combined due to high correlation between technical and biological replicates. The Useq Pipeline was utilized Sam parsed using the SAMTranscriptomeParser followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values. Genome build: Zv10 Supplementary files format and content: RNASeq geneCount minimum10.xlsx: Excel file contains gene count table.	Sperm Stage		Embryos were lysed using Trizol with the addition of 2% SDS then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold		developmental stage:Sperm Stage\|strain:NA\|injection:NA\|mutation:Anp32e Null	GSM2730572	GSM2730572: Anp32e Null Sperm RNA Seq Rep2; Danio rerio; RNA Seq	GSM2730572		1	Embryos were lysed using Trizol with the addition of 2% SDS then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold	GEO Accession:GSM2730572	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP100178			Anp32e_Null_Sperm_RNA-Seq_Rep2.fastq.gz	fastq	2612583700.0	52251674.0	GSM2730572 r1	0:50	A:643932236;C:630114587;G:625850241;T:712599561;N:87075	50		643932236	630114587	625850241	712599561	87075	SRX3058262	SRS2404198	SRA538756	GEO	Huntsman Cancer Institute	1	0.91107	0.05039	0.76108	0.4698	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2017-08-03	Zygote	Embryo	Oocyte	Reproductive System
41848	41848	SRR5892568	SRX3058261	SRS2404197	SRP100178	PRJNA375788	'Placeholder' nucleosomes underlie germline to embryo DNA methylation reprogramming [RNA Seq]	GSE95031	Transcriptome Analysis	The function and retention/reprogramming of epigenetic marks during the germline to embryo transition is a key issue in developmental and cellular biology with relevance to stem cell programming and trans generational inheritance. In zebrafish DNAme patterns are programmed in transcriptionally quiescent early cleavage embryos; paternally inherited patterns are maintained whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a 'placeholder' nucleosome containing the histone H2A variant H2A.ZFV and H3K4me1 occupies virtually all regions lacking DNAme in both sperm and cleavage embryos – residing at promoters encoding housekeeping and early embryonic transcription factors. Upon genome wide transcriptional onset genes with the Placeholder become either active H3K4me3 marked or silent H3K4me3/K27me3 marked bivalent. Importantly functional perturbation causing Placeholder loss confers DNAme acquisition whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation. Thus during transcriptionally quiescent stages gamete zygote cleavage an H2A.ZFV/H3K4me1 containing Placeholder nucleosome deters DNAme poising parental genes for either gene specific activation or facultative repression. Overall design: Transcript abundance was analyzed for zebrafish sperm and cleavage stage embryos that were either wild type or mutant for the anp32e gene.	parent bioproject:PRJNA375781	pubmed:29456083	Anp32e Null Sperm RNA Seq Rep1	GSM2730571		tissue:Sperm Stage\|developmental stage:Sperm Stage\|strain:NA\|injection:NA\|mutation:Anp32e Null	Anp32e Null Sperm RNA Seq Rep1	Reads were aligned to the Zv10 genome using Novoalign v2.8 Novocraft using the following options: o SAM r All 50 Sam files were then combined due to high correlation between technical and biological replicates. The Useq Pipeline was utilized Sam parsed using the SAMTranscriptomeParser followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values. Genome build: Zv10 Supplementary files format and content: RNASeq geneCount minimum10.xlsx: Excel file contains gene count table.	Sperm Stage		Embryos were lysed using Trizol with the addition of 2% SDS then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold		developmental stage:Sperm Stage\|strain:NA\|injection:NA\|mutation:Anp32e Null	GSM2730571	GSM2730571: Anp32e Null Sperm RNA Seq Rep1; Danio rerio; RNA Seq	GSM2730571		1	Embryos were lysed using Trizol with the addition of 2% SDS then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold	GEO Accession:GSM2730571	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP100178			Anp32e_Null_Sperm_RNA-Seq_Rep1.fastq.gz	fastq	3162821050.0	63256421.0	GSM2730571 r1	0:50	A:756571256;C:759039692;G:777010061;T:870095540;N:104501	50		756571256	759039692	777010061	870095540	104501	SRX3058261	SRS2404197	SRA538756	GEO	Huntsman Cancer Institute	1	0.91819	0.04312	0.76307	0.45972	50	B	usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2017-08-03	Zygote	Embryo	Oocyte	Reproductive System
48337	48337	SRR7762357	SRX4617974	SRS3720953	SRP149356	PRJNA473799	Widespread enhancer dememorization and promoter priming during parental to zygotic transition	GSE114954	Other	The epigenome plays critical roles in controlling gene expression and development. However how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast many promoters remain hypomethylated and unexpectedly acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq we systematically examined the genome wide presence of H3K4me3 H3K27ac H3K27me3 and H3K36me3 in sperm oocyte 4 cell 256 cell and dome stage embryos.		pubmed:30444999	oocyte IV RNA seq	GSM3359500		tissue:oocyte\|developmental stage:stage IV\|cell type:metaphase I oocyte\|strain:Tu	oocyte IV RNA seq	RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg 2012 with the parameters –t –q –N 1 –L 25. All unmapped reads non uniquely mapped reads and PCR duplicates were removed. For downstream analysis the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks gene expression table for RNA seq data	oocyte	The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl 136.8 mM NaCl 4.2 mM NaHCO3 0.44 mM KH2PO4 0.25 mM Na2HPO4 and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology and the surrounding follicle cells were detached gently as much as possible.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	The wild type Tu female strain were raised as standard protocol.	developmental stage:stage IV\|cell type:metaphase I oocyte\|strain:Tu	GSM3359500	GSM3359500: oocyte IV RNA seq; Danio rerio; RNA Seq	GSM3359500		1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	GEO Accession:GSM3359500	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500		SRP149356			oocyte_IV_RNA_seq_r1.fq.gz	fastq	636442625.0	12988625.0	GSM3359500 r1	0:49 1:0	A:159884635;C:154136157;G:161233162;T:161078773;N:109898	49	0	159884635	154136157	161233162	161078773	109898	SRX4617974	SRS3720953	SRA712563	GEO	Tsinghua University	1	0.94159	0.02577	0.79933	0.46881	49	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2018-08-28	Zygote	Embryo	Oocyte	Reproductive System
48338	48338	SRR7762356	SRX4617973	SRS3720954	SRP149356	PRJNA473799	Widespread enhancer dememorization and promoter priming during parental to zygotic transition	GSE114954	Other	The epigenome plays critical roles in controlling gene expression and development. However how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast many promoters remain hypomethylated and unexpectedly acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq we systematically examined the genome wide presence of H3K4me3 H3K27ac H3K27me3 and H3K36me3 in sperm oocyte 4 cell 256 cell and dome stage embryos.		pubmed:30444999	oocyte III RNA seq	GSM3359499		tissue:oocyte\|developmental stage:stage III\|cell type:prophase I oocyte\|strain:Tu	oocyte III RNA seq	RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg 2012 with the parameters –t –q –N 1 –L 25. All unmapped reads non uniquely mapped reads and PCR duplicates were removed. For downstream analysis the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks gene expression table for RNA seq data	oocyte	The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl 136.8 mM NaCl 4.2 mM NaHCO3 0.44 mM KH2PO4 0.25 mM Na2HPO4 and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology and the surrounding follicle cells were detached gently as much as possible.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	The wild type Tu female strain were raised as standard protocol.	developmental stage:stage III\|cell type:prophase I oocyte\|strain:Tu	GSM3359499	GSM3359499: oocyte III RNA seq; Danio rerio; RNA Seq	GSM3359499		1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	GEO Accession:GSM3359499	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500		SRP149356			oocyte_III_RNA_seq_r1.fq.gz	fastq	637289296.0	13005904.0	GSM3359499 r1	0:49 1:0	A:160396576;C:153811544;G:160426381;T:162544723;N:110072	49	0	160396576	153811544	160426381	162544723	110072	SRX4617973	SRS3720954	SRA712563	GEO	Tsinghua University	1	0.93382	0.03044	0.729	0.46965	49	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2018-08-28	Zygote	Embryo	Oocyte	Reproductive System
48339	48339	SRR7762355	SRX4617972	SRS3720944	SRP149356	PRJNA473799	Widespread enhancer dememorization and promoter priming during parental to zygotic transition	GSE114954	Other	The epigenome plays critical roles in controlling gene expression and development. However how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast many promoters remain hypomethylated and unexpectedly acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq we systematically examined the genome wide presence of H3K4me3 H3K27ac H3K27me3 and H3K36me3 in sperm oocyte 4 cell 256 cell and dome stage embryos.		pubmed:30444999	oocyte II RNA seq	GSM3359498		tissue:oocyte\|developmental stage:stage II\|cell type:S phase oocyte\|strain:Tu	oocyte II RNA seq	RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg 2012 with the parameters –t –q –N 1 –L 25. All unmapped reads non uniquely mapped reads and PCR duplicates were removed. For downstream analysis the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks gene expression table for RNA seq data	oocyte	The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl 136.8 mM NaCl 4.2 mM NaHCO3 0.44 mM KH2PO4 0.25 mM Na2HPO4 and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology and the surrounding follicle cells were detached gently as much as possible.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	The wild type Tu female strain were raised as standard protocol.	developmental stage:stage II\|cell type:S phase oocyte\|strain:Tu	GSM3359498	GSM3359498: oocyte II RNA seq; Danio rerio; RNA Seq	GSM3359498		1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	GEO Accession:GSM3359498	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500		SRP149356			oocyte_II_RNA_seq_r1.fq.gz	fastq	636518379.0	12990171.0	GSM3359498 r1	0:49 1:0	A:160017029;C:153897668;G:159821522;T:162670200;N:111960	49	0	160017029	153897668	159821522	162670200	111960	SRX4617972	SRS3720944	SRA712563	GEO	Tsinghua University	1	0.9326	0.0241	0.74073	0.47431	49	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2018-08-28	Zygote	Embryo	Oocyte	Reproductive System
48340	48340	SRR7762354	SRX4617971	SRS3720943	SRP149356	PRJNA473799	Widespread enhancer dememorization and promoter priming during parental to zygotic transition	GSE114954	Other	The epigenome plays critical roles in controlling gene expression and development. However how the parental epigenomes transit to the zygotic epigenome in early development remains elusive. Here we show parental to zygotic transition in zebrafish involves extensive erasure of parental epigenetic memory starting by methylating gametic enhancers. Surprisingly this occurs even prior to fertilization for sperm. Both parental enhancers lose histone marks by the 4 cell stage and zygotic enhancers are not activated until around zygotic genome activation ZGA. By contrast many promoters remain hypomethylated and unexpectedly acquire de novo histone acetylation as early as at the 4 cell stage. They then resolve into either activated or repressed promoters upon ZGA. Maternal depletion of histone acetyltransferases results in aberrant ZGA and early embryonic lethality. Finally such reprogramming is largely driven by maternal factors with zygotic products contributing to embryonic enhancer activation. Thus these data revealed widespread enhancer dememorization and promoter priming during parental to zygotic transition. Overall design: By employing STAR ChIP seq and RNA seq we systematically examined the genome wide presence of H3K4me3 H3K27ac H3K27me3 and H3K36me3 in sperm oocyte 4 cell 256 cell and dome stage embryos.		pubmed:30444999	oocyte I RNA seq	GSM3359497		tissue:oocyte\|developmental stage:stage I\|cell type:G1 phase oocyte\|strain:Tu	oocyte I RNA seq	RNA seq data were firstly processed using Trim Galore! with default parameters to trim the adapter containing and low quality reads.The filtered data were then mapped to the zebrafish reference genome danRer7 by STAR version: STAR 2.5.3a modified with following parameters: outSAMstrandField intronMotif outSAMattributes All outSAMunmapped Within outSAMattrIHstart 0 outWigStrand Stranded outFilterMultimapNmax 20 twopassMode Basic. All STAR ChIP seq reads were aligned to the zebrafish reference genome danRer7 using Bowtie2 version 2.2.2 Langmead and Salzberg 2012 with the parameters –t –q –N 1 –L 25. All unmapped reads non uniquely mapped reads and PCR duplicates were removed. For downstream analysis the read counts were normalized by computing the numbers of reads per kilobase of bin per million of reads sequenced RPKM. All STEM seq datasets were mapped to the danRer7 reference genome by Bismark Krueger and Andrews 2011. Reads were trimmed with cutadaptor Martin 2011 using parameters: minimum length 20 pair filter=any. Alignments were performed with the following parameters: N 1 X 600 score min L 0 0.6. Multi mapped reads and PCR duplicates were removed. bismark methylation extractor was used to calculate the DNA methylation level Genome build: danRer7 Supplementary files format and content: Bigwig for ChIP seq and RNA seq tracks gene expression table for RNA seq data	oocyte	The ovaries of adult female were isolated and transferred into specific buffer 5.4 mM KCl 136.8 mM NaCl 4.2 mM NaHCO3 0.44 mM KH2PO4 0.25 mM Na2HPO4 and 0.5% wt/vol BSA. Then stage I V oocytes were separated from the ovary with tweezers under microscope according to their morphology and the surrounding follicle cells were detached gently as much as possible.	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	The wild type Tu female strain were raised as standard protocol.	developmental stage:stage I\|cell type:G1 phase oocyte\|strain:Tu	GSM3359497	GSM3359497: oocyte I RNA seq; Danio rerio; RNA Seq	GSM3359497		1	Total RNA of oocytes were purified using RNeasy Mini kit QIAGEN 74104 as recommended protocols 5 ug RNA was DNase I Fermentas Cat # EN0521 treated at 37C for 1 h. RNA was then purified using AMPure beads. Poly A tailed mRNA was collected using DynabeadsTM mRNA purification kit Invitrogen Cat # 61006. Purified RNA was fragmented with RNA Frag. Buffer NEB Cat # E6186A at 95C for 5 min. Reaction was stopped and RNA was purified by AMPure beads. First stand cDNA was synthesized with a commercial kit using both oligo dT and random primers Invitrogen Cat # 18080 051. Second strand cDNA was synthesized with second strand synthesis buffer Invitrogen Cat # 10812014 MgCl2 DTT dNTP dUTP RNase H Fermentas Cat # EN0202 E. coli DNA ligase NEB Cat # M0205S and DNA polymerase I NEB Cat # M0209S. DNA was purified post 2 hrs incubation on thermomixer at 16C. Synthesized cDNA was subjected to library preparation. DNA was end repaired adenylated and ligated to TruSeq sequencing adaptors. Libraries were then treated with UDG AMPErase Cat # N808 0096 at 37C for 1 hour followed by DNA amplification using Phusion HF DNA polymerase NEB Cat # M0530L. The amplified DNA was size selected using AMPure Beads for 200 500 bp DNA fragments.	GEO Accession:GSM3359497	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 1500		SRP149356			oocyte_I_RNA_seq_r1.fq.gz	fastq	637062181.0	13001269.0	GSM3359497 r1	0:49 1:0	A:161520633;C:153547778;G:156542304;T:165341706;N:109760	49	0	161520633	153547778	156542304	165341706	109760	SRX4617971	SRS3720943	SRA712563	GEO	Tsinghua University	1	0.92933	0.02356	0.73683	0.47367	49	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	China	2018-08-28	Zygote	Embryo	Oocyte	Reproductive System
58431	58431	SRR12436831	SRX8932520	SRS7188865	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O4 R3 RiboMinus	GSM4724750		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	Ski7 O4 R3 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724750	GSM4724750: Ski7 O4 R3 RiboMinus; Danio rerio; RNA Seq	GSM4724750		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724750	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T4_R3_RiboC.fastq	fastq	5953499600.0	59534996.0	GSM4724750 r1	0:100	A:1120262924;C:1886034530;G:1669359412;T:1277719039;N:123695	100		1120262924	1886034530	1669359412	1277719039	123695	SRX8932520	SRS7188865	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.98775	0.27616	0.85561	0.86154	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58432	58432	SRR12436830	SRX8932519	SRS7188864	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O4 R2 RiboMinus	GSM4724749		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	Ski7 O4 R2 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724749	GSM4724749: Ski7 O4 R2 RiboMinus; Danio rerio; RNA Seq	GSM4724749		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724749	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T4_R2_RiboC.fastq	fastq	1483394400.0	14833944.0	GSM4724749 r1	0:100	A:282286056;C:468342445;G:416192774;T:316541929;N:31196	100		282286056	468342445	416192774	316541929	31196	SRX8932519	SRS7188864	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.98708	0.21634	0.84611	0.85636	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58433	58433	SRR12436829	SRX8932518	SRS7188863	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O4 R1 RiboMinus	GSM4724748		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	Ski7 O4 R1 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724748	GSM4724748: Ski7 O4 R1 RiboMinus; Danio rerio; RNA Seq	GSM4724748		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724748	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T4_R1_RiboC.fastq	fastq	1003006700.0	10030067.0	GSM4724748 r1	0:100	A:231770113;C:284279432;G:255931584;T:231004482;N:21089	100		231770113	284279432	255931584	231004482	21089	SRX8932518	SRS7188863	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.97595	0.1875	0.78833	0.7203	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58434	58434	SRR12436828	SRX8932517	SRS7188862	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O3 R3 RiboMinus	GSM4724747		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	Ski7 O3 R3 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	GSM4724747	GSM4724747: Ski7 O3 R3 RiboMinus; Danio rerio; RNA Seq	GSM4724747		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724747	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T3_R3_RiboC.fastq	fastq	1590741700.0	15907417.0	GSM4724747 r1	0:100	A:315819595;C:482378072;G:439500811;T:353009618;N:33604	100		315819595	482378072	439500811	353009618	33604	SRX8932517	SRS7188862	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.98036	0.16863	0.80012	0.76997	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58435	58435	SRR12436827	SRX8932516	SRS7188861	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O3 R2 RiboMinus	GSM4724746		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	Ski7 O3 R2 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	GSM4724746	GSM4724746: Ski7 O3 R2 RiboMinus; Danio rerio; RNA Seq	GSM4724746		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724746	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T3_R2_RiboC.fastq	fastq	1851647100.0	18516471.0	GSM4724746 r1	0:100	A:397602403;C:536394029;G:491276851;T:426334866;N:38951	100		397602403	536394029	491276851	426334866	38951	SRX8932516	SRS7188861	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.96997	0.11852	0.77585	0.66439	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58436	58436	SRR12436826	SRX8932515	SRS7188860	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724745 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724745			Ski7 O3 R1 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	GSM4724745	GSM4724745: Ski7 O3 R1 RiboMinus; Danio rerio; RNA Seq	GSM4724745		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724745	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T3_R1_RiboC.fastq	fastq	1856733400.0	18567334.0	GSM4724745 r1	0:100	A:398467671;C:533331652;G:489602590;T:435279283;N:52204	100		398467671	533331652	489602590	435279283	52204	SRX8932515	SRS7188860	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.96808	0.14968	0.76806	0.67187	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58437	58437	SRR12436825	SRX8932514	SRS7188859	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724744 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724744			Ski7 O2 R3 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage II\|strain:TLAB	GSM4724744	GSM4724744: Ski7 O2 R3 RiboMinus; Danio rerio; RNA Seq	GSM4724744		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724744	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T2_R3_RiboC.fastq	fastq	2638458400.0	26384584.0	GSM4724744 r1	0:100	A:539473608;C:778770363;G:717407077;T:602751798;N:55554	100		539473608	778770363	717407077	602751798	55554	SRX8932514	SRS7188859	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.9783	0.18716	0.79788	0.70432	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58438	58438	SRR12436824	SRX8932513	SRS7188858	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724743 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724743			Ski7 O2 R2 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage II\|strain:TLAB	GSM4724743	GSM4724743: Ski7 O2 R2 RiboMinus; Danio rerio; RNA Seq	GSM4724743		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724743	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T2_R2_RiboC.fastq	fastq	2512073400.0	25120734.0	GSM4724743 r1	0:100	A:616094880;C:635920272;G:606962967;T:653043012;N:52269	100		616094880	635920272	606962967	653043012	52269	SRX8932513	SRS7188858	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95663	0.08667	0.75252	0.52574	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58439	58439	SRR12436823	SRX8932512	SRS7188857	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O2 R1 RiboMinus	GSM4724742		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage II\|strain:TLAB	Ski7 O2 R1 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage II\|strain:TLAB	GSM4724742	GSM4724742: Ski7 O2 R1 RiboMinus; Danio rerio; RNA Seq	GSM4724742		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724742	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T2_R1_RiboC.fastq	fastq	910074400.0	9100744.0	GSM4724742 r1	0:100	A:221922364;C:228583521;G:219452367;T:240097505;N:18643	100		221922364	228583521	219452367	240097505	18643	SRX8932512	SRS7188857	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95527	0.08947	0.74858	0.51463	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58440	58440	SRR12436822	SRX8932511	SRS7188856	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724741 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724741			Ski7 O1 R3 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	GSM4724741	GSM4724741: Ski7 O1 R3 RiboMinus; Danio rerio; RNA Seq	GSM4724741		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724741	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T1_R3_RiboC.fastq	fastq	5943811600.0	59438116.0	GSM4724741 r1	0:100	A:1462644817;C:1467450908;G:1441714266;T:1571912790;N:88819	100		1462644817	1467450908	1441714266	1571912790	88819	SRX8932511	SRS7188856	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95219	0.06874	0.76134	0.48887	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58441	58441	SRR12436821	SRX8932510	SRS7188855	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O1 R2 RiboMinus	GSM4724740		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	Ski7 O1 R2 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	GSM4724740	GSM4724740: Ski7 O1 R2 RiboMinus; Danio rerio; RNA Seq	GSM4724740		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724740	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T1_R2_RiboC.fastq	fastq	1311657500.0	13116575.0	GSM4724740 r1	0:100	A:330391016;C:317678365;G:309923830;T:353636331;N:27958	100		330391016	317678365	309923830	353636331	27958	SRX8932510	SRS7188855	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94932	0.06794	0.75668	0.47546	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58442	58442	SRR12436820	SRX8932509	SRS7188854	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724739 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724739			Ski7 O1 R1 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	GSM4724739	GSM4724739: Ski7 O1 R1 RiboMinus; Danio rerio; RNA Seq	GSM4724739		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724739	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T1_R1_RiboC.fastq	fastq	1075841900.0	10758419.0	GSM4724739 r1	0:100	A:269155883;C:260373486;G:255757791;T:290531791;N:22949	100		269155883	260373486	255757791	290531791	22949	SRX8932509	SRS7188854	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.9501	0.0714	0.75239	0.47851	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58455	58455	SRR12436807	SRX8932496	SRS7188841	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O4 R3 RiboMinus	GSM4724726		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	WT O4 R3 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724726	GSM4724726: WT O4 R3 RiboMinus; Danio rerio; RNA Seq	GSM4724726		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724726	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T4_R3_RiboC.fastq	fastq	3536883000.0	35368830.0	GSM4724726 r1	0:100	A:740435414;C:1028707233;G:946006923;T:821659092;N:74338	100		740435414	1028707233	946006923	821659092	74338	SRX8932496	SRS7188841	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.96899	0.16966	0.77561	0.70876	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58456	58456	SRR12436806	SRX8932495	SRS7188840	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O4 R2 RiboMinus	GSM4724725		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	WT O4 R2 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724725	GSM4724725: WT O4 R2 RiboMinus; Danio rerio; RNA Seq	GSM4724725		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724725	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T4_R2_RiboC.fastq	fastq	1735575800.0	17355758.0	GSM4724725 r1	0:100	A:336997637;C:537535888;G:481185263;T:379820303;N:36709	100		336997637	537535888	481185263	379820303	36709	SRX8932495	SRS7188840	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.98261	0.20886	0.81744	0.82191	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58457	58457	SRR12436805	SRX8932494	SRS7188839	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O4 R1 RiboMinus	GSM4724724		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	WT O4 R1 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724724	GSM4724724: WT O4 R1 RiboMinus; Danio rerio; RNA Seq	GSM4724724		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724724	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T4_R1_RiboC.fastq	fastq	968375900.0	9683759.0	GSM4724724 r1	0:100	A:205812739;C:278650314;G:254581772;T:229311224;N:19851	100		205812739	278650314	254581772	229311224	19851	SRX8932494	SRS7188839	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.97262	0.17599	0.7751	0.69851	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58458	58458	SRR12436804	SRX8932493	SRS7188838	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O3 R3 RiboMinus	GSM4724723		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	WT O3 R3 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	GSM4724723	GSM4724723: WT O3 R3 RiboMinus; Danio rerio; RNA Seq	GSM4724723		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724723	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T3_R3_RiboC.fastq	fastq	1157950000.0	11579500.0	GSM4724723 r1	0:100	A:230959551;C:350911015;G:319781869;T:256262721;N:34844	100		230959551	350911015	319781869	256262721	34844	SRX8932493	SRS7188838	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.97497	0.1512	0.79788	0.77427	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58459	58459	SRR12436803	SRX8932492	SRS7188837	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O3 R2 RiboMinus	GSM4724722		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	WT O3 R2 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	GSM4724722	GSM4724722: WT O3 R2 RiboMinus; Danio rerio; RNA Seq	GSM4724722		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724722	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T3_R2_RiboC.fastq	fastq	2139321300.0	21393213.0	GSM4724722 r1	0:100	A:472163186;C:594579228;G:551625858;T:520908125;N:44903	100		472163186	594579228	551625858	520908125	44903	SRX8932492	SRS7188837	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.96602	0.14064	0.76264	0.63001	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58460	58460	SRR12436802	SRX8932491	SRS7188836	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O3 R1 RiboMinus	GSM4724721		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	WT O3 R1 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	GSM4724721	GSM4724721: WT O3 R1 RiboMinus; Danio rerio; RNA Seq	GSM4724721		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724721	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T3_R1_RiboC.fastq	fastq	2525068300.0	25250683.0	GSM4724721 r1	0:100	A:565744039;C:693096961;G:646577782;T:619596341;N:53177	100		565744039	693096961	646577782	619596341	53177	SRX8932491	SRS7188836	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95787	0.15893	0.7572	0.62249	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58461	58461	SRR12436801	SRX8932490	SRS7188835	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O2 R3 RiboMinus	GSM4724720		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	WT O2 R3 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	GSM4724720	GSM4724720: WT O2 R3 RiboMinus; Danio rerio; RNA Seq	GSM4724720		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724720	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T2_R3_RiboC.fastq	fastq	5992563200.0	59925632.0	GSM4724720 r1	0:100	A:1319977536;C:1660691877;G:1559598039;T:1452225367;N:70381	100		1319977536	1660691877	1559598039	1452225367	70381	SRX8932490	SRS7188835	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.96386	0.11958	0.77191	0.6496	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58462	58462	SRR12436800	SRX8932489	SRS7188834	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O2 R2 RiboMinus	GSM4724719		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	WT O2 R2 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	GSM4724719	GSM4724719: WT O2 R2 RiboMinus; Danio rerio; RNA Seq	GSM4724719		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724719	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T2_R2_RiboC.fastq	fastq	1120112000.0	11201120.0	GSM4724719 r1	0:100	A:278845536;C:275363946;G:266988736;T:298890271;N:23511	100		278845536	275363946	266988736	298890271	23511	SRX8932489	SRS7188834	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95118	0.0769	0.74968	0.49838	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58463	58463	SRR12436799	SRX8932488	SRS7188833	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O2 R1 RiboMinus	GSM4724718		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	WT O2 R1 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	GSM4724718	GSM4724718: WT O2 R1 RiboMinus; Danio rerio; RNA Seq	GSM4724718		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724718	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T2_R1_RiboC.fastq	fastq	1161163900.0	11611639.0	GSM4724718 r1	0:100	A:286378138;C:285298711;G:278971452;T:310491191;N:24408	100		286378138	285298711	278971452	310491191	24408	SRX8932488	SRS7188833	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95348	0.07579	0.75258	0.50375	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58464	58464	SRR12436798	SRX8932487	SRS7188832	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O1 R3 RiboMinus	GSM4724717		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	WT O1 R3 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	GSM4724717	GSM4724717: WT O1 R3 RiboMinus; Danio rerio; RNA Seq	GSM4724717		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724717	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T1_R3_RiboC.fastq	fastq	4193077700.0	41930777.0	GSM4724717 r1	0:100	A:1050014991;C:1016496752;G:997881012;T:1128596351;N:88594	100		1050014991	1016496752	997881012	1128596351	88594	SRX8932487	SRS7188832	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94605	0.07574	0.75903	0.46881	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58465	58465	SRR12436797	SRX8932486	SRS7188831	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O1 R2 RiboMinus	GSM4724716		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	WT O1 R2 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	GSM4724716	GSM4724716: WT O1 R2 RiboMinus; Danio rerio; RNA Seq	GSM4724716		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724716	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T1_R2_RiboC.fastq	fastq	3009030900.0	30090309.0	GSM4724716 r1	0:100	A:756357371;C:732762366;G:713861976;T:805985486;N:63701	100		756357371	732762366	713861976	805985486	63701	SRX8932486	SRS7188831	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94803	0.06904	0.75286	0.47431	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58466	58466	SRR12436796	SRX8932485	SRS7188830	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O1 R1 RiboMinus	GSM4724715		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	WT O1 R1 RiboMinus	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	GSM4724715	GSM4724715: WT O1 R1 RiboMinus; Danio rerio; RNA Seq	GSM4724715		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724715	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T1_R1_RiboC.fastq	fastq	7969559200.0	79695592.0	GSM4724715 r1	0:100	A:1987465338;C:1940306877;G:1899602998;T:2142014898;N:169089	100		1987465338	1940306877	1899602998	2142014898	169089	SRX8932485	SRS7188830	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95073	0.07916	0.7545	0.4763	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58488	58488	SRR12436774	SRX8932463	SRS7188808	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724693 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724693			Ski7 O4 R3 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724693	GSM4724693: Ski7 O4 R3 polyA; Danio rerio; RNA Seq	GSM4724693		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724693	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T4_R3_polyA.fastq	fastq	1385902100.0	13859021.0	GSM4724693 r1	0:100	A:355022344;C:325692901;G:325856286;T:379309245;N:21324	100		355022344	325692901	325856286	379309245	21324	SRX8932463	SRS7188808	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95096	0.05314	0.74397	0.48463	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58489	58489	SRR12436773	SRX8932462	SRS7188807	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724692 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724692			Ski7 O4 R2 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724692	GSM4724692: Ski7 O4 R2 polyA; Danio rerio; RNA Seq	GSM4724692		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724692	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T4_R2_polyA.fastq	fastq	1645095000.0	16450950.0	GSM4724692 r1	0:100	A:419155785;C:388799946;G:390627234;T:446460278;N:51757	100		419155785	388799946	390627234	446460278	51757	SRX8932462	SRS7188807	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94503	0.03717	0.74832	0.48156	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58490	58490	SRR12436772	SRX8932461	SRS7188806	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O4 R1 polyA	GSM4724691		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	Ski7 O4 R1 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724691	GSM4724691: Ski7 O4 R1 polyA; Danio rerio; RNA Seq	GSM4724691		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724691	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T4_R1_polyA.fastq	fastq	1387274300.0	13872743.0	GSM4724691 r1	0:100	A:350864142;C:326857764;G:329326718;T:380199491;N:26185	100		350864142	326857764	329326718	380199491	26185	SRX8932461	SRS7188806	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94828	0.04032	0.74452	0.47597	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58491	58491	SRR12436771	SRX8932460	SRS7188805	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724690 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724690			Ski7 O3 R3 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	GSM4724690	GSM4724690: Ski7 O3 R3 polyA; Danio rerio; RNA Seq	GSM4724690		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724690	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T3_R3_polyA.fastq	fastq	1823940300.0	18239403.0	GSM4724690 r1	0:100	A:465953751;C:430730916;G:432934989;T:494293990;N:26654	100		465953751	430730916	432934989	494293990	26654	SRX8932460	SRS7188805	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94861	0.03314	0.75323	0.47687	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58492	58492	SRR12436770	SRX8932459	SRS7188804	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O3 R2 polyA	GSM4724689		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	Ski7 O3 R2 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	GSM4724689	GSM4724689: Ski7 O3 R2 polyA; Danio rerio; RNA Seq	GSM4724689		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724689	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T3_R2_polyA.fastq	fastq	2475052000.0	24750520.0	GSM4724689 r1	0:100	A:519323476;C:717349825;G:662993394;T:575345089;N:40216	100		519323476	717349825	662993394	575345089	40216	SRX8932459	SRS7188804	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.97546	0.19558	0.79344	0.70626	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58493	58493	SRR12436769	SRX8932458	SRS7188803	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724688 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724688			Ski7 O3 R1 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage III\|strain:TLAB	GSM4724688	GSM4724688: Ski7 O3 R1 polyA; Danio rerio; RNA Seq	GSM4724688		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724688	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T3_R1_polyA.fastq	fastq	1344365700.0	13443657.0	GSM4724688 r1	0:100	A:358902689;C:317990745;G:310901851;T:356551630;N:18785	100		358902689	317990745	310901851	356551630	18785	SRX8932458	SRS7188803	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94986	0.03467	0.75248	0.48024	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58494	58494	SRR12436768	SRX8932457	SRS7188802	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724687 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724687			Ski7 O2 R3 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage II\|strain:TLAB	GSM4724687	GSM4724687: Ski7 O2 R3 polyA; Danio rerio; RNA Seq	GSM4724687		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724687	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T2_R3_polyA.fastq	fastq	5413358400.0	54133584.0	GSM4724687 r1	0:100	A:1388031358;C:1272641126;G:1285955460;T:1466673696;N:56760	100		1388031358	1272641126	1285955460	1466673696	56760	SRX8932457	SRS7188802	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.9472	0.02817	0.76027	0.47983	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58495	58495	SRR12436767	SRX8932456	SRS7188801	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724686 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724686			Ski7 O2 R2 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage II\|strain:TLAB	GSM4724686	GSM4724686: Ski7 O2 R2 polyA; Danio rerio; RNA Seq	GSM4724686		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724686	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T2_R2_polyA.fastq	fastq	1338262100.0	13382621.0	GSM4724686 r1	0:100	A:341009921;C:317021400;G:318286280;T:361902453;N:42046	100		341009921	317021400	318286280	361902453	42046	SRX8932456	SRS7188801	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94175	0.0299	0.75968	0.46945	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58496	58496	SRR12436766	SRX8932455	SRS7188800	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O2 R1 polyA	GSM4724685		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage II\|strain:TLAB	Ski7 O2 R1 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage II\|strain:TLAB	GSM4724685	GSM4724685: Ski7 O2 R1 polyA; Danio rerio; RNA Seq	GSM4724685		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724685	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T2_R1_polyA.fastq	fastq	1713968700.0	17139687.0	GSM4724685 r1	0:100	A:430560645;C:414355275;G:405736622;T:463293152;N:23006	100		430560645	414355275	405736622	463293152	23006	SRX8932455	SRS7188800	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95423	0.04999	0.74815	0.49685	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58497	58497	SRR12436765	SRX8932454	SRS7188799	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O1 R3 polyA	GSM4724684		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	Ski7 O1 R3 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	GSM4724684	GSM4724684: Ski7 O1 R3 polyA; Danio rerio; RNA Seq	GSM4724684		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724684	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T1_R3_polyA.fastq	fastq	719298300.0	7192983.0	GSM4724684 r1	0:100	A:189109969;C:167002756;G:170310269;T:192865064;N:10242	100		189109969	167002756	170310269	192865064	10242	SRX8932454	SRS7188799	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94344	0.02142	0.77053	0.45738	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58498	58498	SRR12436764	SRX8932453	SRS7188798	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	Ski7 O1 R2 polyA	GSM4724683		tissue:zebrafish oocyte\|genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	Ski7 O1 R2 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	GSM4724683	GSM4724683: Ski7 O1 R2 polyA; Danio rerio; RNA Seq	GSM4724683		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724683	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T1_R2_polyA.fastq	fastq	927674100.0	9276741.0	GSM4724683 r1	0:100	A:238134282;C:219286837;G:219778008;T:250446841;N:28132	100		238134282	219286837	219778008	250446841	28132	SRX8932453	SRS7188798	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93928	0.02483	0.7679	0.4858	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58499	58499	SRR12436763	SRX8932452	SRS7188797	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	GEO accession GSM4724682 is currently private and is scheduled to be released on Mar 17 2023.	GSM4724682			Ski7 O1 R1 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:ski7 / \|developmental stage:oocyte stage I\|strain:TLAB	GSM4724682	GSM4724682: Ski7 O1 R1 polyA; Danio rerio; RNA Seq	GSM4724682		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724682	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			Ski7_Ooc_T1_R1_polyA.fastq	fastq	913457600.0	9134576.0	GSM4724682 r1	0:100	A:232865896;C:216322788;G:217434769;T:246805052;N:29095	100		232865896	216322788	217434769	246805052	29095	SRX8932452	SRS7188797	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.9417	0.02723	0.76467	0.47013	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58521	58521	SRR12436741	SRX8932430	SRS7188775	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O4 R3 polyA	GSM4724660		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	WT O4 R3 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724660	GSM4724660: WT O4 R3 polyA; Danio rerio; RNA Seq	GSM4724660		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724660	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T4_R3_polyA.fastq	fastq	1220088000.0	12200880.0	GSM4724660 r1	0:100	A:307655212;C:288667632;G:290013036;T:333731254;N:20866	100		307655212	288667632	290013036	333731254	20866	SRX8932430	SRS7188775	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95191	0.05118	0.74574	0.47723	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58522	58522	SRR12436740	SRX8932429	SRS7188774	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O4 R2 polyA	GSM4724659		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	WT O4 R2 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724659	GSM4724659: WT O4 R2 polyA; Danio rerio; RNA Seq	GSM4724659		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724659	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T4_R2_polyA.fastq	fastq	974054000.0	9740540.0	GSM4724659 r1	0:100	A:245756625;C:231170272;G:232466471;T:264642158;N:18474	100		245756625	231170272	232466471	264642158	18474	SRX8932429	SRS7188774	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95103	0.05355	0.74369	0.49361	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58523	58523	SRR12436739	SRX8932428	SRS7188773	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O4 R1 polyA	GSM4724658		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	WT O4 R1 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage IV V\|strain:TLAB	GSM4724658	GSM4724658: WT O4 R1 polyA; Danio rerio; RNA Seq	GSM4724658		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724658	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T4_R1_polyA.fastq	fastq	1018516000.0	10185160.0	GSM4724658 r1	0:100	A:257744919;C:239788292;G:241035439;T:279928882;N:18468	100		257744919	239788292	241035439	279928882	18468	SRX8932428	SRS7188773	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95651	0.0404	0.74769	0.48301	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58524	58524	SRR12436738	SRX8932427	SRS7188772	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O3 R3 polyA	GSM4724657		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	WT O3 R3 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	GSM4724657	GSM4724657: WT O3 R3 polyA; Danio rerio; RNA Seq	GSM4724657		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724657	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T3_R3_polyA.fastq	fastq	1511221600.0	15112216.0	GSM4724657 r1	0:100	A:360267325;C:384886383;G:376256561;T:389781340;N:29991	100		360267325	384886383	376256561	389781340	29991	SRX8932427	SRS7188772	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95504	0.09847	0.76378	0.53827	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58525	58525	SRR12436737	SRX8932426	SRS7188771	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O3 R2 polyA	GSM4724656		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	WT O3 R2 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	GSM4724656	GSM4724656: WT O3 R2 polyA; Danio rerio; RNA Seq	GSM4724656		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724656	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T3_R2_polyA.fastq	fastq	1819237900.0	18192379.0	GSM4724656 r1	0:100	A:462060132;C:430315975;G:433552644;T:493277344;N:31805	100		462060132	430315975	433552644	493277344	31805	SRX8932426	SRS7188771	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94767	0.03464	0.75148	0.48269	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58526	58526	SRR12436736	SRX8932425	SRS7188770	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O3 R1 polyA	GSM4724655		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	WT O3 R1 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage III\|strain:TLAB	GSM4724655	GSM4724655: WT O3 R1 polyA; Danio rerio; RNA Seq	GSM4724655		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724655	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T3_R1_polyA.fastq	fastq	4207117900.0	42071179.0	GSM4724655 r1	0:100	A:1087102522;C:1013988887;G:993080874;T:1112913159;N:32458	100		1087102522	1013988887	993080874	1112913159	32458	SRX8932425	SRS7188770	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.95096	0.04182	0.74882	0.49243	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58527	58527	SRR12436735	SRX8932424	SRS7188769	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O2 R3 polyA	GSM4724654		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	WT O2 R3 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	GSM4724654	GSM4724654: WT O2 R3 polyA; Danio rerio; RNA Seq	GSM4724654		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724654	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T2_R3_polyA.fastq	fastq	1184155700.0	11841557.0	GSM4724654 r1	0:100	A:305706119;C:277055741;G:280181420;T:321176860;N:35560	100		305706119	277055741	280181420	321176860	35560	SRX8932424	SRS7188769	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93621	0.02475	0.76155	0.48722	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58528	58528	SRR12436734	SRX8932423	SRS7188768	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O2 R2 polyA	GSM4724653		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	WT O2 R2 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	GSM4724653	GSM4724653: WT O2 R2 polyA; Danio rerio; RNA Seq	GSM4724653		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724653	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T2_R2_polyA.fastq	fastq	1883194000.0	18831940.0	GSM4724653 r1	0:100	A:461473532;C:466713142;G:461060681;T:493890140;N:56505	100		461473532	466713142	461060681	493890140	56505	SRX8932423	SRS7188768	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94837	0.07018	0.7612	0.5239	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58529	58529	SRR12436733	SRX8932422	SRS7188767	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O2 R1 polyA	GSM4724652		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	WT O2 R1 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage II\|strain:TLAB	GSM4724652	GSM4724652: WT O2 R1 polyA; Danio rerio; RNA Seq	GSM4724652		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724652	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T2_R1_polyA.fastq	fastq	893055500.0	8930555.0	GSM4724652 r1	0:100	A:228294393;C:211734420;G:210752916;T:242249752;N:24019	100		228294393	211734420	210752916	242249752	24019	SRX8932422	SRS7188767	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94873	0.03454	0.76075	0.49768	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58530	58530	SRR12436732	SRX8932421	SRS7188766	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O1 R3 polyA	GSM4724651		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	WT O1 R3 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	GSM4724651	GSM4724651: WT O1 R3 polyA; Danio rerio; RNA Seq	GSM4724651		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724651	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T1_R3_polyA.fastq	fastq	1690049000.0	16900490.0	GSM4724651 r1	0:100	A:433170251;C:397976643;G:403752898;T:455117766;N:31442	100		433170251	397976643	403752898	455117766	31442	SRX8932421	SRS7188766	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93925	0.0267	0.76921	0.47685	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58531	58531	SRR12436731	SRX8932420	SRS7188765	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O1 R2 polyA	GSM4724650		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	WT O1 R2 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	GSM4724650	GSM4724650: WT O1 R2 polyA; Danio rerio; RNA Seq	GSM4724650		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724650	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T1_R2_polyA.fastq	fastq	1118013500.0	11180135.0	GSM4724650 r1	0:100	A:287670338;C:261590511;G:265103395;T:303614321;N:34935	100		287670338	261590511	265103395	303614321	34935	SRX8932420	SRS7188765	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.93851	0.02215	0.76351	0.47327	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
58532	58532	SRR12436730	SRX8932419	SRS7188764	SRP253077	PRJNA613025	Zebrafish Ski7 tunes RNA levels during the oocyte to embryo transition	GSE147112	Transcriptome Analysis	Post transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte to embryo transition which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte to embryo transition. Here we focused on the auxiliary three prime to five prime degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte to embryo transition transcriptome profiling identified stage specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall our results provide first insights into the physiological role of vertebrate Ski7 as an important post transcriptional regulator during the oocyte to embryo transition. Overall design: Transcriptome profiles of eleven time points of WT and ski7 mutant zebrafish samples during the oocyte to embryo transition. Every time point from each genotype was performed in triplicates.		pubmed:33600438;pubmed:34556579	WT O1 R1 polyA	GSM4724649		tissue:zebrafish oocyte\|genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	WT O1 R1 polyA	Libraries were sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0 using the Ensembl transcriptome release 92. The following parameters were used: hisat2 q dta rna strandness R k 12 no unal Quantification of uniquely mapped reads raw reads was done with HTSeq v0.9.1 Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing raw reads or TPM	zebrafish oocyte		Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14/10 hour light/dark cycle	genotype:wild type\|developmental stage:oocyte stage I\|strain:TLAB	GSM4724649	GSM4724649: WT O1 R1 polyA; Danio rerio; RNA Seq	GSM4724649		1	Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA the polyA selection kit from LEXOGEN was used. For rRNA depleted samples RiboCop rRNA depletion kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina	GEO Accession:GSM4724649	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP253077			WT_Ooc_T1_R1_polyA.fastq	fastq	911081300.0	9110813.0	GSM4724649 r1	0:100	A:233869154;C:213268857;G:216850859;T:247064879;N:27551	100		233869154	213268857	216850859	247064879	27551	SRX8932419	SRS7188764	SRA1055855	GEO	Pauli lab, Research Institute of Molecular Pathology	1	0.94808	0.02169	0.76501	0.47032	100	B	usable mapping rate	illumina	hiseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown	Austria	2020-08-12	Zygote	Embryo	Oocyte	Reproductive System
66236	66236	SRR16195512	SRX12480000	SRS10443550	SRP339965	PRJNA768450	Time resolved RNA sequencing reveals distinct post transcriptional regimes during zebrafish embryogenesis	GSE185283	Other	We report the characterization of transcript dynamics during maternal to zygotic transition in Zebrafish MZT using thiol linked alkylation for the metabolic sequencing of RNA SLAMseq. Overall design: Quantification of de novo transcription during MZT		pubmed:36757845	Fertilized oocyte replicate 3 Fertilized oocyte 3	GSM5610104		tissue:Zebrafish oocytes\|cell type:oocyte\|strain:TLAB TL X AB\|chip antibody:3 prime end sequencing\|treatment:Untreated	Fertilized oocyte replicate 3 Fertilized oocyte 3	three prime end sequencing data were used to creat custom annotations using three prime GAmES SLAMseq was mapped and counted using SLAMdunk 3.4.1. Reads were alingned to the dr11 genome Additional SNP filtering was performed using samtools pileup TTSLAMseq data were sequentially mapped to rRNA sequences mitochondrial sequences and then the genome. other RNAseq data were mapped to dr11 using STAR and counted using featureCounts Genome build: dr11 Supplementary files format and content: count files of SLAMseq data were created using custom scripts post SNP filtering Supplementary files format and content: bedgraph files were genererated using deeptools Supplementary files format and content: Count files of TTSLAmseq data were obtained from SLAMdunk	Zebrafish oocytes	Zebrafish embryos were injected with 4sU or incubated in 4sU	QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. NEB. Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs and indexed with NEBNext Multiplex Oligos for Illumina Dual Index Primer Set I New England Biolabs.	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14 hour light/10 hour dark cycle. TLAB fish were generated by crossing zebrafish AB and the natural variant TL Tupfel Longfin stocks and used for all experiments.	cell type:oocyte\|strain:TLAB TL X AB\|chip antibody:3 prime end sequencing\|treatment:Untreated	GSM5610104	GSM5610104: Fertilized oocyte replicate 3 Fertilized oocyte 3; Danio rerio; RNA Seq	GSM5610104		1	QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. NEB. Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs and indexed with NEBNext Multiplex Oligos for Illumina Dual Index Primer Set I New England Biolabs.	GEO Accession:GSM5610104	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP339965			WT_Ooc_FER_R3.fastq.gz	fastq	1117096200.0	11170962.0	GSM5610104 r1	0:100	A:382619405;C:202583344;G:250919891;T:280906801;N:66759	100		382619405	202583344	250919891	280906801	66759	SRX12480000	SRS10443550	SRA1305700	GEO	Institute of Molecular Biotechnology	1	0.64947	0.10219	0.83905	0.60833	100	B	usable mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	nebnext	bulk	unknown	unknown	Austria	2021-10-04	Zygote	Embryo	Oocyte	Reproductive System
66237	66237	SRR16195511	SRX12479999	SRS10443549	SRP339965	PRJNA768450	Time resolved RNA sequencing reveals distinct post transcriptional regimes during zebrafish embryogenesis	GSE185283	Other	We report the characterization of transcript dynamics during maternal to zygotic transition in Zebrafish MZT using thiol linked alkylation for the metabolic sequencing of RNA SLAMseq. Overall design: Quantification of de novo transcription during MZT		pubmed:36757845	Fertilized oocyte replicate 2 Fertilized oocyte 2	GSM5610103		tissue:Zebrafish oocytes\|cell type:oocyte\|strain:TLAB TL X AB\|chip antibody:3 prime end sequencing\|treatment:Untreated	Fertilized oocyte replicate 2 Fertilized oocyte 2	three prime end sequencing data were used to creat custom annotations using three prime GAmES SLAMseq was mapped and counted using SLAMdunk 3.4.1. Reads were alingned to the dr11 genome Additional SNP filtering was performed using samtools pileup TTSLAMseq data were sequentially mapped to rRNA sequences mitochondrial sequences and then the genome. other RNAseq data were mapped to dr11 using STAR and counted using featureCounts Genome build: dr11 Supplementary files format and content: count files of SLAMseq data were created using custom scripts post SNP filtering Supplementary files format and content: bedgraph files were genererated using deeptools Supplementary files format and content: Count files of TTSLAmseq data were obtained from SLAMdunk	Zebrafish oocytes	Zebrafish embryos were injected with 4sU or incubated in 4sU	QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. NEB. Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs and indexed with NEBNext Multiplex Oligos for Illumina Dual Index Primer Set I New England Biolabs.	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14 hour light/10 hour dark cycle. TLAB fish were generated by crossing zebrafish AB and the natural variant TL Tupfel Longfin stocks and used for all experiments.	cell type:oocyte\|strain:TLAB TL X AB\|chip antibody:3 prime end sequencing\|treatment:Untreated	GSM5610103	GSM5610103: Fertilized oocyte replicate 2 Fertilized oocyte 2; Danio rerio; RNA Seq	GSM5610103		1	QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. NEB. Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs and indexed with NEBNext Multiplex Oligos for Illumina Dual Index Primer Set I New England Biolabs.	GEO Accession:GSM5610103	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP339965			WT_Ooc_FER_R2.fastq.gz	fastq	727606300.0	7276063.0	GSM5610103 r1	0:100	A:255161621;C:130820008;G:159259242;T:182321712;N:43717	100		255161621	130820008	159259242	182321712	43717	SRX12479999	SRS10443549	SRA1305700	GEO	Institute of Molecular Biotechnology	1	0.60979	0.06401	0.83871	0.58404	100	B	usable mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	nebnext	bulk	unknown	unknown	Austria	2021-10-04	Zygote	Embryo	Oocyte	Reproductive System
66238	66238	SRR16195510	SRX12479998	SRS10443548	SRP339965	PRJNA768450	Time resolved RNA sequencing reveals distinct post transcriptional regimes during zebrafish embryogenesis	GSE185283	Other	We report the characterization of transcript dynamics during maternal to zygotic transition in Zebrafish MZT using thiol linked alkylation for the metabolic sequencing of RNA SLAMseq. Overall design: Quantification of de novo transcription during MZT		pubmed:36757845	Fertilized oocyte replicate 1 Fertilized oocyte 1	GSM5610102		tissue:Zebrafish oocytes\|cell type:oocyte\|strain:TLAB TL X AB\|chip antibody:3 prime end sequencing\|treatment:Untreated	Fertilized oocyte replicate 1 Fertilized oocyte 1	three prime end sequencing data were used to creat custom annotations using three prime GAmES SLAMseq was mapped and counted using SLAMdunk 3.4.1. Reads were alingned to the dr11 genome Additional SNP filtering was performed using samtools pileup TTSLAMseq data were sequentially mapped to rRNA sequences mitochondrial sequences and then the genome. other RNAseq data were mapped to dr11 using STAR and counted using featureCounts Genome build: dr11 Supplementary files format and content: count files of SLAMseq data were created using custom scripts post SNP filtering Supplementary files format and content: bedgraph files were genererated using deeptools Supplementary files format and content: Count files of TTSLAmseq data were obtained from SLAMdunk	Zebrafish oocytes	Zebrafish embryos were injected with 4sU or incubated in 4sU	QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. NEB. Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs and indexed with NEBNext Multiplex Oligos for Illumina Dual Index Primer Set I New England Biolabs.	Zebrafish Danio rerio were raised according to standard protocols 28°C water temperature; 14 hour light/10 hour dark cycle. TLAB fish were generated by crossing zebrafish AB and the natural variant TL Tupfel Longfin stocks and used for all experiments.	cell type:oocyte\|strain:TLAB TL X AB\|chip antibody:3 prime end sequencing\|treatment:Untreated	GSM5610102	GSM5610102: Fertilized oocyte replicate 1 Fertilized oocyte 1; Danio rerio; RNA Seq	GSM5610102		1	QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. NEB. Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina New England Biolabs and indexed with NEBNext Multiplex Oligos for Illumina Dual Index Primer Set I New England Biolabs.	GEO Accession:GSM5610102	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP339965			WT_Ooc_FER_R1.fastq.gz	fastq	1319550100.0	13195501.0	GSM5610102 r1	0:100	A:446810012;C:237425862;G:301380045;T:333855325;N:78856	100		446810012	237425862	301380045	333855325	78856	SRX12479998	SRS10443548	SRA1305700	GEO	Institute of Molecular Biotechnology	1	0.6572	0.10662	0.83575	0.59976	100	B	usable mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	nebnext	bulk	unknown	unknown	Austria	2021-10-04	Zygote	Embryo	Oocyte	Reproductive System
69433	69433	SRR18685191	SRX14786403	SRS12545308	SRP368241	PRJNA824784	Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes	GSE200470	Other	We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species except mouse. We found endo siRNAs resulted from the truncated Dicer isoform were mouse specific and os piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2' three prime O methylation. The sequences of many highly expressed piRNA clusters are fast evolving compared with their syntenic genomic locations and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.		pubmed:38532500	zebrafish oxidation	GSM6034633		source name:oocyte\|tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|treatment:NaIO4 oxidation\|geo loc name:missing\|collection date:missing	zebrafish oxidation	We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs tsRNA tRNA derived small non coding RNA rsRNA rRNA derived small non coding RNA small snoRNAs lncRNA and mRNA successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others. We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM transcripts per kilobase of exon model per million mapped reads by StringTie. Assembly: GRCh38 GRCm38 Supplementary files format and content: tab delimited text files include TPM values or raw counts for each Sample	oocyte		Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|treatment:NaIO4 oxidation	GSM6034633	GSM6034633: zebrafish oxidation; Danio rerio; RNA Seq	GSM6034633 r1	GSM6034633	1	Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP368241			ZebrafishO_combined_R1.fastq.gz	fastq	729583350.0	4863889.0	GSM6034633 r1	0:150 1:0	A:107993751;C:106112485;G:397809615;T:117666119;N:1380	150	0	107993751	106112485	397809615	117666119	1380	SRX14786403	SRS12545308	SRA1400916	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	1	0.0	0.0	1.0		150	T	under 1.2% mapping rate	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-04-08	Zygote	Embryo	Oocyte	Reproductive System
69434	69434	SRR18685192	SRX14786402	SRS12545307	SRP368241	PRJNA824784	Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes	GSE200470	Other	We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species except mouse. We found endo siRNAs resulted from the truncated Dicer isoform were mouse specific and os piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2' three prime O methylation. The sequences of many highly expressed piRNA clusters are fast evolving compared with their syntenic genomic locations and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.		pubmed:38532500	zebrafish control	GSM6034632		source name:oocyte\|tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|treatment:control\|geo loc name:missing\|collection date:missing	zebrafish control	We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs tsRNA tRNA derived small non coding RNA rsRNA rRNA derived small non coding RNA small snoRNAs lncRNA and mRNA successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others. We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM transcripts per kilobase of exon model per million mapped reads by StringTie. Assembly: GRCh38 GRCm38 Supplementary files format and content: tab delimited text files include TPM values or raw counts for each Sample	oocyte		Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|treatment:control	GSM6034632	GSM6034632: zebrafish control; Danio rerio; RNA Seq	GSM6034632 r1	GSM6034632	1	Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP368241			ZebrafishB_combined_R1.fastq.gz	fastq	1146821100.0	7645474.0	GSM6034632 r1	0:150 1:0	A:173086143;C:178233645;G:594358274;T:201140843;N:2195	150	0	173086143	178233645	594358274	201140843	2195	SRX14786402	SRS12545307	SRA1400916	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	1	0.0	0.0	1.0		150	T	under 1.2% mapping rate	illumina	novaseq_era	unknown	small_rna	unknown	bulk	unknown	unknown	China	2022-04-08	Zygote	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");;