{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_strategy = \"RNA-Seq\" and tissue_curation = \"Oocyte\"", "rows": [[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\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 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 needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage IV  rep2", "GSM8147872", null, "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", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s 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\u2019s 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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "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, null, null, null, 588246161, 609187233, 593122683, 665837765, 120490, "SRX23954975", "SRS20755396", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [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\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 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 needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage IV  rep1", "GSM8147871", null, "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", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s 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\u2019s 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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "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, null, null, null, 649971632, 640667370, 632570967, 727447552, 127175, "SRX23954974", "SRS20755395", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [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\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 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 needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage III  rep2", "GSM8147870", null, "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", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s 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\u2019s 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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "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, null, null, null, 679041537, 690924547, 702857353, 736996218, 138301, "SRX23954973", "SRS20755394", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [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\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 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 needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage III  rep1", "GSM8147869", null, "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", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s 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\u2019s 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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "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, null, null, null, 701751055, 680571938, 664212213, 781698241, 138929, "SRX23954972", "SRS20755393", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [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\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 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 needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage II  rep2", "GSM8147868", null, "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", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s 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\u2019s 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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "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, null, null, null, 698931608, 681467909, 683751172, 773364392, 137351, "SRX23954971", "SRS20755392", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [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\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 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 needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage II  rep1", "GSM8147867", null, "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", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s 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\u2019s 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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "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, null, null, null, 829333798, 802089215, 804982077, 923557236, 164494, "SRX23954970", "SRS20755391", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [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\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 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 needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage I  rep2", "GSM8147866", null, "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", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s 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\u2019s 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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "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, null, null, null, 653441701, 681445567, 663740568, 740918288, 128096, "SRX23954969", "SRS20755390", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [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\u201311 days post purging dpp. Stage I and II oocytes were collected at 1\u20132 dpp  stage III oocytes germinal vesicle in central position at 4\u20137 dpp  and stage IV oocytes germinal vesicle asymmetrically located at 8\u201310 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 needle without xxx use of Collagenases. Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer's protocols. Three biological replicate samples containing 20 dechorionated zebrafish embryos were snap frozen in TRIzol Invitrogen #15596026. Four time points of embryonic development were included: 1 cell stage 0 hpf  hpf  2 hpf  4 hpf  and 6 hpf. RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer's protocols.", null, "pubmed:39302832", null, "Zebrafish Oocyte  Stage I  rep1", "GSM8147865", null, "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", null, "Isolated oocytes were snap frozen and RNA was extracted with TRIzol Invitrogen #15596026 following manufacturer\u2019s protocols. 0   2   4  and 6 hpf zebrafish embryo RNA was extracted with Direct zol RNA MicroPrep kit Zymo Research #R2062 following manufacturer\u2019s 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\u2019s 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\u2019s 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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP495323", null, null, "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, null, null, null, 815134657, 817210346, 809175239, 907149915, 161695, "SRX23954968", "SRS20755389", "SRA1824599", "Computational Biology, Stowers Institute for Medical Research", "Computational Biology, Stowers Institute for Medical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-03-14", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [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", null, "pubmed:21555364;pubmed:24586560;pubmed:23676078", null, "Maternal", "GSM564427", null, "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:\u00a0 Mapping was done using Applied Biosystems\u2019 SOLiD BioScope alignment for whole transcriptome analysis pipeline.\u00a0 Two mismatches were allowed in the 25bp color space seed sequence with extension alignment performed to find the full mapping location.\u00a0 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\u2122 Sequencing kit ABI according to manufacturer\u2019s instructions. About 200 280 \u00b5g 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 \u221280\u00b0C. Total RNA was extracted from whole embryos using Trizol Invitrogen according to manufacturer\u2019s 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", null, "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", null, null, null, null, 1566199300.0, 31323986.0, "GSM564427 1", "0:50", null, 50, null, null, null, null, null, null, null, null, "SRX025025", "SRS085804", "SRA022850", "GEO", "Computational and Systems Biology, Genome Institute of Singapore", 1, 0.72688, null, 0.05657, null, 0.876, null, 0.51223, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "full_length", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2010-07-08", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:27870856", null, "60mg arm 3", "GSM2140605", null, "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 \u00b0C 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", null, "1", "The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 \u00b0C 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", null, "SRP074244", null, null, "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, null, null, null, 550921675, 559384489, 553530174, 689218350, 13112, "SRX1738401", "SRS1418771", "SRA422860", "GEO", "Chromosome Structure and Development Group, Department of Pathology, University of Otago", 1, 0.95538, null, 0.04454, null, 0.7512, null, 0.62731, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "New Zealand", "2016-05-02", "Multi-stage", "Multi-stage", "Oocyte", "Reproductive System"], [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.", null, "pubmed:27870856", null, "60mg arm 2", "GSM2140604", null, "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 \u00b0C 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", null, "1", "The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 \u00b0C 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", null, "SRP074244", null, null, "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, null, null, null, 598028827, 604381782, 600136410, 749858137, 14044, "SRX1738399", "SRS1418770", "SRA422860", "GEO", "Chromosome Structure and Development Group, Department of Pathology, University of Otago", 1, 0.95953, null, 0.04033, null, 0.75408, null, 0.63549, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "New Zealand", "2016-05-02", "Multi-stage", "Multi-stage", "Oocyte", "Reproductive System"], [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.", null, "pubmed:27870856", null, "60mg arm 1", "GSM2140603", null, "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 \u00b0C 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", null, "1", "The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 \u00b0C 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", null, "SRP074244", null, null, "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, null, null, null, 578536744, 593318438, 586674975, 713299111, 14032, "SRX1738397", "SRS1418769", "SRA422860", "GEO", "Chromosome Structure and Development Group, Department of Pathology, University of Otago", 1, 0.95474, null, 0.04276, null, 0.75625, null, 0.61194, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "New Zealand", "2016-05-02", "Multi-stage", "Multi-stage", "Oocyte", "Reproductive System"], [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.", null, "pubmed:27870856", null, "5mg arm 3", "GSM2140602", null, "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 \u00b0C 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", null, "1", "The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 \u00b0C 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", null, "SRP074244", null, null, "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, null, null, null, 599122965, 614407524, 605967391, 742824547, 14073, "SRX1738395", "SRS1418767", "SRA422860", "GEO", "Chromosome Structure and Development Group, Department of Pathology, University of Otago", 1, 0.95071, null, 0.0461, null, 0.74483, null, 0.61788, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "New Zealand", "2016-05-02", "Multi-stage", "Multi-stage", "Oocyte", "Reproductive System"], [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.", null, "pubmed:27870856", null, "5mg arm 2", "GSM2140601", null, "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 \u00b0C 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", null, "1", "The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 \u00b0C 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", null, "SRP074244", null, null, "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, null, null, null, 663485391, 679416584, 665850494, 832942768, 15463, "SRX1738393", "SRS1418765", "SRA422860", "GEO", "Chromosome Structure and Development Group, Department of Pathology, University of Otago", 1, 0.94998, null, 0.04837, null, 0.75442, null, 0.63571, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "New Zealand", "2016-05-02", "Multi-stage", "Multi-stage", "Oocyte", "Reproductive System"], [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.", null, "pubmed:27870856", null, "5mg arm 1", "GSM2140600", null, "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 \u00b0C 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", null, "1", "The eggs were transferred to tube containing RA1 buffer Macherey Nagel  cat. 740955.250 with b mercaptoethanol  and stored at  80 \u00b0C 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", null, "SRP074244", null, null, "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, null, null, null, 519836883, 638777587, 641445656, 609475335, 13339, "SRX1738391", "SRS1418764", "SRA422860", "GEO", "Chromosome Structure and Development Group, Department of Pathology, University of Otago", 1, 0.88003, null, 0.04264, null, 0.76138, null, 0.66721, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "New Zealand", "2016-05-02", "Multi-stage", "Multi-stage", "Oocyte", "Reproductive System"], [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 \u2013 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", null, "Anp32e Null Sperm RNA Seq Rep2", "GSM2730572", null, "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", null, "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", null, "developmental stage:Sperm Stage|strain:NA|injection:NA|mutation:Anp32e Null", "GSM2730572", "GSM2730572: Anp32e Null Sperm RNA Seq Rep2; Danio rerio; RNA Seq", "GSM2730572", null, "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", null, "SRP100178", null, null, "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, null, null, null, 643932236, 630114587, 625850241, 712599561, 87075, "SRX3058262", "SRS2404198", "SRA538756", "GEO", "Huntsman Cancer Institute", 1, 0.91107, null, 0.05039, null, 0.76108, null, 0.4698, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-03", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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 \u2013 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", null, "Anp32e Null Sperm RNA Seq Rep1", "GSM2730571", null, "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", null, "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", null, "developmental stage:Sperm Stage|strain:NA|injection:NA|mutation:Anp32e Null", "GSM2730571", "GSM2730571: Anp32e Null Sperm RNA Seq Rep1; Danio rerio; RNA Seq", "GSM2730571", null, "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", null, "SRP100178", null, null, "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, null, null, null, 756571256, 759039692, 777010061, 870095540, 104501, "SRX3058261", "SRS2404197", "SRA538756", "GEO", "Huntsman Cancer Institute", 1, 0.91819, null, 0.04312, null, 0.76307, null, 0.45972, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-03", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:30444999", null, "oocyte IV RNA seq", "GSM3359500", null, "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 \u2013t \u2013q \u2013N 1 \u2013L 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", null, "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", null, "SRP149356", null, null, "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, null, null, 159884635, 154136157, 161233162, 161078773, 109898, "SRX4617974", "SRS3720953", "SRA712563", "GEO", "Tsinghua University", 1, 0.94159, null, 0.02577, null, 0.79933, null, 0.46881, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-08-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:30444999", null, "oocyte III RNA seq", "GSM3359499", null, "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 \u2013t \u2013q \u2013N 1 \u2013L 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", null, "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", null, "SRP149356", null, null, "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, null, null, 160396576, 153811544, 160426381, 162544723, 110072, "SRX4617973", "SRS3720954", "SRA712563", "GEO", "Tsinghua University", 1, 0.93382, null, 0.03044, null, 0.729, null, 0.46965, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-08-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:30444999", null, "oocyte II RNA seq", "GSM3359498", null, "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 \u2013t \u2013q \u2013N 1 \u2013L 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", null, "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", null, "SRP149356", null, null, "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, null, null, 160017029, 153897668, 159821522, 162670200, 111960, "SRX4617972", "SRS3720944", "SRA712563", "GEO", "Tsinghua University", 1, 0.9326, null, 0.0241, null, 0.74073, null, 0.47431, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-08-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:30444999", null, "oocyte I RNA seq", "GSM3359497", null, "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 \u2013t \u2013q \u2013N 1 \u2013L 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", null, "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", null, "SRP149356", null, null, "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, null, null, 161520633, 153547778, 156542304, 165341706, 109760, "SRX4617971", "SRS3720943", "SRA712563", "GEO", "Tsinghua University", 1, 0.92933, null, 0.02356, null, 0.73683, null, 0.47367, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2018-08-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O4 R3 RiboMinus", "GSM4724750", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 1120262924, 1886034530, 1669359412, 1277719039, 123695, "SRX8932520", "SRS7188865", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.98775, null, 0.27616, null, 0.85561, null, 0.86154, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O4 R2 RiboMinus", "GSM4724749", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 282286056, 468342445, 416192774, 316541929, 31196, "SRX8932519", "SRS7188864", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.98708, null, 0.21634, null, 0.84611, null, 0.85636, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O4 R1 RiboMinus", "GSM4724748", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 231770113, 284279432, 255931584, 231004482, 21089, "SRX8932518", "SRS7188863", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.97595, null, 0.1875, null, 0.78833, null, 0.7203, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O3 R3 RiboMinus", "GSM4724747", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 315819595, 482378072, 439500811, 353009618, 33604, "SRX8932517", "SRS7188862", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.98036, null, 0.16863, null, 0.80012, null, 0.76997, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O3 R2 RiboMinus", "GSM4724746", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 397602403, 536394029, 491276851, 426334866, 38951, "SRX8932516", "SRS7188861", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96997, null, 0.11852, null, 0.77585, null, 0.66439, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724745 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724745", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 398467671, 533331652, 489602590, 435279283, 52204, "SRX8932515", "SRS7188860", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96808, null, 0.14968, null, 0.76806, null, 0.67187, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724744 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724744", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 539473608, 778770363, 717407077, 602751798, 55554, "SRX8932514", "SRS7188859", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.9783, null, 0.18716, null, 0.79788, null, 0.70432, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724743 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724743", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 616094880, 635920272, 606962967, 653043012, 52269, "SRX8932513", "SRS7188858", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95663, null, 0.08667, null, 0.75252, null, 0.52574, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O2 R1 RiboMinus", "GSM4724742", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 221922364, 228583521, 219452367, 240097505, 18643, "SRX8932512", "SRS7188857", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95527, null, 0.08947, null, 0.74858, null, 0.51463, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724741 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724741", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 1462644817, 1467450908, 1441714266, 1571912790, 88819, "SRX8932511", "SRS7188856", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95219, null, 0.06874, null, 0.76134, null, 0.48887, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O1 R2 RiboMinus", "GSM4724740", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 330391016, 317678365, 309923830, 353636331, 27958, "SRX8932510", "SRS7188855", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94932, null, 0.06794, null, 0.75668, null, 0.47546, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724739 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724739", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 269155883, 260373486, 255757791, 290531791, 22949, "SRX8932509", "SRS7188854", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.9501, null, 0.0714, null, 0.75239, null, 0.47851, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O4 R3 RiboMinus", "GSM4724726", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 740435414, 1028707233, 946006923, 821659092, 74338, "SRX8932496", "SRS7188841", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96899, null, 0.16966, null, 0.77561, null, 0.70876, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O4 R2 RiboMinus", "GSM4724725", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 336997637, 537535888, 481185263, 379820303, 36709, "SRX8932495", "SRS7188840", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.98261, null, 0.20886, null, 0.81744, null, 0.82191, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O4 R1 RiboMinus", "GSM4724724", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 205812739, 278650314, 254581772, 229311224, 19851, "SRX8932494", "SRS7188839", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.97262, null, 0.17599, null, 0.7751, null, 0.69851, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O3 R3 RiboMinus", "GSM4724723", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 230959551, 350911015, 319781869, 256262721, 34844, "SRX8932493", "SRS7188838", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.97497, null, 0.1512, null, 0.79788, null, 0.77427, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O3 R2 RiboMinus", "GSM4724722", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 472163186, 594579228, 551625858, 520908125, 44903, "SRX8932492", "SRS7188837", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96602, null, 0.14064, null, 0.76264, null, 0.63001, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O3 R1 RiboMinus", "GSM4724721", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 565744039, 693096961, 646577782, 619596341, 53177, "SRX8932491", "SRS7188836", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95787, null, 0.15893, null, 0.7572, null, 0.62249, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O2 R3 RiboMinus", "GSM4724720", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 1319977536, 1660691877, 1559598039, 1452225367, 70381, "SRX8932490", "SRS7188835", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.96386, null, 0.11958, null, 0.77191, null, 0.6496, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O2 R2 RiboMinus", "GSM4724719", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 278845536, 275363946, 266988736, 298890271, 23511, "SRX8932489", "SRS7188834", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95118, null, 0.0769, null, 0.74968, null, 0.49838, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O2 R1 RiboMinus", "GSM4724718", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 286378138, 285298711, 278971452, 310491191, 24408, "SRX8932488", "SRS7188833", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95348, null, 0.07579, null, 0.75258, null, 0.50375, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O1 R3 RiboMinus", "GSM4724717", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 1050014991, 1016496752, 997881012, 1128596351, 88594, "SRX8932487", "SRS7188832", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94605, null, 0.07574, null, 0.75903, null, 0.46881, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O1 R2 RiboMinus", "GSM4724716", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 756357371, 732762366, 713861976, 805985486, 63701, "SRX8932486", "SRS7188831", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94803, null, 0.06904, null, 0.75286, null, 0.47431, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O1 R1 RiboMinus", "GSM4724715", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 1987465338, 1940306877, 1899602998, 2142014898, 169089, "SRX8932485", "SRS7188830", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95073, null, 0.07916, null, 0.7545, null, 0.4763, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724693 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724693", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 355022344, 325692901, 325856286, 379309245, 21324, "SRX8932463", "SRS7188808", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95096, null, 0.05314, null, 0.74397, null, 0.48463, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724692 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724692", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 419155785, 388799946, 390627234, 446460278, 51757, "SRX8932462", "SRS7188807", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94503, null, 0.03717, null, 0.74832, null, 0.48156, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O4 R1 polyA", "GSM4724691", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 350864142, 326857764, 329326718, 380199491, 26185, "SRX8932461", "SRS7188806", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94828, null, 0.04032, null, 0.74452, null, 0.47597, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724690 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724690", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 465953751, 430730916, 432934989, 494293990, 26654, "SRX8932460", "SRS7188805", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94861, null, 0.03314, null, 0.75323, null, 0.47687, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O3 R2 polyA", "GSM4724689", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 519323476, 717349825, 662993394, 575345089, 40216, "SRX8932459", "SRS7188804", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.97546, null, 0.19558, null, 0.79344, null, 0.70626, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724688 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724688", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 358902689, 317990745, 310901851, 356551630, 18785, "SRX8932458", "SRS7188803", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94986, null, 0.03467, null, 0.75248, null, 0.48024, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724687 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724687", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 1388031358, 1272641126, 1285955460, 1466673696, 56760, "SRX8932457", "SRS7188802", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.9472, null, 0.02817, null, 0.76027, null, 0.47983, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724686 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724686", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 341009921, 317021400, 318286280, 361902453, 42046, "SRX8932456", "SRS7188801", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94175, null, 0.0299, null, 0.75968, null, 0.46945, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O2 R1 polyA", "GSM4724685", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 430560645, 414355275, 405736622, 463293152, 23006, "SRX8932455", "SRS7188800", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95423, null, 0.04999, null, 0.74815, null, 0.49685, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O1 R3 polyA", "GSM4724684", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 189109969, 167002756, 170310269, 192865064, 10242, "SRX8932454", "SRS7188799", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94344, null, 0.02142, null, 0.77053, null, 0.45738, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "Ski7 O1 R2 polyA", "GSM4724683", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 238134282, 219286837, 219778008, 250446841, 28132, "SRX8932453", "SRS7188798", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93928, null, 0.02483, null, 0.7679, null, 0.4858, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "GEO accession GSM4724682 is currently private and is scheduled to be released on Mar 17  2023.", "GSM4724682", null, null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 232865896, 216322788, 217434769, 246805052, 29095, "SRX8932452", "SRS7188797", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.9417, null, 0.02723, null, 0.76467, null, 0.47013, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O4 R3 polyA", "GSM4724660", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 307655212, 288667632, 290013036, 333731254, 20866, "SRX8932430", "SRS7188775", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95191, null, 0.05118, null, 0.74574, null, 0.47723, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O4 R2 polyA", "GSM4724659", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 245756625, 231170272, 232466471, 264642158, 18474, "SRX8932429", "SRS7188774", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95103, null, 0.05355, null, 0.74369, null, 0.49361, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O4 R1 polyA", "GSM4724658", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 257744919, 239788292, 241035439, 279928882, 18468, "SRX8932428", "SRS7188773", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95651, null, 0.0404, null, 0.74769, null, 0.48301, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O3 R3 polyA", "GSM4724657", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 360267325, 384886383, 376256561, 389781340, 29991, "SRX8932427", "SRS7188772", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95504, null, 0.09847, null, 0.76378, null, 0.53827, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O3 R2 polyA", "GSM4724656", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 462060132, 430315975, 433552644, 493277344, 31805, "SRX8932426", "SRS7188771", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94767, null, 0.03464, null, 0.75148, null, 0.48269, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O3 R1 polyA", "GSM4724655", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 1087102522, 1013988887, 993080874, 1112913159, 32458, "SRX8932425", "SRS7188770", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95096, null, 0.04182, null, 0.74882, null, 0.49243, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O2 R3 polyA", "GSM4724654", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 305706119, 277055741, 280181420, 321176860, 35560, "SRX8932424", "SRS7188769", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93621, null, 0.02475, null, 0.76155, null, 0.48722, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O2 R2 polyA", "GSM4724653", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 461473532, 466713142, 461060681, 493890140, 56505, "SRX8932423", "SRS7188768", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94837, null, 0.07018, null, 0.7612, null, 0.5239, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O2 R1 polyA", "GSM4724652", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 228294393, 211734420, 210752916, 242249752, 24019, "SRX8932422", "SRS7188767", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94873, null, 0.03454, null, 0.76075, null, 0.49768, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O1 R3 polyA", "GSM4724651", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 433170251, 397976643, 403752898, 455117766, 31442, "SRX8932421", "SRS7188766", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93925, null, 0.0267, null, 0.76921, null, 0.47685, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O1 R2 polyA", "GSM4724650", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 287670338, 261590511, 265103395, 303614321, 34935, "SRX8932420", "SRS7188765", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.93851, null, 0.02215, null, 0.76351, null, 0.47327, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:33600438;pubmed:34556579", null, "WT O1 R1 polyA", "GSM4724649", null, "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", null, "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\u00b0C 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", null, "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", null, "SRP253077", null, null, "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, null, null, null, 233869154, 213268857, 216850859, 247064879, 27551, "SRX8932419", "SRS7188764", "SRA1055855", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94808, null, 0.02169, null, 0.76501, null, 0.47032, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2020-08-12", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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", null, "pubmed:36757845", null, "Fertilized oocyte replicate 3 Fertilized oocyte 3", "GSM5610104", null, "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\u00ae Ultra II Directional RNA Library Prep Kit for Illumina\u00ae. 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\u00b0C 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", null, "1", "QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext\u00ae Ultra II Directional RNA Library Prep Kit for Illumina\u00ae. 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", null, "SRP339965", null, null, "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, null, null, null, 382619405, 202583344, 250919891, 280906801, 66759, "SRX12480000", "SRS10443550", "SRA1305700", "GEO", "Institute of Molecular Biotechnology", 1, 0.64947, null, 0.10219, null, 0.83905, null, 0.60833, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-10-04", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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", null, "pubmed:36757845", null, "Fertilized oocyte replicate 2 Fertilized oocyte 2", "GSM5610103", null, "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\u00ae Ultra II Directional RNA Library Prep Kit for Illumina\u00ae. 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\u00b0C 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", null, "1", "QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext\u00ae Ultra II Directional RNA Library Prep Kit for Illumina\u00ae. 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", null, "SRP339965", null, null, "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, null, null, null, 255161621, 130820008, 159259242, 182321712, 43717, "SRX12479999", "SRS10443549", "SRA1305700", "GEO", "Institute of Molecular Biotechnology", 1, 0.60979, null, 0.06401, null, 0.83871, null, 0.58404, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-10-04", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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", null, "pubmed:36757845", null, "Fertilized oocyte replicate 1 Fertilized oocyte 1", "GSM5610102", null, "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\u00ae Ultra II Directional RNA Library Prep Kit for Illumina\u00ae. 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\u00b0C 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", null, "1", "QuantSeq three prime end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext\u00ae Ultra II Directional RNA Library Prep Kit for Illumina\u00ae. 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", null, "SRP339965", null, null, "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, null, null, null, 446810012, 237425862, 301380045, 333855325, 78856, "SRX12479998", "SRS10443548", "SRA1305700", "GEO", "Institute of Molecular Biotechnology", 1, 0.6572, null, 0.10662, null, 0.83575, null, 0.59976, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-10-04", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:38532500", null, "zebrafish oxidation", "GSM6034633", null, "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", null, "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 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation  the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 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 \u00b0C for 3 min and then cooled on ice. For every single oocyte  1 \u03bcl 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.", null, "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 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation  the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 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 \u00b0C for 3 min and then cooled on ice. For every single oocyte  1 \u03bcl 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP368241", null, null, "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, null, null, 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, null, 0.0, null, 1.0, null, null, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-08", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [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.", null, "pubmed:38532500", null, "zebrafish control", "GSM6034632", null, "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", null, "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 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation  the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 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 \u00b0C for 3 min and then cooled on ice. For every single oocyte  1 \u03bcl 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.", null, "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 \u00b0C for 3 min then cooled in ice. post 3\u2032 adapter ligation  the samples were incubated with 5 U of lambda exonuclease and 25 U of 5\u2032 de adenylates. Small RNAs were reverse transcribed post 5\u2032 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 \u00b0C for 3 min and then cooled on ice. For every single oocyte  1 \u03bcl 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP368241", null, null, "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, null, null, 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, null, 0.0, null, 1.0, null, null, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-04-08", "Zygote", "Embryo", "Oocyte", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 74, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", 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