{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Multi-stage\" 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"], [34904, "SRR32321882", "SRX27657151", "SRS24062618", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Mild par2a mutant Enew", "GSM8790746", null, "source name:1hpf|tissue:1hpf|genotype:par2a mutant Mild|batch:biol rep 3|geo loc name:missing|collection date:missing", "Mild par2a mutant Enew", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:par2a mutant Mild|batch:biol rep 3", "GSM8790746", "GSM8790746: Mild par2a mutant Enew; Danio rerio; RNA Seq", "GSM8790746 r1", "GSM8790746", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "ENew_R1.fq.gz ENew_R2.fq.gz", "fastq fastq", 10329910500.0, 34433035.0, "GSM8790746 r1", "0:150 1:150", "A:2799891916;C:2357268078;G:2464224845;T:2708331200;N:194461", 150, 150, null, null, 2799891916, 2357268078, 2464224845, 2708331200, 194461, "SRX27657151", "SRS24062618", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34905, "SRR32321883", "SRX27657150", "SRS24062617", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Mild par2a mutant Dnew", "GSM8790745", null, "source name:1hpf|tissue:1hpf|genotype:par2a mutant Mild|batch:biol rep 2|geo loc name:missing|collection date:missing", "Mild par2a mutant Dnew", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:par2a mutant Mild|batch:biol rep 2", "GSM8790745", "GSM8790745: Mild par2a mutant Dnew; Danio rerio; RNA Seq", "GSM8790745 r1", "GSM8790745", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "DNew_R1.fq.gz DNew_R2.fq.gz", "fastq fastq", 10248079200.0, 34160264.0, "GSM8790745 r1", "0:150 1:150", "A:2793260638;C:2326676658;G:2420206143;T:2707745384;N:190377", 150, 150, null, null, 2793260638, 2326676658, 2420206143, 2707745384, 190377, "SRX27657150", "SRS24062617", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34906, "SRR32321884", "SRX27657149", "SRS24062616", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Mild par2a mutant D2", "GSM8790744", null, "source name:1hpf|tissue:1hpf|genotype:par2a mutant Mild|batch:biol rep 1|geo loc name:missing|collection date:missing", "Mild par2a mutant D2", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:par2a mutant Mild|batch:biol rep 1", "GSM8790744", "GSM8790744: Mild par2a mutant D2; Danio rerio; RNA Seq", "GSM8790744 r1", "GSM8790744", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "D2_R1.fq.gz D2_R2.fq.gz", "fastq fastq", 11762172300.0, 39207241.0, "GSM8790744 r1", "0:150 1:150", "A:3175985473;C:2693452522;G:2817123539;T:3074667110;N:943656", 150, 150, null, null, 3175985473, 2693452522, 2817123539, 3074667110, 943656, "SRX27657149", "SRS24062616", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34907, "SRR32321885", "SRX27657148", "SRS24062615", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Severe par2a mutant Cnew", "GSM8790743", null, "source name:1hpf|tissue:1hpf|genotype:par2a mutant Severe|batch:biol rep 3|geo loc name:missing|collection date:missing", "Severe par2a mutant Cnew", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:par2a mutant Severe|batch:biol rep 3", "GSM8790743", "GSM8790743: Severe par2a mutant Cnew; Danio rerio; RNA Seq", "GSM8790743 r1", "GSM8790743", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "CNew_R1.fq.gz CNew_R2.fq.gz", "fastq fastq", 10738375500.0, 35794585.0, "GSM8790743 r1", "0:150 1:150", "A:2913601251;C:2451840201;G:2552925604;T:2819808486;N:199958", 150, 150, null, null, 2913601251, 2451840201, 2552925604, 2819808486, 199958, "SRX27657148", "SRS24062615", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34908, "SRR32321886", "SRX27657147", "SRS24062614", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Severe par2a mutant Bnew", "GSM8790742", null, "source name:1hpf|tissue:1hpf|genotype:par2a mutant Severe|batch:biol rep 2|geo loc name:missing|collection date:missing", "Severe par2a mutant Bnew", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:par2a mutant Severe|batch:biol rep 2", "GSM8790742", "GSM8790742: Severe par2a mutant Bnew; Danio rerio; RNA Seq", "GSM8790742 r1", "GSM8790742", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "BNew_R1.fq.gz BNew_R2.fq.gz", "fastq fastq", 10032138000.0, 33440460.0, "GSM8790742 r1", "0:150 1:150", "A:2725263740;C:2280983708;G:2404101885;T:2621602178;N:186489", 150, 150, null, null, 2725263740, 2280983708, 2404101885, 2621602178, 186489, "SRX27657147", "SRS24062614", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34909, "SRR32321887", "SRX27657146", "SRS24062613", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Severe par2a mutant B3", "GSM8790741", null, "source name:1hpf|tissue:1hpf|genotype:par2a mutant Severe|batch:biol rep 1|geo loc name:missing|collection date:missing", "Severe par2a mutant B3", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:par2a mutant Severe|batch:biol rep 1", "GSM8790741", "GSM8790741: Severe par2a mutant B3; Danio rerio; RNA Seq", "GSM8790741 r1", "GSM8790741", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "B3_R1.fq.gz B3_R2.fq.gz", "fastq fastq", 10602259500.0, 35340865.0, "GSM8790741 r1", "0:150 1:150", "A:2890092630;C:2407378053;G:2504194258;T:2799754016;N:840543", 150, 150, null, null, 2890092630, 2407378053, 2504194258, 2799754016, 840543, "SRX27657146", "SRS24062613", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34910, "SRR32321888", "SRX27657145", "SRS24062612", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Sibling3 S3 New", "GSM8790740", null, "source name:1hpf|tissue:1hpf|genotype:Sibling|batch:biol rep 3|geo loc name:missing|collection date:missing", "Sibling3 S3 New", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:Sibling|batch:biol rep 3", "GSM8790740", "GSM8790740: Sibling3 S3 New; Danio rerio; RNA Seq", "GSM8790740 r1", "GSM8790740", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "S3New_R1.fq.gz S3New_R2.fq.gz", "fastq fastq", 10090266900.0, 33634223.0, "GSM8790740 r1", "0:150 1:150", "A:2751527796;C:2286318705;G:2376241359;T:2675989647;N:189393", 150, 150, null, null, 2751527796, 2286318705, 2376241359, 2675989647, 189393, "SRX27657145", "SRS24062612", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34911, "SRR32321889", "SRX27657144", "SRS24062611", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Sibling2 S2 New", "GSM8790739", null, "source name:1hpf|tissue:1hpf|genotype:Sibling|batch:biol rep 2|geo loc name:missing|collection date:missing", "Sibling2 S2 New", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:Sibling|batch:biol rep 2", "GSM8790739", "GSM8790739: Sibling2 S2 New; Danio rerio; RNA Seq", "GSM8790739 r1", "GSM8790739", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "S2New_R1.fq.gz S2New_R2.fq.gz", "fastq fastq", 10203807000.0, 34012690.0, "GSM8790739 r1", "0:150 1:150", "A:2771950983;C:2329534166;G:2415425258;T:2686709429;N:187164", 150, 150, null, null, 2771950983, 2329534166, 2415425258, 2686709429, 187164, "SRX27657144", "SRS24062611", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [34912, "SRR32321890", "SRX27657143", "SRS24062610", "SRP563479", "PRJNA1222877", "Protease activated receptor 2 links protease activity with calcium waves during egg activation and blastomere cleavage", "GSE289416", "Transcriptome Analysis", "Successful initiation of animal development requires activation of the egg immediately prior to fusion of gamete pronucleii. In all taxa  this is initiated by waves of calcium transients which transverse across the egg. Calcium waves also occur at cleavage furrows during later blastula cytokinesis. Calcium is released from the endoplasmic reticulum through activation of 1 4 5 trisphosphate IP3 receptors. Only a subset of the mechanisms employed to generate IP3 during vertebrate egg activation are defined  with strong evidence that other critical mechanisms exist. Serine proteases have been long implicated in egg activation and fertilisation. Here we report that treatment of zebrafish eggs with serine protease inhibitors leads to defective calcium wave propagation and failed egg activation. We further show that mutation of zebrafish Protease activated receptor 2a Par2a also results in severe disruption of egg activation  leading to failed chorion elevation and ooplasmic segregation. Milder par2a mutants progress further  but then show abnormal blastomere cleavage. We observed that par2a mutants show decreased amplitude and duration of calcium transients. Restoring Ca++ or direct injection of IP3 ligand rescues egg activation aborted by either serine protease inhibitor treatment or by mutation of Par2a. We thus show that serine protease activity is a critical regulator of IP3 and subsequent calcium wave amplification during zebrafish egg activation  and link this to intracellular calcium release via the protease receptor  Par2a.  This constitutes a novel signalling pathway critical for successful fertilisation. Overall design: RNA seq from 1 hpf zygotes of severe and mild par2a mutant zebrafish and sibling controls", null, null, null, "Sibling1 S1 New", "GSM8790738", null, "source name:1hpf|tissue:1hpf|genotype:Sibling|batch:biol rep 1|geo loc name:missing|collection date:missing", "Sibling1 S1 New", "In order to remove technical sequences  including adapters  polymerase chain reaction PCR primers  or fragments thereof  and quality of bases lower than 20  pass filter data of fastq format were processed by Cutadapt V1.9.1  phred cutoff: 20  error rate: 0.1  adapter overlap: 1bp  min. length: 75  proportion of N: 0.1 to be high quality clean data. Assembly: Zebrafish Genome assembly GRCz11 Supplementary files format and content: all.fpkm anno.xls    Excel file with all samples raw counts and FPKM in alternating columns", "1hpf", null, "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", "Mutant or sibling f2rl1.1 females were crossed to sibling males by natural crossing. Zygotes were collected at 1 hour post egg laying and maternal RNA extracted", "tissue:1hpf|genotype:Sibling|batch:biol rep 1", "GSM8790738", "GSM8790738: Sibling1 S1 New; Danio rerio; RNA Seq", "GSM8790738 r1", "GSM8790738", "1", "RNA was extracted using TRI Zol Invitrogen and precipitated by isopropanol. polyA mRNA isolated by OligodT beads mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP563479", null, null, "S1New_R1.fq.gz S1New_R2.fq.gz", "fastq fastq", 10109834700.0, 33699449.0, "GSM8790738 r1", "0:150 1:150", "A:2734326027;C:2315919523;G:2410121939;T:2649275286;N:191925", 150, 150, null, null, 2734326027, 2315919523, 2410121939, 2649275286, 191925, "SRX27657143", "SRS24062610", "SRA2077074", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", "Cancer Discovery & Regenerative Medicine Programme, Lee Kong Chian School of Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2025-02-12", "Multi-stage", "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"], [49742, "SRR8197481", "SRX5016863", "SRS4049994", "SRP169068", "PRJNA495892", "Danio rerio Genome sequencing", "PRJNA495892", "Whole Genome Sequencing", "Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, null, "three samples of zebrafish unfertilized eggs  and three samples zebrafish fries at the stage of prim5.", "Model organism or animal sample from Danio rerio", "The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, "isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage|dev stage:2 stages of unfertilized egg and prim 5|sex:pooled male and female|tissue:zebrafish in 2 stages of unfertilized egg and prim 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: prim5 stage", "Z2 3 F", "Z2 3 F", "The unfertilized eggs of zebrafish were taken as three samples Z1 1  Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1  Z2 2 and Z2 3 in the prim5 stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP169068", null, null, "Z2_3_1.fq.gz Z2_3_2.fq.gz", "fastq fastq", 6979181500.0, 27916726.0, "Z2 3 1.fq.gz", "0:125 1:125", "A:1822429760;C:1670132153;G:1694226275;T:1791552753;N:840559", 125, 125, null, null, 1822429760, 1670132153, 1694226275, 1791552753, 840559, "SRX5016863", "SRS4049994", "SRA810793", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.9586, 0.9518, 0.02217, 0.02129, 0.81022, 0.80921, 0.50342, 0.51319, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-11-16", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [49743, "SRR8197482", "SRX5016862", "SRS4049994", "SRP169068", "PRJNA495892", "Danio rerio Genome sequencing", "PRJNA495892", "Whole Genome Sequencing", "Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, null, "three samples of zebrafish unfertilized eggs  and three samples zebrafish fries at the stage of prim5.", "Model organism or animal sample from Danio rerio", "The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, "isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage|dev stage:2 stages of unfertilized egg and prim 5|sex:pooled male and female|tissue:zebrafish in 2 stages of unfertilized egg and prim 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: prim5 stage", "Z2 1 F", "Z2 1 F", "The unfertilized eggs of zebrafish were taken as three samples Z1 1  Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1  Z2 2 and Z2 3 in the prim5 stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP169068", null, null, "Z2_1_2.fq.gz Z2_1_1.fq.gz", "fastq fastq", 6728695750.0, 26914783.0, "Z2 1 1.fq.gz", "0:125 1:125", "A:1732100690;C:1624557456;G:1649046037;T:1722193010;N:798557", 125, 125, null, null, 1732100690, 1624557456, 1649046037, 1722193010, 798557, "SRX5016862", "SRS4049994", "SRA810793", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.9585, 0.95335, 0.01902, 0.01833, 0.8131, 0.81014, 0.48431, 0.493, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-11-16", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [49744, "SRR8197483", "SRX5016861", "SRS4049994", "SRP169068", "PRJNA495892", "Danio rerio Genome sequencing", "PRJNA495892", "Whole Genome Sequencing", "Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, null, "three samples of zebrafish unfertilized eggs  and three samples zebrafish fries at the stage of prim5.", "Model organism or animal sample from Danio rerio", "The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, "isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage|dev stage:2 stages of unfertilized egg and prim 5|sex:pooled male and female|tissue:zebrafish in 2 stages of unfertilized egg and prim 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: unfertilized egg", "Z1 3 F", "Z1 3 F", "The unfertilized eggs of zebrafish were taken as three samples Z1 1  Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1  Z2 2 and Z2 3 in the prim5 stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP169068", null, null, "Z1_3_1.fq.gz Z1_3_2.fq.gz", "fastq fastq", 6657035500.0, 26628142.0, "Z1 3 1.fq.gz", "0:125 1:125", "A:1796541492;C:1535300915;G:1557971133;T:1766443902;N:778058", 125, 125, null, null, 1796541492, 1535300915, 1557971133, 1766443902, 778058, "SRX5016861", "SRS4049994", "SRA810793", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.95543, 0.94989, 0.02312, 0.02201, 0.79689, 0.79421, 0.51212, 0.51203, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-11-16", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [49745, "SRR8197484", "SRX5016860", "SRS4049994", "SRP169068", "PRJNA495892", "Danio rerio Genome sequencing", "PRJNA495892", "Whole Genome Sequencing", "Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, null, "three samples of zebrafish unfertilized eggs  and three samples zebrafish fries at the stage of prim5.", "Model organism or animal sample from Danio rerio", "The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, "isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage|dev stage:2 stages of unfertilized egg and prim 5|sex:pooled male and female|tissue:zebrafish in 2 stages of unfertilized egg and prim 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: unfertilized egg", "Z1 2 F", "Z1 2 F", "The unfertilized eggs of zebrafish were taken as three samples Z1 1  Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1  Z2 2 and Z2 3 in the prim5 stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP169068", null, null, "Z1_2_1.fq.gz Z1_2_2.fq.gz", "fastq fastq", 8869328500.0, 35477314.0, "Z1 2 1.fq.gz", "0:125 1:125", "A:2367358711;C:2085652811;G:2116692954;T:2298597848;N:1026176", 125, 125, null, null, 2367358711, 2085652811, 2116692954, 2298597848, 1026176, "SRX5016860", "SRS4049994", "SRA810793", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.95776, 0.95084, 0.01896, 0.01811, 0.79823, 0.79608, 0.49565, 0.49345, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-11-18", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [49746, "SRR8197485", "SRX5016859", "SRS4049994", "SRP169068", "PRJNA495892", "Danio rerio Genome sequencing", "PRJNA495892", "Whole Genome Sequencing", "Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, null, "three samples of zebrafish unfertilized eggs  and three samples zebrafish fries at the stage of prim5.", "Model organism or animal sample from Danio rerio", "The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, "isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage|dev stage:2 stages of unfertilized egg and prim 5|sex:pooled male and female|tissue:zebrafish in 2 stages of unfertilized egg and prim 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: unfertilized egg", "Z1 1 F", "Z1 1 F", "The unfertilized eggs of zebrafish were taken as three samples Z1 1  Z1 2 and Z1 3 respectively. And the fries of zebrafish were taken as three samples Z2 1  Z2 2 and Z2 3 in the prim5 stage.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP169068", null, null, "Z1_1_1.fq.gz Z1_1_2.fq.gz", "fastq fastq", 7205390500.0, 28821562.0, "Z1 1 1.fq.gz", "0:125 1:125", "A:1900562357;C:1700185416;G:1728383049;T:1875415232;N:844446", 125, 125, null, null, 1900562357, 1700185416, 1728383049, 1875415232, 844446, "SRX5016859", "SRS4049994", "SRA810793", "Institute of Hydrobiology, Chinese Academy of Sciences|State Key Laboratory of Freshwater Ecology and Bio", "Institute of Hydrobiology, Chinese Academy of Sciences", 2, 0.95593, 0.95003, 0.01844, 0.01778, 0.80064, 0.80008, 0.4858, 0.48331, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-11-18", "Multi-stage", "Embryo", "Oocyte", "Reproductive System"], [49747, "SRR8197486", "SRX5016858", "SRS4049994", "SRP169068", "PRJNA495892", "Danio rerio Genome sequencing", "PRJNA495892", "Whole Genome Sequencing", "Transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, null, "three samples of zebrafish unfertilized eggs  and three samples zebrafish fries at the stage of prim5.", "Model organism or animal sample from Danio rerio", "The transcriptome data of zebrafish in two stages of unfertilized egg and prim 5.", null, "isolate:zebrafish unfertilized eggs and zebrafish fries at the prim5 stage|dev stage:2 stages of unfertilized egg and prim 5|sex:pooled male and female|tissue:zebrafish in 2 stages of unfertilized egg and prim 5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: prim5 stage", "Z2 2 F", "Z2 2 F", "The unfertilized eggs of zebrafish were taken as three samples Z1 1  Z1 2 and Z1 3 respectively. 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"truncated": false, "filtered_table_rows_count": 29, "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", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", 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