{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"bulk\" and tissue_curation_coarse = \"Reproductive System\"", "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"], [67554, "SRR17210893", "SRX13390812", "SRS11294344", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep6", "GSM5730194", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep6", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730194", "GSM5730194: RNAseq PCB126 10nM Rep6; Danio rerio; RNA Seq", "GSM5730194", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730194", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T24_S18_R1_001.fastq.gz", "fastq", 1912515249.0, 37500299.0, "GSM5730194 r1", "0:51 1:0", "A:477251176;C:466929755;G:439380761;T:528825431;N:128126", 51, 0, null, null, 477251176, 466929755, 439380761, 528825431, 128126, "SRX13390812", "SRS11294344", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95015, null, 0.10454, null, 0.64922, null, 0.53267, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67555, "SRR17210892", "SRX13390811", "SRS11294345", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep5", "GSM5730193", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep5", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730193", "GSM5730193: RNAseq PCB126 10nM Rep5; Danio rerio; RNA Seq", "GSM5730193", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730193", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T23_S17_R1_001.fastq.gz", "fastq", 1344965778.0, 26371878.0, "GSM5730193 r1", "0:51 1:0", "A:347349418;C:318051347;G:301879882;T:377595413;N:89718", 51, 0, null, null, 347349418, 318051347, 301879882, 377595413, 89718, "SRX13390811", "SRS11294345", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.94726, null, 0.10386, null, 0.64948, null, 0.5434, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67556, "SRR17210891", "SRX13390810", "SRS11294343", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep4", "GSM5730192", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep4", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730192", "GSM5730192: RNAseq PCB126 10nM Rep4; Danio rerio; RNA Seq", "GSM5730192", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730192", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T21_S16_R1_001.fastq.gz", "fastq", 2077575474.0, 40736774.0, "GSM5730192 r1", "0:51 1:0", "A:507322408;C:503941476;G:510925051;T:555250063;N:136476", 51, 0, null, null, 507322408, 503941476, 510925051, 555250063, 136476, "SRX13390810", "SRS11294343", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95021, null, 0.06976, null, 0.6464, null, 0.50296, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67557, "SRR17210890", "SRX13390809", "SRS11294342", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep3", "GSM5730191", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep3", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730191", "GSM5730191: RNAseq PCB126 10nM Rep3; Danio rerio; RNA Seq", "GSM5730191", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730191", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T19_S15_R1_001.fastq.gz", "fastq", 1514204127.0, 29690277.0, "GSM5730191 r1", "0:51 1:0", "A:362659383;C:370554761;G:356314539;T:424574865;N:100579", 51, 0, null, null, 362659383, 370554761, 356314539, 424574865, 100579, "SRX13390809", "SRS11294342", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95191, null, 0.07368, null, 0.62509, null, 0.48965, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67558, "SRR17210889", "SRX13390808", "SRS11294341", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep2", "GSM5730190", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep2", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730190", "GSM5730190: RNAseq PCB126 10nM Rep2; Danio rerio; RNA Seq", "GSM5730190", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730190", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T18_S14_R1_001.fastq.gz", "fastq", 1381687155.0, 27091905.0, "GSM5730190 r1", "0:51 1:0", "A:333912162;C:335458932;G:326378401;T:385845588;N:92072", 51, 0, null, null, 333912162, 335458932, 326378401, 385845588, 92072, "SRX13390808", "SRS11294341", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95313, null, 0.07433, null, 0.63177, null, 0.50475, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67559, "SRR17210888", "SRX13390807", "SRS11294340", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 10nM Rep1", "GSM5730189", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "RNAseq PCB126 10nM Rep1", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 10nM", "GSM5730189", "GSM5730189: RNAseq PCB126 10nM Rep1; Danio rerio; RNA Seq", "GSM5730189", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730189", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T17_S13_R1_001.fastq.gz", "fastq", 1508524920.0, 29578920.0, "GSM5730189 r1", "0:51 1:0", "A:393426431;C:349348415;G:337538750;T:428110887;N:100437", 51, 0, null, null, 393426431, 349348415, 337538750, 428110887, 100437, "SRX13390807", "SRS11294340", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.94765, null, 0.0935, null, 0.64743, null, 0.53646, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67560, "SRR17210887", "SRX13390806", "SRS11294338", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep6", "GSM5730188", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep6", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730188", "GSM5730188: RNAseq PCB126 3nM Rep6; Danio rerio; RNA Seq", "GSM5730188", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730188", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T16_S12_R1_001.fastq.gz", "fastq", 1840726935.0, 36092685.0, "GSM5730188 r1", "0:51 1:0", "A:466997928;C:437493060;G:421124744;T:514986449;N:124754", 51, 0, null, null, 466997928, 437493060, 421124744, 514986449, 124754, "SRX13390806", "SRS11294338", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.9474, null, 0.0984, null, 0.64165, null, 0.51348, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67561, "SRR17210886", "SRX13390805", "SRS11294339", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep5", "GSM5730187", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep5", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730187", "GSM5730187: RNAseq PCB126 3nM Rep5; Danio rerio; RNA Seq", "GSM5730187", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730187", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T15_S11_R1_001.fastq.gz", "fastq", 1384282545.0, 27142795.0, "GSM5730187 r1", "0:51 1:0", "A:325552702;C:343473865;G:329054590;T:386110707;N:90681", 51, 0, null, null, 325552702, 343473865, 329054590, 386110707, 90681, "SRX13390805", "SRS11294339", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95623, null, 0.06621, null, 0.63345, null, 0.49688, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67562, "SRR17210885", "SRX13390804", "SRS11294337", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep4", "GSM5730186", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep4", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730186", "GSM5730186: RNAseq PCB126 3nM Rep4; Danio rerio; RNA Seq", "GSM5730186", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730186", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T14_S10_R1_001.fastq.gz", "fastq", 2099071260.0, 41158260.0, "GSM5730186 r1", "0:51 1:0", "A:525168723;C:513155313;G:482406202;T:578202593;N:138429", 51, 0, null, null, 525168723, 513155313, 482406202, 578202593, 138429, "SRX13390804", "SRS11294337", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.94639, null, 0.10285, null, 0.64942, null, 0.50757, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67563, "SRR17210884", "SRX13390803", "SRS11294336", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep3", "GSM5730185", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep3", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730185", "GSM5730185: RNAseq PCB126 3nM Rep3; Danio rerio; RNA Seq", "GSM5730185", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730185", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T13_S9_R1_001.fastq.gz", "fastq", 1877300055.0, 36809805.0, "GSM5730185 r1", "0:51 1:0", "A:447373671;C:463401185;G:439915337;T:526483226;N:126636", 51, 0, null, null, 447373671, 463401185, 439915337, 526483226, 126636, "SRX13390803", "SRS11294336", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95301, null, 0.06979, null, 0.64319, null, 0.49994, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67564, "SRR17210883", "SRX13390802", "SRS11294335", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep2", "GSM5730184", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep2", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730184", "GSM5730184: RNAseq PCB126 3nM Rep2; Danio rerio; RNA Seq", "GSM5730184", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730184", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T11_S8_R1_001.fastq.gz", "fastq", 1788165621.0, 35062071.0, "GSM5730184 r1", "0:51 1:0", "A:420221044;C:445407082;G:423493165;T:498924231;N:120099", 51, 0, null, null, 420221044, 445407082, 423493165, 498924231, 120099, "SRX13390802", "SRS11294335", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95488, null, 0.06451, null, 0.63126, null, 0.49662, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67565, "SRR17210882", "SRX13390801", "SRS11294334", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq PCB126 3nM Rep1", "GSM5730183", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "RNAseq PCB126 3nM Rep1", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:PCB126 3nM", "GSM5730183", "GSM5730183: RNAseq PCB126 3nM Rep1; Danio rerio; RNA Seq", "GSM5730183", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730183", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T9_S7_R1_001.fastq.gz", "fastq", 1855410702.0, 36380602.0, "GSM5730183 r1", "0:51 1:0", "A:459292963;C:465999847;G:421852734;T:508143917;N:121241", 51, 0, null, null, 459292963, 465999847, 421852734, 508143917, 121241, "SRX13390801", "SRS11294334", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95181, null, 0.07794, null, 0.65141, null, 0.51342, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67566, "SRR17210881", "SRX13390800", "SRS11294333", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep6", "GSM5730182", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep6", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730182", "GSM5730182: RNAseq DMSO Rep6; Danio rerio; RNA Seq", "GSM5730182", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730182", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T8_S6_R1_001.fastq.gz", "fastq", 1923223464.0, 37710264.0, "GSM5730182 r1", "0:51 1:0", "A:451684628;C:481126641;G:454781274;T:535502647;N:128274", 51, 0, null, null, 451684628, 481126641, 454781274, 535502647, 128274, "SRX13390800", "SRS11294333", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95508, null, 0.07375, null, 0.63183, null, 0.49887, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67567, "SRR17210880", "SRX13390799", "SRS11294332", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep5", "GSM5730181", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep5", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730181", "GSM5730181: RNAseq DMSO Rep5; Danio rerio; RNA Seq", "GSM5730181", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730181", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T6_S5_R1_001.fastq.gz", "fastq", 1752584247.0, 34364397.0, "GSM5730181 r1", "0:51 1:0", "A:413763719;C:434326065;G:412787803;T:491589762;N:116898", 51, 0, null, null, 413763719, 434326065, 412787803, 491589762, 116898, "SRX13390799", "SRS11294332", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95515, null, 0.06656, null, 0.63859, null, 0.49877, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67568, "SRR17210879", "SRX13390798", "SRS11294331", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep4", "GSM5730180", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep4", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730180", "GSM5730180: RNAseq DMSO Rep4; Danio rerio; RNA Seq", "GSM5730180", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730180", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T5_S4_R1_001.fastq.gz", "fastq", 1783559199.0, 34971749.0, "GSM5730180 r1", "0:51 1:0", "A:426389805;C:442827488;G:416807133;T:497417118;N:117655", 51, 0, null, null, 426389805, 442827488, 416807133, 497417118, 117655, "SRX13390798", "SRS11294331", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95322, null, 0.0736, null, 0.6354, null, 0.49805, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67569, "SRR17210878", "SRX13390797", "SRS11294329", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep3", "GSM5730179", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep3", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730179", "GSM5730179: RNAseq DMSO Rep3; Danio rerio; RNA Seq", "GSM5730179", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730179", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T4_S3_R1_001.fastq.gz", "fastq", 1907367207.0, 37399357.0, "GSM5730179 r1", "0:51 1:0", "A:508707164;C:436434670;G:414734236;T:547363631;N:127506", 51, 0, null, null, 508707164, 436434670, 414734236, 547363631, 127506, "SRX13390797", "SRS11294329", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.50915, null, 0.03593, null, 0.70147, null, 0.49838, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67570, "SRR17210877", "SRX13390796", "SRS11294330", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep2", "GSM5730178", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep2", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730178", "GSM5730178: RNAseq DMSO Rep2; Danio rerio; RNA Seq", "GSM5730178", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730178", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T3_S2_R1_001.fastq.gz", "fastq", 1756085856.0, 34433056.0, "GSM5730178 r1", "0:51 1:0", "A:409690032;C:438746739;G:419437935;T:488094432;N:116718", 51, 0, null, null, 409690032, 438746739, 419437935, 488094432, 116718, "SRX13390796", "SRS11294330", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95577, null, 0.06639, null, 0.64076, null, 0.49674, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"], [67571, "SRR17210876", "SRX13390795", "SRS11294328", "SRP350440", "PRJNA788302", "PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis", "GSE190741", "Other", "The objective of this study is to determine the effects of pre conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin like PCB 3  three prime  4  4'  5 pentachlorobiphenyl; PCB126 as a model environmental chemical because the mechanism of action is well characterized  involving activation of aryl hydrocarbon receptor  a ligand activated transcription factor. Adult zebrafish were exposed to 3 and 10?nM PCB126 for 24?h water borne exposure and testis tissue was sampled at 7?days post exposure for histology  DNA methylation and gene expression profiling. We used enhanced Reduced Representation Bisulfite Sequencing RRBS and RNAseq to quantify DNA methylation and gene expression  respectively. RRBS revealed 37 and 92 differentially methylated regions DMRs in response to 3 and 10nM PCB126 exposures  respectively. We observed 19 DMRs to be common between the two PCB126 treatment groups. Among them 14 and 5 are hypomethylated and hypermethylated  respectively. Majority of these DMRs are hypomethylated and gene ontology analysis revealed that these regions are regulate genes associated with RNA processing  nucleoside metabolic process  iron sulfur cluster assembly and gluconeogenesis. Dysregulation of all these pathways have been associated with spermatogenic defects such as infertility. RNAseq results revealed differential expression of genes related to xenobiotic metabolism  oxidative stress and immune function. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting complex and multiple layers of regulation. Overall  the results from this study provide new understanding about the mechanisms of action of dioxin like PCBs in affecting testicular function and potential multigenerational phenotypes. Overall design: 5 6 biological replicates per treatment condition. Three treatment conditions DMSO control   3nM PCB126 and 10 nM PCB126", null, "pubmed:35477799", null, "RNAseq DMSO Rep1", "GSM5730177", null, "source name:testis|tissue:testis|developmental stage:Adult|treatment:DMSO", "RNAseq DMSO Rep1", "DNA methylation analysis was carried out following Bisulfite Analysis Toolkit BAT. The details are provided in this website: https://www.bioinf.uni leipzig.de/Software/BAT/. This contains 4 different modules   Mapping   Calling  Analysis and DMRs RNAseq   pre processing using FASTQC RNAseq   mapping the reads to the genome using STAR RNAseq   counting the reads using HT seq count RNAseq   statistical analysis using edgeR Genome build: GRCz10 Supplementary files format and content: Text format; RNAseq data files Htseq count contains read counts. DMR data contains statistically significant DMRs and statistical data. Supplementary files format and content: P0 3.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 3nM PCB126 group in comparison to DMSO Supplementary files format and content: P10.metilene qval.0.05.txt: Statistically significant Differentially Methylated Regions in 10nM PCB126 group in comparison to DMSO Supplementary files format and content: P0 3 overlap P10.txt: Common DMRs between 3 and 10nM PCB126 groups", "testis", "Adult zebrafish were exposed to 3 or 10 nM PCB126 for 24 hours and raised in contaminant free water for xxx days prior to sampling the testis tissue.", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", null, "tissue:testis|developmental stage:Adult|treatment:DMSO", "GSM5730177", "GSM5730177: RNAseq DMSO Rep1; Danio rerio; RNA Seq", "GSM5730177", null, "1", "Total RNA and DNA were isolated using the ZR Duet\u2122 DNA/RNA Mini Prep kit Zymo Research  CA. Stranded RNAseq library preparation using the Illumina TruSeq total RNA library prep kit and 50\u2009bp single ends sequencing on the HiSeq2000 platform were performed at the Tufts University Core Facility. RRBS library preparation and sequencing was conducted by NXT Dx  a Diagenode company Ghent  Belgium. Briefly  libraries were prepared from 500\u2009ng of genomic DNA digested with 30 units of MspI New England Biolabs  MA  followed by end repair and A tailing of DNA fragments. Fragments were ligated with methylated Illumina adapters. Adaptor ligated fragments were size selected and then bisulfite converted using a commercial kit. Ligated fragments were amplified and the resulting products were purified and 50 bp paired end PE sequencing was performed on an Illumina HiSeq2500 platform.", "GEO Accession:GSM5730177", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP350440", null, null, "4170_mix-T1_S1_R1_001.fastq.gz", "fastq", 1791620310.0, 35129810.0, "GSM5730177 r1", "0:51 1:0", "A:422311870;C:442811083;G:428686648;T:497691822;N:118887", 51, 0, null, null, 422311870, 442811083, 428686648, 497691822, 118887, "SRX13390795", "SRS11294328", "SRA1342092", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.95683, null, 0.06919, null, 0.6495, null, 0.49403, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-12-12", "Adult", "Adult", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 26, "expanded_columns": 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