{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"other\", experiment.library_strategy = \"RIP-Seq\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[41548, "SRR5017075", "SRX2345570", "SRS1796136", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "input shield rep2", "GSM2390028", null, "tissue:Embryos|developmental stage:Shield stage embryos|strain:AB wild type", "input shield rep2", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:Shield stage embryos|strain:AB wild type", "GSM2390028", "GSM2390028: input shield rep2; Danio rerio; RIP Seq", "GSM2390028", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390028", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "input_shield_rep2.fastq.gz", "fastq", 6559838034.0, 69785511.0, "GSM2390028 r1", "0:94", "A:1785772532;C:1552902091;G:1571407685;T:1649464013;N:291713", 94, null, null, null, 1785772532, 1552902091, 1571407685, 1649464013, 291713, "SRX2345570", "SRS1796136", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03627, null, 0.01, null, 0.96676, null, 0.66777, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41549, "SRR5017074", "SRX2345569", "SRS1796134", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "input shield rep1", "GSM2390027", null, "tissue:Embryos|developmental stage:Shield stage embryos|strain:AB wild type", "input shield rep1", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:Shield stage embryos|strain:AB wild type", "GSM2390027", "GSM2390027: input shield rep1; Danio rerio; RIP Seq", "GSM2390027", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390027", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "input_shield_rep1.fastq.gz", "fastq", 3765873214.0, 40062481.0, "GSM2390027 r1", "0:94", "A:1002751444;C:902509483;G:908627718;T:951814220;N:170349", 94, null, null, null, 1002751444, 902509483, 908627718, 951814220, 170349, "SRX2345569", "SRS1796134", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03936, null, 0.01095, null, 0.96518, null, 0.68725, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41550, "SRR5017073", "SRX2345568", "SRS1796132", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "ip shield rep2", "GSM2390026", null, "tissue:Embryos|developmental stage:Shield stage embryos|strain:AB wild type", "ip shield rep2", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:Shield stage embryos|strain:AB wild type", "GSM2390026", "GSM2390026: ip shield rep2; Danio rerio; RIP Seq", "GSM2390026", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390026", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "ip_shield_rep2.fastq", "fastq", 3855863926.0, 41019829.0, "GSM2390026 r1", "0:94", "A:1044010018;C:931492803;G:952890289;T:926349254;N:1121562", 94, null, null, null, 1044010018, 931492803, 952890289, 926349254, 1121562, "SRX2345568", "SRS1796132", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03311, null, 0.00481, null, 0.96337, null, 0.68612, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41551, "SRR5017072", "SRX2345567", "SRS1796131", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "ip shield rep1", "GSM2390025", null, "tissue:Embryos|developmental stage:Shield stage embryos|strain:AB wild type", "ip shield rep1", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:Shield stage embryos|strain:AB wild type", "GSM2390025", "GSM2390025: ip shield rep1; Danio rerio; RIP Seq", "GSM2390025", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390025", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "ip_shield_rep1.fastq.gz", "fastq", 4107624502.0, 43698133.0, "GSM2390025 r1", "0:94", "A:1087077899;C:996101257;G:1020588721;T:1002667943;N:1188682", 94, null, null, null, 1087077899, 996101257, 1020588721, 1002667943, 1188682, "SRX2345567", "SRS1796131", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.01898, null, 0.00264, null, 0.97238, null, 0.59809, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41552, "SRR5017071", "SRX2345566", "SRS1796152", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "input sphere rep2", "GSM2390024", null, "tissue:Embryos|developmental stage:sphere stage embryos|strain:AB wild type", "input sphere rep2", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:sphere stage embryos|strain:AB wild type", "GSM2390024", "GSM2390024: input sphere rep2; Danio rerio; RIP Seq", "GSM2390024", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390024", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "input_sphere_rep2.fastq.gz", "fastq", 3684856024.0, 39200596.0, "GSM2390024 r1", "0:94", "A:991404019;C:883789087;G:892976599;T:916520929;N:165390", 94, null, null, null, 991404019, 883789087, 892976599, 916520929, 165390, "SRX2345566", "SRS1796152", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03619, null, 0.00867, null, 0.96051, null, 0.63934, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41553, "SRR5017070", "SRX2345565", "SRS1796139", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "input sphere rep1", "GSM2390023", null, "tissue:Embryos|developmental stage:sphere stage embryos|strain:AB wild type", "input sphere rep1", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:sphere stage embryos|strain:AB wild type", "GSM2390023", "GSM2390023: input sphere rep1; Danio rerio; RIP Seq", "GSM2390023", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390023", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "input_sphere_rep1.fastq.gz", "fastq", 3774515574.0, 40154421.0, "GSM2390023 r1", "0:94", "A:1014569244;C:912257296;G:925742711;T:921776107;N:170216", 94, null, null, null, 1014569244, 912257296, 925742711, 921776107, 170216, "SRX2345565", "SRS1796139", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.04287, null, 0.00892, null, 0.95085, null, 0.50435, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41554, "SRR5017069", "SRX2345564", "SRS1796133", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "ip sphere rep2", "GSM2390022", null, "tissue:Embryos|developmental stage:sphere stage embryos|strain:AB wild type", "ip sphere rep2", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:sphere stage embryos|strain:AB wild type", "GSM2390022", "GSM2390022: ip sphere rep2; Danio rerio; RIP Seq", "GSM2390022", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390022", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "ip_sphere_rep2.fastq.gz", "fastq", 3926426624.0, 41770496.0, "GSM2390022 r1", "0:94", "A:1037910962;C:957162730;G:963824694;T:966381238;N:1147000", 94, null, null, null, 1037910962, 957162730, 963824694, 966381238, 1147000, "SRX2345564", "SRS1796133", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03492, null, 0.00427, null, 0.95026, null, 0.60529, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41555, "SRR5017068", "SRX2345563", "SRS1796143", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "ip sphere rep1", "GSM2390021", null, "tissue:Embryos|developmental stage:sphere stage embryos|strain:AB wild type", "ip sphere rep1", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:sphere stage embryos|strain:AB wild type", "GSM2390021", "GSM2390021: ip sphere rep1; Danio rerio; RIP Seq", "GSM2390021", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390021", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "ip_sphere_rep1.fastq.gz", "fastq", 4185867000.0, 44530500.0, "GSM2390021 r1", "0:94", "A:1114959829;C:1018236207;G:1019156922;T:1032304051;N:1209991", 94, null, null, null, 1114959829, 1018236207, 1019156922, 1032304051, 1209991, "SRX2345563", "SRS1796143", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03035, null, 0.00288, null, 0.94757, null, 0.5787, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41556, "SRR5017067", "SRX2345562", "SRS1796129", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "input 64cell rep2", "GSM2390020", null, "tissue:Embryos|developmental stage:64 cell embryos|strain:AB wild type", "input 64cell rep2", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:64 cell embryos|strain:AB wild type", "GSM2390020", "GSM2390020: input 64cell rep2; Danio rerio; RIP Seq", "GSM2390020", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390020", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "input_64cell_rep2.fastq.gz", "fastq", 3598782386.0, 38284919.0, "GSM2390020 r1", "0:94", "A:953869445;C:864903757;G:875832539;T:903947732;N:228913", 94, null, null, null, 953869445, 864903757, 875832539, 903947732, 228913, "SRX2345562", "SRS1796129", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.04289, null, 0.00757, null, 0.9418, null, 0.6078, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41557, "SRR5017066", "SRX2345561", "SRS1796141", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "input 64cell rep1", "GSM2390019", null, "tissue:Embryos|developmental stage:64 cell embryos|strain:AB wild type", "input 64cell rep1", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:64 cell embryos|strain:AB wild type", "GSM2390019", "GSM2390019: input 64cell rep1; Danio rerio; RIP Seq", "GSM2390019", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390019", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "input_64cell_rep1.fastq.gz", "fastq", 3538898746.0, 37647859.0, "GSM2390019 r1", "0:94", "A:916878511;C:870431252;G:873611680;T:877750503;N:226800", 94, null, null, null, 916878511, 870431252, 873611680, 877750503, 226800, "SRX2345561", "SRS1796141", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03397, null, 0.00616, null, 0.95268, null, 0.62545, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41558, "SRR5017065", "SRX2345560", "SRS1796153", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "ip 64cell rep2", "GSM2390018", null, "tissue:Embryos|developmental stage:64 cell embryos|strain:AB wild type", "ip 64cell rep2", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:64 cell embryos|strain:AB wild type", "GSM2390018", "GSM2390018: ip 64cell rep2; Danio rerio; RIP Seq", "GSM2390018", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390018", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "ip_64cell_rep2.fastq.gz", "fastq", 3530677976.0, 37560404.0, "GSM2390018 r1", "0:94", "A:966880666;C:841411144;G:858285224;T:862983808;N:1117134", 94, null, null, null, 966880666, 841411144, 858285224, 862983808, 1117134, "SRX2345560", "SRS1796153", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.04775, null, 0.00421, null, 0.92845, null, 0.5748, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41559, "SRR5017064", "SRX2345559", "SRS1796135", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "ip 64cell rep1", "GSM2390017", null, "tissue:Embryos|developmental stage:64 cell embryos|strain:AB wild type", "ip 64cell rep1", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:64 cell embryos|strain:AB wild type", "GSM2390017", "GSM2390017: ip 64cell rep1; Danio rerio; RIP Seq", "GSM2390017", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390017", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "ip_64cell_rep1.fastq.gz", "fastq", 3912003734.0, 41617061.0, "GSM2390017 r1", "0:94", "A:1040276279;C:945311584;G:953598043;T:971589029;N:1228799", 94, null, null, null, 1040276279, 945311584, 953598043, 971589029, 1228799, "SRX2345559", "SRS1796135", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03544, null, 0.00268, null, 0.93914, null, 0.53712, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41560, "SRR5017063", "SRX2345558", "SRS1796155", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "input 1cell rep2", "GSM2390016", null, "tissue:Embryos|developmental stage:1cell embryos|strain:AB wild type", "input 1cell rep2", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:1cell embryos|strain:AB wild type", "GSM2390016", "GSM2390016: input 1cell rep2; Danio rerio; RIP Seq", "GSM2390016", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390016", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "input_1cell_rep2.fastq.gz", "fastq", 3379762010.0, 35954915.0, "GSM2390016 r1", "0:94", "A:898920912;C:816234808;G:823428476;T:840956466;N:221348", 94, null, null, null, 898920912, 816234808, 823428476, 840956466, 221348, "SRX2345558", "SRS1796155", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.04513, null, 0.00864, null, 0.95085, null, 0.51692, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41561, "SRR5017062", "SRX2345557", "SRS1796128", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "input 1cell rep1", "GSM2390015", null, "tissue:Embryos|developmental stage:1cell embryos|strain:AB wild type", "input 1cell rep1", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:1cell embryos|strain:AB wild type", "GSM2390015", "GSM2390015: input 1cell rep1; Danio rerio; RIP Seq", "GSM2390015", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390015", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "input_1cell_rep1.fastq.gz", "fastq", 3650321646.0, 38833209.0, "GSM2390015 r1", "0:94", "A:951411355;C:878458528;G:890250453;T:929968044;N:233266", 94, null, null, null, 951411355, 878458528, 890250453, 929968044, 233266, "SRX2345557", "SRS1796128", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.03728, null, 0.00668, null, 0.94901, null, 0.60038, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41562, "SRR5017061", "SRX2345556", "SRS1796127", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "ip 1cell rep2", "GSM2390014", null, "tissue:Embryos|developmental stage:1cell embryos|strain:AB wild type", "ip 1cell rep2", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:1cell embryos|strain:AB wild type", "GSM2390014", "GSM2390014: ip 1cell rep2; Danio rerio; RIP Seq", "GSM2390014", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390014", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "ip_1cell_rep2.fastq.gz", "fastq", 3485432580.0, 37079070.0, "GSM2390014 r1", "0:94", "A:953699047;C:835179152;G:846963064;T:848487912;N:1103405", 94, null, null, null, 953699047, 835179152, 846963064, 848487912, 1103405, "SRX2345556", "SRS1796127", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.02534, null, 0.00219, null, 0.95891, null, 0.5975, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41563, "SRR5017060", "SRX2345555", "SRS1796130", "SRP093295", "PRJNA353372", "N6 methyladenosine dynamics during early vertebrate embryogenesis", "GSE89815", "Other", "Early vertebrate embryogenesis is characterized by extensive post transcriptional regulation during the maternal to zygotic transition. The N6 methyladenosine m6A modifications on mRNA has been shown to affect both translation and stability of transcripts. Here we investigate the m6A topology during early vertebrate embryogenesis and its association with RNA stability  translation efficiency and effect on miR 430 degradation kinetics. Notably  we find a strong association of m6A with cytoplasmic polyadenylation and translational efficiency prior to zygotic genome activation. Genes required for zygotic genome activation such as nanog and pou5f3 display dynamic m6A levels. post zygotic genome activation m6A is associated with improved stability and dampens the effect of miR 430 mediated degradation. Through sequence analyses we identified enrichment of motifs for RNA binding proteins involved in translational regulation and RNA degradation. We propose a role for m6A in multiple mRNA regulatory mechanisms  for the first time in an in vivo system and improve our understanding of the combinatorial code behind the complex post transcriptional regulation of reprogramming during early vertebrate development. Overall design: Examination of m6A in four different developmental stages", null, null, null, "ip 1cell rep1", "GSM2390013", null, "tissue:Embryos|developmental stage:1cell embryos|strain:AB wild type", "ip 1cell rep1", "Base calling The sequencing output from each of the 4 lanes the sequencing run was trimmed 7 nucleotides in the 5\u2019end  and de multiplexed 4 samples in each lane. Reads were mapped to Zv10 using the STAR aligner Dobin et al.  2013 with options   seedSearchStartLmax 15   clip3pNbases 10   clip5pNbases 10   outFilterMultimapNmax 20   outFilterMismatchNoverLmax 0.05   outFilterMatchNminOverLread 0.0   outFilterMatchNmin 15   outFilterScoreMinOverLread 0.0. We performed peak calling and detection of differentially methylated genes using ExomePeak Meng et al.  2013. Genome build: Zv10 Supplementary files format and content: Bed files with enriched regions from each developmental stage  and txt file with raw and normalized read counts for each gene using the input samples", "Embryos", null, "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "Embryos from the AB wild type strain were obtained from the NMBU zebrafish facility where the zebrafish were kept at 28\u00b11\u00b0C on a 14 10 hour light dark cycle at a density of 5 10 fish/L. System water SW was prepared from particle and active charcoal filtrated tap water  deionized by reverse osmosis RO and kept sterile by UV irradiation. The water was conditioned to a conductivity of 500\u00b5S/cm  general hardness GH 4 5 and pH 7.5 by addition of 155g synthetic sea salt Instant Ocean  Blacksburg  USA  53g sodium carbonate and 15g calcium chloride Sigma Aldrich per liter RO water. Adult fish were fed with Gemma Micro 300 Skretting  Stavanger  Norway dry feed twice a day and live artemia Scanbur  Karlslunde  Denmark once a day. Health monitoring was by daily inspection  use of sentinel fish sent for pathology ZIRC  Eugene  Oregon and water microbiology analysis NMBU Vetbio  Oslo every six month. Adult fish were allowed to mate for 30 minutes in standard 1L breeding tanks Aquatic Habitats  Apopka  FL. Harvested embryos were kept in autoclaved SW at 28 \u00b0C  harvested by snap freezing liquid nitrogen and visually controlled for stage and lack of abnormalities at the selected time points. All experiments were performed according to Norwegian Animal Welfare Act 2009  the EU Directive 2010/63.", "developmental stage:1cell embryos|strain:AB wild type", "GSM2390013", "GSM2390013: ip 1cell rep1; Danio rerio; RIP Seq", "GSM2390013", null, "1", "We isolated total RNA from 4 stages 1 cell/20 minutes post fertilization  2   4  and 6 hpf in batches of 200 embryos using TRIzol Invitrogen  cat.no. 15596 018. We added ERCC spike in RNA TermoFisher scientific  cat.no. 4456740 to the trizol. For each sequencing library two batches of total RNA from 200 embryos were merged and enriched for polyA+ RNA using Dynabeads\u00ae mRNA Purification Kit Ambion  #61006. The m6A RIP experiment was carried out as previously described Ke et al.  2015 and the protocol can be found in supplementary file 1. Briefly  polyA+ enriched RNA was partially fragmented by alkaline hydrolysis  ethanol precipitated and SDS PAGE size selected for 20 80nt. Part of the fragmented RNA was used as input and the rest was immunoprecipitated at 4oC for 2 h using Dynabeads Protein A Life Technologies  # 10008D conjugated anti m6A antibody Synaptic systems  # 202003. post stringent washing  the bound RNA was eluted with 0.5mg/ml N6 methyladenosine sodium salt Sigma Aldrich  # M2780  ethanol precipitated  and resuspended with RNase free water. The eluted RNA and input RNA were subjected to 3\u2019pre adenylated DNA liker ligation with T4 RNA ligase2  truncated KQ NEB  #M0373L  at 16 oC over night. The sequencing library was constructed with bromodeoxyuridine BrdU CLIP protocol described in Weyn Vanhentenryck et al. 2014  with improved RT primers indicated in Ke et al. 2015.", "GEO Accession:GSM2390013", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP093295", null, null, "ip_1cell_rep1.fastq.gz", "fastq", 3610167102.0, 38406033.0, "GSM2390013 r1", "0:94", "A:961438376;C:875781200;G:891055201;T:880749228;N:1143097", 94, null, null, null, 961438376, 875781200, 891055201, 880749228, 1143097, "SRX2345555", "SRS1796130", "SRA492943", "GEO", "Klungland Lab, Dept of microbiology, Oslo University Hospital", 1, 0.01939, null, 0.00159, null, 0.96457, null, 0.53652, null, 94, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Norway", "2016-11-14", "Zygote", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42000, "SRR5379364", "SRX2674572", "SRS2073700", "SRP102513", "PRJNA380609", "Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing", "GSE97067", "Other", "DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development  we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.", null, "pubmed:29636379", null, "ddx39a 24hpf RIPseq", "GSM2550918", null, "source name:embryos|genotype:ddx39a mutant|tissue:embryo|developmental stage:24hpf", "ddx39a 24hpf RIPseq", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "embryos", null, "Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "genotype:ddx39a mutant|tissue:embryo|developmental stage:24hpf", "GSM2550918", "GSM2550918: ddx39a 24hpf RIPseq; Danio rerio; RIP Seq", "GSM2550918", null, "1", "Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2550918", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP102513", null, null, "RDWHDANwwwCAABRAAPEI-206_1.fq.gz RDWHDANwwwCAABRAAPEI-206_2.fq.gz", "fastq fastq", 3819239400.0, 19096197.0, "GSM2550918 r1", "0:100 1:100", "A:751858949;C:1169790479;G:1139713624;T:756987876;N:888472", 100, 100, null, null, 751858949, 1169790479, 1139713624, 756987876, 888472, "SRX2674572", "SRS2073700", "SRA549449", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.98659, 0.98572, 0.28836, 0.28975, 0.89422, 0.89558, 0.75396, 0.78553, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-03-27", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42001, "SRR5379363", "SRX2674571", "SRS2073697", "SRP102513", "PRJNA380609", "Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing", "GSE97067", "Other", "DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development  we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.", null, "pubmed:29636379", null, "WT 24hpf RIPseq", "GSM2550917", null, "source name:embryos|genotype:wild type|tissue:embryo|developmental stage:24hpf", "WT 24hpf RIPseq", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "embryos", null, "Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "genotype:wild type|tissue:embryo|developmental stage:24hpf", "GSM2550917", "GSM2550917: WT 24hpf RIPseq; Danio rerio; RIP Seq", "GSM2550917", null, "1", "Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2550917", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP102513", null, null, "RDWHDANwwwCAAARAAPEI-205_2.fq.gz RDWHDANwwwCAAARAAPEI-205_1.fq.gz", "fastq fastq", 3802882200.0, 19014411.0, "GSM2550917 r1", "0:100 1:100", "A:733911232;C:1178365174;G:1154031422;T:735690235;N:884137", 100, 100, null, null, 733911232, 1178365174, 1154031422, 735690235, 884137, "SRX2674571", "SRS2073697", "SRA549449", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.9866, 0.98469, 0.30567, 0.30486, 0.90796, 0.90928, 0.82926, 0.83029, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-03-27", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [43458, "SRR5952027", "SRX3110521", "SRS2445614", "SRP115900", "PRJNA399133", "RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN", "GSE102861", "Transcriptome Analysis", "We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.", null, "pubmed:29765956", null, "IP HCtranslatome RNAseq rep3", "GSM2747294", null, "source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "IP HCtranslatome RNAseq rep3", "Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample", "Tgmyo6b:GFP 2A rpl10a 3xHA", "Untreated", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "GSM2747294", "GSM2747294: IP HCtranslatome RNAseq rep3; Danio rerio; RIP Seq", "GSM2747294", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747294", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "RiboZF_IP4_R1.fastq.gz RiboZF_IP4_R2.fastq.gz", "fastq fastq", 4994833580.0, 33330363.0, "GSM2747294 r1", "0:74.96 1:74.90", "A:1202677579;C:1288784412;G:1278463604;T:1223941397;N:966588", 74, 74, null, null, 1202677579, 1288784412, 1278463604, 1223941397, 966588, "SRX3110521", "SRS2445614", "SRA601675", "GEO", "Department: Institute for Genome Sciences, University of Maryland in Baltimore", 2, 0.61854, 0.6151, 0.20328, 0.19651, 0.83599, 0.84104, 0.60632, 0.59954, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-21", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [43459, "SRR5952026", "SRX3110520", "SRS2445613", "SRP115900", "PRJNA399133", "RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN", "GSE102861", "Transcriptome Analysis", "We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.", null, "pubmed:29765956", null, "IP HCtranslatome RNAseq rep2", "GSM2747293", null, "source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "IP HCtranslatome RNAseq rep2", "Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample", "Tgmyo6b:GFP 2A rpl10a 3xHA", "Untreated", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "GSM2747293", "GSM2747293: IP HCtranslatome RNAseq rep2; Danio rerio; RIP Seq", "GSM2747293", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747293", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "RiboZF_IP2_R1.fastq.gz RiboZF_IP2_R2.fastq.gz", "fastq fastq", 4530855300.0, 30205702.0, "GSM2747293 r1", "0:75 1:75", "A:1112381418;C:1153277132;G:1147183468;T:1117133915;N:879367", 75, 75, null, null, 1112381418, 1153277132, 1147183468, 1117133915, 879367, "SRX3110520", "SRS2445613", "SRA601675", "GEO", "Department: Institute for Genome Sciences, University of Maryland in Baltimore", 2, 0.64948, 0.64878, 0.15967, 0.15683, 0.80756, 0.81288, 0.56438, 0.56275, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-21", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [43460, "SRR5952025", "SRX3110519", "SRS2445612", "SRP115900", "PRJNA399133", "RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN", "GSE102861", "Transcriptome Analysis", "We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.", null, "pubmed:29765956", null, "IP HCtranslatome RNAseq rep1", "GSM2747292", null, "source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "IP HCtranslatome RNAseq rep1", "Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample", "Tgmyo6b:GFP 2A rpl10a 3xHA", "Untreated", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "GSM2747292", "GSM2747292: IP HCtranslatome RNAseq rep1; Danio rerio; RIP Seq", "GSM2747292", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747292", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "RiboZF_IP1_R1.fastq.gz RiboZF_IP1_R2.fastq.gz", "fastq fastq", 5261113350.0, 35074089.0, "GSM2747292 r1", "0:75 1:75", "A:1356848229;C:1276483567;G:1260001700;T:1366757927;N:1021927", 75, 75, null, null, 1356848229, 1276483567, 1260001700, 1366757927, 1021927, "SRX3110519", "SRS2445612", "SRA601675", "GEO", "Department: Institute for Genome Sciences, University of Maryland in Baltimore", 2, 0.66363, 0.6599, 0.15644, 0.15316, 0.76808, 0.7725, 0.48538, 0.48933, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-21", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [54307, "SRR10129555", "SRX6857975", "SRS5395856", "SRP221863", "PRJNA565584", "The functions of igf2bp3 during zebrafish early development", "PRJNA565584", "Whole Genome Sequencing", "RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.", null, null, null, "Model organism or animal sample from Danio rerio", "RIP seq zebrafish embryo HA rabbit", null, "strain:AB|dev stage:embryo|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RIP seq zebrafish embryo sphere HA", "HA sphere", "HA sphere", "RIP seq", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP221863", null, null, "IP2_R1.fq.gz IP2_R2.fq.gz", "fastq fastq", 7528561800.0, 25095206.0, "IP2 R1.fq.gz", "0:150 1:150", "A:1638987252;C:1830922014;G:2628590112;T:1430016657;N:45765", 150, 150, null, null, 1638987252, 1830922014, 2628590112, 1430016657, 45765, "SRX6857975", "SRS5395856", "SRA962995", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", 2, 0.92316, 0.96332, 0.32571, 0.34771, 0.89173, 0.88962, 0.89557, 0.89793, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-17", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [54308, "SRR10129346", "SRX6857766", "SRS5395649", "SRP221863", "PRJNA565584", "The functions of igf2bp3 during zebrafish early development", "PRJNA565584", "Whole Genome Sequencing", "RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.", null, null, null, "Model organism or animal sample from Danio rerio", "RIP seq zebrafish embryo IgG rabbit", null, "strain:AB|dev stage:embryo|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RIP seq zebrafish embryo sphere IgG", "IgG sphere", "IgG sphere", "RIP seq", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP221863", null, null, "IgG1_R1.fq.gz IgG1_R2.fq.gz", "fastq fastq", 2647374600.0, 8824582.0, "IgG1 R1.fq.gz", "0:150 1:150", "A:565620765;C:650153559;G:936592543;T:494992101;N:15632", 150, 150, null, null, 565620765, 650153559, 936592543, 494992101, 15632, "SRX6857766", "SRS5395649", "SRA962944", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", 2, 0.95349, 0.96423, 0.33504, 0.34458, 0.93748, 0.93726, 0.85176, 0.91118, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-17", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [60025, "SRR12103783", "SRX8627954", "SRS6916259", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB4 IP", "GSM4644253", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217", "PCB4 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217", "GSM4644253", "GSM4644253: PCB4 IP; Danio rerio; RIP Seq", "GSM4644253", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644253", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P4_m6A-IP_S16_R1_001.fastq.gz P4_m6A-IP_S16_R2_001.fastq.gz", "fastq fastq", 2309150560.0, 15191780.0, "GSM4644253 r1", "0:76 1:76", "A:490672579;C:656568819;G:666651729;T:495020365;N:237068", 76, 76, null, null, 490672579, 656568819, 666651729, 495020365, 237068, "SRX8627954", "SRS6916259", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94474, 0.944, 0.18094, 0.18203, 0.7515, 0.75554, 0.60771, 0.6152, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60026, "SRR12103782", "SRX8627953", "SRS6916258", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB3 IP", "GSM4644252", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216", "PCB3 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216", "GSM4644252", "GSM4644252: PCB3 IP; Danio rerio; RIP Seq", "GSM4644252", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644252", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P3_m6A-IP_S15_R2_001.fastq.gz P3_m6A-IP_S15_R1_001.fastq.gz", "fastq fastq", 2965972504.0, 19512977.0, "GSM4644252 r1", "0:76 1:76", "A:620624207;C:853765538;G:874990332;T:616281897;N:310530", 76, 76, null, null, 620624207, 853765538, 874990332, 616281897, 310530, "SRX8627953", "SRS6916258", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93433, 0.93213, 0.16543, 0.16208, 0.75043, 0.753, 0.62186, 0.64359, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60027, "SRR12103781", "SRX8627952", "SRS6916257", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB2 IP", "GSM4644251", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215", "PCB2 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215", "GSM4644251", "GSM4644251: PCB2 IP; Danio rerio; RIP Seq", "GSM4644251", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644251", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P2_m6A-IP_S14_R2_001.fastq.gz P2_m6A-IP_S14_R1_001.fastq.gz", "fastq fastq", 2687973472.0, 17684036.0, "GSM4644251 r1", "0:76 1:76", "A:585901626;C:744255122;G:756993274;T:600539454;N:283996", 76, 76, null, null, 585901626, 744255122, 756993274, 600539454, 283996, "SRX8627952", "SRS6916257", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.9445, 0.94466, 0.16876, 0.17035, 0.74728, 0.75022, 0.57878, 0.57933, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60028, "SRR12103780", "SRX8627951", "SRS6916256", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB1 IP", "GSM4644250", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214", "PCB1 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214", "GSM4644250", "GSM4644250: PCB1 IP; Danio rerio; RIP Seq", "GSM4644250", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644250", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P1_m6A-IP_S13_R1_001.fastq.gz P1_m6A-IP_S13_R2_001.fastq.gz", "fastq fastq", 2596174288.0, 17080094.0, "GSM4644250 r1", "0:76 1:76", "A:564523297;C:723443207;G:735894528;T:572044392;N:268864", 76, 76, null, null, 564523297, 723443207, 735894528, 572044392, 268864, "SRX8627951", "SRS6916256", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93494, 0.93528, 0.17469, 0.17518, 0.746, 0.74803, 0.60114, 0.60005, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60029, "SRR12103779", "SRX8627950", "SRS6916255", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB4 Input", "GSM4644249", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1", "PCB4 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:input control|antibody:n1", "GSM4644249", "GSM4644249: PCB4 Input; Danio rerio; RIP Seq", "GSM4644249", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644249", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P4_INPUT_S8_R1_001.fastq.gz P4_INPUT_S8_R2_001.fastq.gz", "fastq fastq", 3655473384.0, 24049167.0, "GSM4644249 r1", "0:76 1:76", "A:680110064;C:1145409769;G:1179103219;T:650470372;N:379960", 76, 76, null, null, 680110064, 1145409769, 1179103219, 650470372, 379960, "SRX8627950", "SRS6916255", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93037, 0.96319, 0.21668, 0.22563, 0.86338, 0.86385, 0.77257, 0.70059, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60030, "SRR12103778", "SRX8627949", "SRS6916254", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB3 Input", "GSM4644248", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1", "PCB3 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:input control|antibody:n1", "GSM4644248", "GSM4644248: PCB3 Input; Danio rerio; RIP Seq", "GSM4644248", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644248", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P3_INPUT_S7_R1_001.fastq.gz P3_INPUT_S7_R2_001.fastq.gz", "fastq fastq", 4926238376.0, 32409463.0, "GSM4644248 r1", "0:76 1:76", "A:929043061;C:1530175131;G:1577898210;T:888604850;N:517124", 76, 76, null, null, 929043061, 1530175131, 1577898210, 888604850, 517124, "SRX8627949", "SRS6916254", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92875, 0.95698, 0.21539, 0.22073, 0.85253, 0.85431, 0.76235, 0.68659, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60031, "SRR12103777", "SRX8627948", "SRS6916253", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB2 Input", "GSM4644247", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1", "PCB2 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:input control|antibody:n1", "GSM4644247", "GSM4644247: PCB2 Input; Danio rerio; RIP Seq", "GSM4644247", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644247", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P2_INPUT_S6_R1_001.fastq.gz P2_INPUT_S6_R2_001.fastq.gz", "fastq fastq", 5669611400.0, 37300075.0, "GSM4644247 r1", "0:76 1:76", "A:1050955836;C:1780355588;G:1829450728;T:1008257255;N:591993", 76, 76, null, null, 1050955836, 1780355588, 1829450728, 1008257255, 591993, "SRX8627948", "SRS6916253", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93297, 0.93791, 0.21298, 0.21667, 0.85902, 0.86302, 0.7387, 0.69759, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60032, "SRR12103776", "SRX8627947", "SRS6916252", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB1 Input", "GSM4644246", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1", "PCB1 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:input control|antibody:n1", "GSM4644246", "GSM4644246: PCB1 Input; Danio rerio; RIP Seq", "GSM4644246", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644246", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P1_INPUT_S5_R1_001.fastq.gz P1_INPUT_S5_R2_001.fastq.gz", "fastq fastq", 4154972744.0, 27335347.0, "GSM4644246 r1", "0:76 1:76", "A:764769282;C:1310937656;G:1344287240;T:734545457;N:433109", 76, 76, null, null, 764769282, 1310937656, 1344287240, 734545457, 433109, "SRX8627947", "SRS6916252", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92033, 0.95428, 0.21666, 0.2245, 0.86571, 0.8678, 0.74089, 0.68247, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60033, "SRR12103775", "SRX8627946", "SRS6916251", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO4 IP", "GSM4644245", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217", "DMSO4 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217", "GSM4644245", "GSM4644245: DMSO4 IP; Danio rerio; RIP Seq", "GSM4644245", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644245", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D4_m6A-IP_S12_R1_001.fastq.gz D4_m6A-IP_S12_R2_001.fastq.gz", "fastq fastq", 2415539920.0, 15891710.0, "GSM4644245 r1", "0:76 1:76", "A:519904759;C:674887600;G:688106098;T:532387711;N:253752", 76, 76, null, null, 519904759, 674887600, 688106098, 532387711, 253752, "SRX8627946", "SRS6916251", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94931, 0.94824, 0.16515, 0.16656, 0.74858, 0.7497, 0.57724, 0.58102, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60034, "SRR12103774", "SRX8627945", "SRS6916250", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO3 IP", "GSM4644244", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216", "DMSO3 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216", "GSM4644244", "GSM4644244: DMSO3 IP; Danio rerio; RIP Seq", "GSM4644244", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644244", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D3_m6A-IP_S11_R1_001.fastq.gz D3_m6A-IP_S11_R2_001.fastq.gz", "fastq fastq", 2419255408.0, 15916154.0, "GSM4644244 r1", "0:76 1:76", "A:524637988;C:675158080;G:687344217;T:531861650;N:253473", 76, 76, null, null, 524637988, 675158080, 687344217, 531861650, 253473, "SRX8627945", "SRS6916250", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93623, 0.93621, 0.18212, 0.18165, 0.74308, 0.74426, 0.60527, 0.60757, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60035, "SRR12103773", "SRX8627944", "SRS6916249", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO2 IP", "GSM4644243", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215", "DMSO2 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215", "GSM4644243", "GSM4644243: DMSO2 IP; Danio rerio; RIP Seq", "GSM4644243", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644243", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D2_m6A-IP_S10_R1_001.fastq.gz D2_m6A-IP_S10_R2_001.fastq.gz", "fastq fastq", 2698406448.0, 17752674.0, "GSM4644243 r1", "0:76 1:76", "A:578126060;C:760791571;G:775423382;T:583783650;N:281785", 76, 76, null, null, 578126060, 760791571, 775423382, 583783650, 281785, "SRX8627944", "SRS6916249", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.9433, 0.94318, 0.17976, 0.1816, 0.74992, 0.75215, 0.58844, 0.61497, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60036, "SRR12103772", "SRX8627943", "SRS6916248", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO1 IP", "GSM4644242", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214", "DMSO1 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214", "GSM4644242", "GSM4644242: DMSO1 IP; Danio rerio; RIP Seq", "GSM4644242", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644242", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D1_m6A-IP_S9_R1_001.fastq.gz D1_m6A-IP_S9_R2_001.fastq.gz", "fastq fastq", 2588221344.0, 17027772.0, "GSM4644242 r1", "0:76 1:76", "A:552076254;C:730948542;G:744135059;T:560788856;N:272633", 76, 76, null, null, 552076254, 730948542, 744135059, 560788856, 272633, "SRX8627943", "SRS6916248", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93871, 0.9398, 0.17681, 0.17588, 0.74688, 0.74915, 0.59376, 0.61045, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60037, "SRR12103771", "SRX8627942", "SRS6916247", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO4 Input", "GSM4644241", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "DMSO4 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "GSM4644241", "GSM4644241: DMSO4 Input; Danio rerio; RIP Seq", "GSM4644241", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644241", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D4_INPUT_S4_R1_001.fastq.gz D4_INPUT_S4_R2_001.fastq.gz", "fastq fastq", 4085824752.0, 26880426.0, "GSM4644241 r1", "0:76 1:76", "A:734095239;C:1307425224;G:1339970208;T:703907493;N:426588", 76, 76, null, null, 734095239, 1307425224, 1339970208, 703907493, 426588, "SRX8627942", "SRS6916247", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94341, 0.94693, 0.21035, 0.21294, 0.86306, 0.86571, 0.66228, 0.69648, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60038, "SRR12103770", "SRX8627941", "SRS6916246", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO3 Input", "GSM4644240", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "DMSO3 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "GSM4644240", "GSM4644240: DMSO3 Input; Danio rerio; RIP Seq", "GSM4644240", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644240", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D3_INPUT_S3_R1_001.fastq.gz D3_INPUT_S3_R2_001.fastq.gz", "fastq fastq", 3627749800.0, 23866775.0, "GSM4644240 r1", "0:76 1:76", "A:677883991;C:1133504965;G:1166401920;T:649582074;N:376850", 76, 76, null, null, 677883991, 1133504965, 1166401920, 649582074, 376850, "SRX8627941", "SRS6916246", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92028, 0.96282, 0.2164, 0.22913, 0.86517, 0.8661, 0.73802, 0.70578, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60039, "SRR12103769", "SRX8627940", "SRS6916245", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO2 Input", "GSM4644239", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "DMSO2 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "GSM4644239", "GSM4644239: DMSO2 Input; Danio rerio; RIP Seq", "GSM4644239", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644239", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D2_INPUT_S2_R2_001.fastq.gz D2_INPUT_S2_R1_001.fastq.gz", "fastq fastq", 2991355592.0, 19679971.0, "GSM4644239 r1", "0:76 1:76", "A:555548434;C:937287598;G:965607991;T:532600162;N:311407", 76, 76, null, null, 555548434, 937287598, 965607991, 532600162, 311407, "SRX8627940", "SRS6916245", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92966, 0.96538, 0.21752, 0.22835, 0.86137, 0.86701, 0.71065, 0.70316, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60040, "SRR12103768", "SRX8627939", "SRS6916244", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO1 Input", "GSM4644238", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "DMSO1 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "GSM4644238", "GSM4644238: DMSO1 Input; Danio rerio; RIP Seq", "GSM4644238", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644238", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D1_INPUT_S1_R1_001.fastq.gz D1_INPUT_S1_R2_001.fastq.gz", "fastq fastq", 3551567552.0, 23365576.0, "GSM4644238 r1", "0:76 1:76", "A:659305531;C:1112775748;G:1146213503;T:632894453;N:378317", 76, 76, null, null, 659305531, 1112775748, 1146213503, 632894453, 378317, "SRX8627939", "SRS6916244", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92942, 0.96366, 0.21295, 0.2231, 0.8574, 0.85934, 0.75989, 0.75855, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [63731, "SRR13998081", "SRX10375447", "SRS8490053", "SRP311218", "PRJNA715461", "RIP seq for Ddx3xb in zebrafish embryos", "GSE169161", "Other", "We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs  and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation  further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb  but not the Ddx3xb without xxx ability. Mechanistically  the condensation of Ddx3xb is vital for its RNA helicase activity  which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT  highlighting the critical role of protein phase separation in translational control and animal early development.    Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates", "parent bioproject:PRJNA715459", "pubmed:35661831", null, "rip 4h WT rep1", "GSM5179333", null, "source name:control 4h RIP seq rep1|tissue:zebrafish embryos|genotype:wild type|age:4 hpf", "rip 4h WT rep1", "low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options \u2018\u2013nomodel\u2019   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 \u00d7 10\u22122 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein", "control 4h RIP seq rep1", null, "flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4. Ddx3xb RIP was carried out following a published protocol  but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech  635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.", null, "tissue:zebrafish embryos|genotype:wild type|age:4 hpf", "GSM5179333", "GSM5179333: rip 4h WT rep1; Danio rerio; RIP Seq", "GSM5179333", null, "1", "RIP was carried out as previously described Despic et al.  2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc", "GEO Accession:GSM5179333", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311218", null, "loader:fastq load.py", "rip_4h_WT1.fq.gz", "fastq", 11966922300.0, 79779482.0, "GSM5179333 r1", "0:150", "A:3779410126;C:2709781787;G:3301583942;T:2175291644;N:854801", 150, null, null, null, 3779410126, 2709781787, 3301583942, 2175291644, 854801, "SRX10375447", "SRS8490053", "SRA1207702", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.30752, null, 0.13393, null, 0.90575, null, 0.74028, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2021-03-18", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63732, "SRR13998080", "SRX10375446", "SRS8490052", "SRP311218", "PRJNA715461", "RIP seq for Ddx3xb in zebrafish embryos", "GSE169161", "Other", "We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs  and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation  further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb  but not the Ddx3xb without xxx ability. Mechanistically  the condensation of Ddx3xb is vital for its RNA helicase activity  which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT  highlighting the critical role of protein phase separation in translational control and animal early development.    Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates", "parent bioproject:PRJNA715459", "pubmed:35661831", null, "rip 2h WT rep2", "GSM5179332", null, "source name:control 2h RIP seq rep2|tissue:zebrafish embryos|genotype:wild type|age:2 hpf", "rip 2h WT rep2", "low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options \u2018\u2013nomodel\u2019   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 \u00d7 10\u22122 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein", "control 2h RIP seq rep2", null, "flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4. Ddx3xb RIP was carried out following a published protocol  but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech  635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.", null, "tissue:zebrafish embryos|genotype:wild type|age:2 hpf", "GSM5179332", "GSM5179332: rip 2h WT rep2; Danio rerio; RIP Seq", "GSM5179332", null, "1", "RIP was carried out as previously described Despic et al.  2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc", "GEO Accession:GSM5179332", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311218", null, "loader:fastq load.py", "rip_2h_WT2.fq.gz", "fastq", 12320805000.0, 82138700.0, "GSM5179332 r1", "0:150", "A:3686415626;C:2826613772;G:3732955088;T:2073945227;N:875287", 150, null, null, null, 3686415626, 2826613772, 3732955088, 2073945227, 875287, "SRX10375446", "SRS8490052", "SRA1207702", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.1848, null, 0.11194, null, 0.9669, null, 0.82171, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2021-03-18", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63733, "SRR13998079", "SRX10375445", "SRS8490051", "SRP311218", "PRJNA715461", "RIP seq for Ddx3xb in zebrafish embryos", "GSE169161", "Other", "We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs  and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation  further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb  but not the Ddx3xb without xxx ability. Mechanistically  the condensation of Ddx3xb is vital for its RNA helicase activity  which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT  highlighting the critical role of protein phase separation in translational control and animal early development.    Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates", "parent bioproject:PRJNA715459", "pubmed:35661831", null, "rip 2h WT rep1", "GSM5179331", null, "source name:control 2h RIP seq rep1|tissue:zebrafish embryos|genotype:wild type|age:2 hpf", "rip 2h WT rep1", "low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options \u2018\u2013nomodel\u2019   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 \u00d7 10\u22122 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein", "control 2h RIP seq rep1", null, "flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4. Ddx3xb RIP was carried out following a published protocol  but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech  635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.", null, "tissue:zebrafish embryos|genotype:wild type|age:2 hpf", "GSM5179331", "GSM5179331: rip 2h WT rep1; Danio rerio; RIP Seq", "GSM5179331", null, "1", "RIP was carried out as previously described Despic et al.  2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc", "GEO Accession:GSM5179331", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311218", null, "loader:fastq load.py", "rip_2h_WT1.fq.gz", "fastq", 8787958800.0, 58586392.0, "GSM5179331 r1", "0:150", "A:2671043775;C:2046825976;G:2545406298;T:1524056303;N:626448", 150, null, null, null, 2671043775, 2046825976, 2545406298, 1524056303, 626448, "SRX10375445", "SRS8490051", "SRA1207702", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.30731, null, 0.17665, null, 0.94117, null, 0.79653, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2021-03-18", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [63734, "SRR13998082", "SRX10375444", "SRS8490050", "SRP311218", "PRJNA715461", "RIP seq for Ddx3xb in zebrafish embryos", "GSE169161", "Other", "We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs  and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation  further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb  but not the Ddx3xb without xxx ability. Mechanistically  the condensation of Ddx3xb is vital for its RNA helicase activity  which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT  highlighting the critical role of protein phase separation in translational control and animal early development.    Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates", "parent bioproject:PRJNA715459", "pubmed:35661831", null, "rip 4h WT rep2", "GSM5179334", null, "source name:control 4h RIP seq rep2|tissue:zebrafish embryos|genotype:wild type|age:4 hpf", "rip 4h WT rep2", "low quality bases were trimmed and filtered by cutadapt V 1.13 and Trimmomatic V 0.36. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome Zv9 using TopHat v2.1.1 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options \u2018\u2013nomodel\u2019   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 \u00d7 10\u22122 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein", "control 4h RIP seq rep2", null, "flag ddx3xb mRNA injected embryos were collected at xxx hpf or 4 hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4. Ddx3xb RIP was carried out following a published protocol  but with some modifications. Lysate was incubated with anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA Seq kit Clontech  635031. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc.", null, "tissue:zebrafish embryos|genotype:wild type|age:4 hpf", "GSM5179334", "GSM5179334: rip 4h WT rep2; Danio rerio; RIP Seq", "GSM5179334", null, "1", "RIP was carried out as previously described Despic et al.  2017. flag ddx3xb mRNA injected embryos were collected at xxx hpf and 6 hpf. 400 zebrafish embryos were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed  and subjected to mild RNA fragmentation. Crosslinked RNA proteins complexes were immunopurified using Anti FLAG M2 Magnetic Beads Merck  M8823 for 4 h. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Clontech Laboratories Inc", "GEO Accession:GSM5179334", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP311218", null, "loader:fastq load.py", "rip_4h_WT2.fq.gz", "fastq", 13945270350.0, 92968469.0, "GSM5179334 r1", "0:150", "A:4325573323;C:3059456045;G:4094407908;T:2464843410;N:989664", 150, null, null, null, 4325573323, 3059456045, 4094407908, 2464843410, 989664, "SRX10375444", "SRS8490050", "SRA1207702", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 1, 0.19992, null, 0.08953, null, 0.93046, null, 0.71052, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2021-03-18", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70712, "SRR20077343", "SRX16115141", "SRS13777745", "SRP385866", "PRJNA857663", "RIP seq for Cpeb1b in zebrafish embryos", "GSE207904", "Transcriptome Analysis", "Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates", "parent bioproject:PRJNA857656", null, null, "Flag Cpeb1b replicate 2", "GSM6322839", null, "source name:Flag Cpeb1b replicate 2|tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "Flag Cpeb1b replicate 2", "The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples", "Flag Cpeb1b replicate 2", null, "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.", null, "tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "GSM6322839", "GSM6322839: Flag Cpeb1b replicate 2; Danio rerio; RIP Seq", "GSM6322839 r1", "GSM6322839", "1", "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP385866", null, "loader:fastq load.py", "Flag_Cpeb1b_replicate_2.R1.fq.gz Flag_Cpeb1b_replicate_2.R2.fq.gz", "fastq fastq", 14733801000.0, 49112670.0, "GSM6322839 r1", "0:150 1:150", "A:4141614412;C:3363207101;G:3881752054;T:3344596903;N:2630530", 150, 150, null, null, 4141614412, 3363207101, 3881752054, 3344596903, 2630530, "SRX16115141", "SRS13777745", "SRA1452503", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.05175, 0.02071, 0.01394, 0.00703, 0.99383, 0.99758, 0.80854, 0.85616, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2022-07-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70713, "SRR20077344", "SRX16115140", "SRS13777744", "SRP385866", "PRJNA857663", "RIP seq for Cpeb1b in zebrafish embryos", "GSE207904", "Transcriptome Analysis", "Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates", "parent bioproject:PRJNA857656", null, null, "Flag Cpeb1b replicate 1", "GSM6322838", null, "source name:Flag Cpeb1b replicate 1|tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "Flag Cpeb1b replicate 1", "The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples", "Flag Cpeb1b replicate 1", null, "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.", null, "tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "GSM6322838", "GSM6322838: Flag Cpeb1b replicate 1; Danio rerio; RIP Seq", "GSM6322838 r1", "GSM6322838", "1", "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP385866", null, "loader:fastq load.py", "Flag_Cpeb1b_replicate_1.R1.fq.gz Flag_Cpeb1b_replicate_1.R2.fq.gz", "fastq fastq", 15482669700.0, 51608899.0, "GSM6322838 r1", "0:150 1:150", "A:4303443264;C:3570990345;G:4030059369;T:3575508224;N:2668498", 150, 150, null, null, 4303443264, 3570990345, 4030059369, 3575508224, 2668498, "SRX16115140", "SRS13777744", "SRA1452503", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.03751, 0.01773, 0.01056, 0.00621, 0.99346, 0.99736, 0.89693, 0.8036, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2022-07-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [75639, "SRR24746222", "SRX20523357", "SRS17832947", "SRP439774", "PRJNA976671", "RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos", "GSE233570", "Other", "To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c  we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.", null, "pubmed:38177902", null, "eIF4E1c RIP biol rep 2", "GSM7430662", null, "source name:Embryo lysate RIP|tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c|geo loc name:missing|collection date:missing", "eIF4E1c RIP biol rep 2", "RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter  s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts", "Embryo lysate RIP", null, "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c", "GSM7430662", "GSM7430662: eIF4E1c RIP biol rep 2; Danio rerio; RIP Seq", "GSM7430662 r1", "GSM7430662", "1", "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP439774", null, "loader:fastq load.py", "e1c-RIP_3_1.fastq.gz e1c-RIP_3_2.fastq.gz", "fastq fastq", 3658509264.0, 18111432.0, "GSM7430662 r1", "0:101 1:101", "A:1021449118;C:787165883;G:803394137;T:1046320964;N:179162", 101, 101, null, null, 1021449118, 787165883, 803394137, 1046320964, 179162, "SRX20523357", "SRS17832947", "SRA1645065", "IMP", "IMP", 2, 0.89621, 0.89533, 0.04125, 0.04128, 0.7722, 0.77244, 0.5895, 0.5976, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [75640, "SRR24746223", "SRX20523356", "SRS17832945", "SRP439774", "PRJNA976671", "RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos", "GSE233570", "Other", "To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c  we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.", null, "pubmed:38177902", null, "eIF4E1c RIP biol rep 1", "GSM7430661", null, "source name:Embryo lysate RIP|tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c|geo loc name:missing|collection date:missing", "eIF4E1c RIP biol rep 1", "RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter  s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts", "Embryo lysate RIP", null, "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c", "GSM7430661", "GSM7430661: eIF4E1c RIP biol rep 1; Danio rerio; RIP Seq", "GSM7430661 r1", "GSM7430661", "1", "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP439774", null, "loader:fastq load.py", "e1c-RIP_1_1.fastq.gz e1c-RIP_1_2.fastq.gz", "fastq fastq", 3661517448.0, 18126324.0, "GSM7430661 r1", "0:101 1:101", "A:1033737040;C:769143038;G:789231169;T:1069383557;N:22644", 101, 101, null, null, 1033737040, 769143038, 789231169, 1069383557, 22644, "SRX20523356", "SRS17832945", "SRA1645065", "IMP", "IMP", 2, 0.63898, 0.63654, 0.0292, 0.02977, 0.8202, 0.8216, 0.63773, 0.65353, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [75641, "SRR24746224", "SRX20523355", "SRS17832943", "SRP439774", "PRJNA976671", "RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos", "GSE233570", "Other", "To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c  we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.", null, "pubmed:38177902", null, "eIF4E1b RIP biol rep 3", "GSM7430660", null, "source name:Embryo lysate RIP|tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1b|geo loc name:missing|collection date:missing", "eIF4E1b RIP biol rep 3", "RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter  s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts", "Embryo lysate RIP", null, "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1b", "GSM7430660", "GSM7430660: eIF4E1b RIP biol rep 3; Danio rerio; RIP Seq", "GSM7430660 r1", "GSM7430660", "1", "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP439774", null, "loader:fastq load.py", "e1b-RIP_3_1.fastq.gz e1b-RIP_3_2.fastq.gz", "fastq fastq", 3668401608.0, 18160404.0, "GSM7430660 r1", "0:101 1:101", "A:994142435;C:809751406;G:823521552;T:1040962762;N:23453", 101, 101, null, null, 994142435, 809751406, 823521552, 1040962762, 23453, "SRX20523355", "SRS17832943", "SRA1645065", "IMP", "IMP", 2, 0.89614, 0.8938, 0.02204, 0.02191, 0.77968, 0.77938, 0.46572, 0.46433, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [75642, "SRR24746225", "SRX20523354", "SRS17832942", "SRP439774", "PRJNA976671", "RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos", "GSE233570", "Other", "To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c  we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.", null, "pubmed:38177902", null, "eIF4E1b RIP biol rep 2", "GSM7430659", null, "source name:Embryo lysate RIP|tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1b|geo loc name:missing|collection date:missing", "eIF4E1b RIP biol rep 2", "RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter  s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. 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Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.", null, "pubmed:38177902", null, "eIF4E1b RIP biol rep 1", "GSM7430658", null, "source name:Embryo lysate RIP|tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1b|geo loc name:missing|collection date:missing", "eIF4E1b RIP biol rep 1", "RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter  s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts", "Embryo lysate RIP", null, "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "tissue:Embryo lysate RIP|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1b", "GSM7430658", "GSM7430658: eIF4E1b RIP biol rep 1; Danio rerio; RIP Seq", "GSM7430658 r1", "GSM7430658", "1", "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP439774", null, "loader:fastq load.py", "e1b-RIP_1_1.fastq.gz e1b-RIP_1_2.fastq.gz", "fastq fastq", 3664341206.0, 18140303.0, "GSM7430658 r1", "0:101 1:101", "A:1002079901;C:797505762;G:819102400;T:1045629643;N:23500", 101, 101, null, null, 1002079901, 797505762, 819102400, 1045629643, 23500, "SRX20523353", "SRS17832941", "SRA1645065", "IMP", "IMP", 2, 0.89693, 0.89111, 0.03355, 0.03395, 0.77009, 0.77157, 0.48797, 0.48637, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 50, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", 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[run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_selection\" = :p0 and \"experiment.library_strategy\" = :p1 and \"tissue_curation\" = :p2 order 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