{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Blastula\" and experiment.library_strategy = \"RIP-Seq\"", "rows": [[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"], [49549, "SRR7942636", "SRX4776901", "SRS3857441", "SRP162876", "PRJNA493828", "Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.", "GSE120646", "Other", "The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP 4hpf rep2", "GSM3406902", null, "source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo", "RIP 4hpf rep2", "RIP seq and iCLIP seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10  respectively. RIP seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools\u2019 intersectBed. iCLIP: To identify the Ybx1 targets\u2019 locus  the mode of truncation calling was performed. For each truncation position  the coverages of unique tag k and truncations m were determined by CIMS.pl program CLIP Tool Kit  CTK. The sites were annotated by applying BEDTools\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "Zebrafish embryo", null, "RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u03bcl RNasin by rotating at 4\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00b0C for 1 h. 50 \u03bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u03bcl Protein A Dynabeads for 4 h at 4\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00d7 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u2122 DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.", null, "strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo", "GSM3406902", "GSM3406902: RIP 4hpf rep2; Danio rerio; RIP Seq", "GSM3406902", null, "1", "RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u03bcl RNasin by rotating at 4\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00b0C for 1 h. 50 \u03bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u03bcl Protein A Dynabeads for 4 h at 4\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00d7 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u2122 DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.", "GEO Accession:GSM3406902", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162876", null, null, "RIP_4hpf_rep2_R1.fastq.gz RIP_4hpf_rep2_R2.fastq.gz", "fastq fastq", 22888305600.0, 76294352.0, "GSM3406902 r1", "0:150 1:150", "A:5927520807;C:4846894836;G:4996844576;T:7111789925;N:5255456", 150, 150, null, null, 5927520807, 4846894836, 4996844576, 7111789925, 5255456, "SRX4776901", "SRS3857441", "SRA786939", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.2704, 0.17205, 0.06114, 0.06961, 0.95879, 0.9698, 0.94515, 0.83252, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "hiseq_era", "full_length", "random_priming", "smarter", "bulk", "clip", "iclip", null, "China", "2018-09-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [49550, "SRR7942635", "SRX4776900", "SRS3857440", "SRP162876", "PRJNA493828", "Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.", "GSE120646", "Other", "The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP 4hpf rep1", "GSM3406901", null, "source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo", "RIP 4hpf rep1", "RIP seq and iCLIP seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10  respectively. RIP seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools\u2019 intersectBed. iCLIP: To identify the Ybx1 targets\u2019 locus  the mode of truncation calling was performed. For each truncation position  the coverages of unique tag k and truncations m were determined by CIMS.pl program CLIP Tool Kit  CTK. The sites were annotated by applying BEDTools\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "Zebrafish embryo", null, "RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u03bcl RNasin by rotating at 4\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00b0C for 1 h. 50 \u03bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u03bcl Protein A Dynabeads for 4 h at 4\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00d7 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u2122 DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.", null, "strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo", "GSM3406901", "GSM3406901: RIP 4hpf rep1; Danio rerio; RIP Seq", "GSM3406901", null, "1", "RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u03bcl RNasin by rotating at 4\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00b0C for 1 h. 50 \u03bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u03bcl Protein A Dynabeads for 4 h at 4\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00d7 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u2122 DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.", "GEO Accession:GSM3406901", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162876", null, null, "RIP_4hpf_rep1_R1.fastq.gz RIP_4hpf_rep1_R2.fastq.gz", "fastq fastq", 19929300600.0, 66431002.0, "GSM3406901 r1", "0:150 1:150", "A:5076575451;C:4235012507;G:4442151234;T:6170975339;N:4586069", 150, 150, null, null, 5076575451, 4235012507, 4442151234, 6170975339, 4586069, "SRX4776900", "SRS3857440", "SRA786939", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.27932, 0.16557, 0.06585, 0.06178, 0.95692, 0.96844, 0.94238, 0.84334, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "hiseq_era", "full_length", "random_priming", "smarter", "bulk", "clip", "iclip", null, "China", "2018-09-28", "Blastula", "Embryo", "Whole Organism", "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"], [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"], [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"], [75646, "SRR24754508", "SRX20530612", "SRS17839502", "SRP439912", "PRJNA976946", "MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model", "PRJNA976946", "Other", "MeRIP seq for embryotoxicity evaluation of Gentamicin  an aminoglycoside antibiotic added to human embryo culture medium  using the zebrafish Danio rerio model", null, null, null, "m6A Embryos 5hpf", "m6A Embryos 5hpf", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "MeRIP Seq of Embryo 5hpf Gentanicin", "2", "2", "Embryo 5hpf Gentanicin", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP439912", null, null, "QingdaIP_1.fq.gz QingdaIP_2.fq.gz Qingdainput_1.fq.gz Qingdainput_2.fq.gz", "fastq fastq fastq fastq", 16015155900.0, 53383853.0, "QingdaIP 1.fq.gz", "0:150 1:150", "A:3341079522;C:3427050846;G:6045646273;T:3201293287;N:85972", 150, 150, null, null, 3341079522, 3427050846, 6045646273, 3201293287, 85972, "SRX20530612", "SRS17839502", "SRA1645459", "Sichuan University|West China Second University Hospital", "Sichuan University", 2, 0.75159, 0.73659, 0.1359, 0.13542, 0.8117, 0.81172, 0.51543, 0.51251, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-05-27", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [75647, "SRR24754509", "SRX20530611", "SRS17839502", "SRP439912", "PRJNA976946", "MeRIP seq of Embryotoxicity evaluation of Gentamicin using the zebrafish model", "PRJNA976946", "Other", "MeRIP seq for embryotoxicity evaluation of Gentamicin  an aminoglycoside antibiotic added to human embryo culture medium  using the zebrafish Danio rerio model", null, null, null, "m6A Embryos 5hpf", "m6A Embryos 5hpf", null, "strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "MeRIP Seq of WT Embryo 5hpf", "1", "1", "WT Embryo 5hpf", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "RT-PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP439912", null, null, "WT-blankIP_1.fq.gz WT-blankIP_2.fq.gz WT-blankinput_1.fq.gz WT-blankinput_2.fq.gz", "fastq fastq fastq fastq", 15326922600.0, 51089742.0, "WT blankIP 1.fq.gz", "0:150 1:150", "A:3289509867;C:3239692571;G:5510216977;T:3287142341;N:360844", 150, 150, null, null, 3289509867, 3239692571, 5510216977, 3287142341, 360844, "SRX20530611", "SRS17839502", "SRA1645459", "Sichuan University|West China Second University Hospital", "Sichuan University", 2, 0.71182, 0.69789, 0.02169, 0.02058, 0.80409, 0.80395, 0.47813, 0.48125, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-05-27", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 12, "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", "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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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], [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 \"devstage_curation\" = :p0 and \"experiment.library_strategy\" = :p1 order by rowid limit 101", "params": {"p0": "Blastula", "p1": "RIP-Seq"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Blastula&experiment.library_strategy=RIP-Seq", "results": [{"value": "RIP-Seq", "label": "RIP-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Blastula", "selected": true}], "truncated": false}, 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