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
40576,SRR3228716,SRX1634616,SRS1345843,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A CLIP 8,GSM2088181,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A CLIP 8,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:8|genotype:WT|treatment:n1,GSM2088181,GSM2088181: m6A CLIP 8; Danio rerio; RIP Seq,GSM2088181,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088181,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_8h-IP.fastq.gz,fastq,921977050.0,18439541.0,GSM2088181 r1,0:50,A:233396466;C:263744643;G:252737160;T:172064890;N:33891,50,,,,233396466,263744643,252737160,172064890,33891,SRX1634616,SRS1345843,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.61408,,0.1783,,0.88032,,0.72361,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40577,SRR3228715,SRX1634615,SRS1345844,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A CLIP 6,GSM2088180,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A CLIP 6,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:6|genotype:WT|treatment:n1,GSM2088180,GSM2088180: m6A CLIP 6; Danio rerio; RIP Seq,GSM2088180,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088180,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_6h-IP.fastq.gz,fastq,811777600.0,16235552.0,GSM2088180 r1,0:50,A:214241727;C:241830821;G:208608337;T:147066789;N:29926,50,,,,214241727,241830821,208608337,147066789,29926,SRX1634615,SRS1345844,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.68946,,0.17622,,0.9194,,0.62968,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40578,SRR3228714,SRX1634614,SRS1345845,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A CLIP 4,GSM2088179,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A CLIP 4,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:4|genotype:WT|treatment:n1,GSM2088179,GSM2088179: m6A CLIP 4; Danio rerio; RIP Seq,GSM2088179,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088179,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_4h-IP.fastq.gz,fastq,746223800.0,14924476.0,GSM2088179 r1,0:50,A:185147085;C:236139555;G:187875436;T:137034934;N:26790,50,,,,185147085,236139555,187875436,137034934,26790,SRX1634614,SRS1345845,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.80174,,0.17015,,0.86164,,0.77262,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40579,SRR3228713,SRX1634613,SRS1345846,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A CLIP 2,GSM2088178,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A CLIP 2,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:2|genotype:WT|treatment:n1,GSM2088178,GSM2088178: m6A CLIP 2; Danio rerio; RIP Seq,GSM2088178,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088178,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_2h-IP.fastq.gz,fastq,937426800.0,18748536.0,GSM2088178 r1,0:50,A:263526034;C:262864870;G:241415141;T:169586820;N:33935,50,,,,263526034,262864870,241415141,169586820,33935,SRX1634613,SRS1345846,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.75612,,0.2242,,0.87823,,0.61308,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40580,SRR3228712,SRX1634612,SRS1345847,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A CLIP 0,GSM2088177,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A CLIP 0,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:0|genotype:WT|treatment:n1,GSM2088177,GSM2088177: m6A CLIP 0; Danio rerio; RIP Seq,GSM2088177,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088177,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_0h-IP.fastq.gz,fastq,1320186200.0,26403724.0,GSM2088177 r1,0:50,A:362282258;C:387362464;G:326692598;T:243799324;N:49556,50,,,,362282258,387362464,326692598,243799324,49556,SRX1634612,SRS1345847,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.50689,,0.10395,,0.89755,,0.72663,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40581,SRR3228711,SRX1634611,SRS1345848,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input CLIP 8,GSM2088176,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input CLIP 8,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:8|genotype:WT|treatment:n1,GSM2088176,GSM2088176: input CLIP 8; Danio rerio; RIP Seq,GSM2088176,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088176,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_8h-input.fastq.gz,fastq,1971263900.0,39425278.0,GSM2088176 r1,0:50,A:530986171;C:559974651;G:547087685;T:333110850;N:104543,50,,,,530986171,559974651,547087685,333110850,104543,SRX1634611,SRS1345848,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.64576,,0.23563,,0.91618,,0.71461,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40582,SRR3228710,SRX1634610,SRS1345849,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input CLIP 6,GSM2088175,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input CLIP 6,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:6|genotype:WT|treatment:n1,GSM2088175,GSM2088175: input CLIP 6; Danio rerio; RIP Seq,GSM2088175,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088175,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_6h-input.fastq.gz,fastq,2424925650.0,48498513.0,GSM2088175 r1,0:50,A:622469966;C:699224547;G:701719139;T:401382845;N:129153,50,,,,622469966,699224547,701719139,401382845,129153,SRX1634610,SRS1345849,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.68121,,0.23857,,0.93123,,0.73919,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40583,SRR3228709,SRX1634609,SRS1345850,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input CLIP 4,GSM2088174,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input CLIP 4,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:4|genotype:WT|treatment:n1,GSM2088174,GSM2088174: input CLIP 4; Danio rerio; RIP Seq,GSM2088174,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088174,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_4h-input.fastq.gz,fastq,1996829250.0,39936585.0,GSM2088174 r1,0:50,A:527211013;C:600800804;G:528828160;T:339883128;N:106145,50,,,,527211013,600800804,528828160,339883128,106145,SRX1634609,SRS1345850,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.60745,,0.19305,,0.92537,,0.74508,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40584,SRR3228708,SRX1634608,SRS1345851,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input CLIP 2,GSM2088173,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input CLIP 2,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:2|genotype:WT|treatment:n1,GSM2088173,GSM2088173: input CLIP 2; Danio rerio; RIP Seq,GSM2088173,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088173,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_2h-input.fastq.gz,fastq,2119606350.0,42392127.0,GSM2088173 r1,0:50,A:555894042;C:598667411;G:609233481;T:355698501;N:112915,50,,,,555894042,598667411,609233481,355698501,112915,SRX1634608,SRS1345851,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.65392,,0.2263,,0.9049,,0.72736,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40585,SRR3228707,SRX1634607,SRS1345852,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input CLIP 0,GSM2088172,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input CLIP 0,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:0|genotype:WT|treatment:n1,GSM2088172,GSM2088172: input CLIP 0; Danio rerio; RIP Seq,GSM2088172,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088172,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,CLIP_0h-input.fastq.gz,fastq,2150269400.0,43005388.0,GSM2088172 r1,,,,,,,,,,,,SRX1634607,SRS1345852,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.57233,,0.18947,,0.91323,,0.75741,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40586,SRR3228706,SRX1634606,SRS1345853,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A IP 8,GSM2088171,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A IP 8,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:8|genotype:WT|treatment:n1,GSM2088171,GSM2088171: m6A IP 8; Danio rerio; RIP Seq,GSM2088171,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088171,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_8h.IP.fastq.gz,fastq,527347000.0,10546940.0,GSM2088171 r1,0:50,A:90387238;C:157767772;G:129133581;T:150048442;N:9967,50,,,,90387238,157767772,129133581,150048442,9967,SRX1634606,SRS1345853,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.90207,,0.11796,,0.80208,,0.51587,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40587,SRR3228705,SRX1634605,SRS1345854,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A IP 6,GSM2088170,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A IP 6,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:6|genotype:WT|treatment:n1,GSM2088170,GSM2088170: m6A IP 6; Danio rerio; RIP Seq,GSM2088170,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088170,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_6h.IP.fastq.gz,fastq,606551300.0,12131026.0,GSM2088170 r1,0:50,A:100429722;C:200919401;G:156361859;T:148828837;N:11481,50,,,,100429722,200919401,156361859,148828837,11481,SRX1634605,SRS1345854,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.94517,,0.23269,,0.84571,,0.73203,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40588,SRR3228704,SRX1634604,SRS1345855,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A IP 4,GSM2088169,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A IP 4,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:4|genotype:WT|treatment:n1,GSM2088169,GSM2088169: m6A IP 4; Danio rerio; RIP Seq,GSM2088169,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088169,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_4h.IP.fastq.gz,fastq,616373350.0,12327467.0,GSM2088169 r1,0:50,A:103511937;C:199101152;G:159952372;T:153796186;N:11703,50,,,,103511937,199101152,159952372,153796186,11703,SRX1634604,SRS1345855,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.9484,,0.20806,,0.81349,,0.68893,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40589,SRR3228703,SRX1634603,SRS1345856,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A IP 2,GSM2088168,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A IP 2,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:2|genotype:WT|treatment:n1,GSM2088168,GSM2088168: m6A IP 2; Danio rerio; RIP Seq,GSM2088168,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088168,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_2h.IP.fastq.gz,fastq,560037350.0,11200747.0,GSM2088168 r1,0:50,A:90079119;C:192220024;G:154098019;T:123629702;N:10486,50,,,,90079119,192220024,154098019,123629702,10486,SRX1634603,SRS1345856,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.95056,,0.25053,,0.87322,,0.82008,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40590,SRR3228702,SRX1634602,SRS1345857,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,m6A IP 0,GSM2088167,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,m6A IP 0,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:0|genotype:WT|treatment:n1,GSM2088167,GSM2088167: m6A IP 0; Danio rerio; RIP Seq,GSM2088167,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088167,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_0h.IP.fastq.gz,fastq,458827450.0,9176549.0,GSM2088167 r1,0:50,A:74889651;C:150121353;G:121032505;T:112775237;N:8704,50,,,,74889651,150121353,121032505,112775237,8704,SRX1634602,SRS1345857,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.96567,,0.22221,,0.84471,,0.70341,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40591,SRR3228701,SRX1634601,SRS1345858,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input 8,GSM2088166,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input 8,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:8|genotype:WT|treatment:n1,GSM2088166,GSM2088166: input 8; Danio rerio; RIP Seq,GSM2088166,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088166,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_8h.input.fastq.gz,fastq,575536100.0,11510722.0,GSM2088166 r1,0:50,A:111158012;C:168916114;G:151564939;T:143886262;N:10773,50,,,,111158012,168916114,151564939,143886262,10773,SRX1634601,SRS1345858,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.95515,,0.19883,,0.79245,,0.6247,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40592,SRR3228700,SRX1634600,SRS1345859,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input 6,GSM2088165,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input 6,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:6|genotype:WT|treatment:n1,GSM2088165,GSM2088165: input 6; Danio rerio; RIP Seq,GSM2088165,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088165,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_6h.input.fastq.gz,fastq,613333150.0,12266663.0,GSM2088165 r1,0:50,A:113451661;C:194144306;G:164598114;T:141127589;N:11480,50,,,,113451661,194144306,164598114,141127589,11480,SRX1634600,SRS1345859,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.97989,,0.33526,,0.84798,,0.72512,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40593,SRR3228699,SRX1634599,SRS1345860,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input 4,GSM2088164,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input 4,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:4|genotype:WT|treatment:n1,GSM2088164,GSM2088164: input 4; Danio rerio; RIP Seq,GSM2088164,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088164,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_4h.input.fastq.gz,fastq,576058200.0,11521164.0,GSM2088164 r1,0:50,A:108062480;C:178888385;G:153976688;T:135119699;N:10948,50,,,,108062480,178888385,153976688,135119699,10948,SRX1634599,SRS1345860,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.97495,,0.29544,,0.81162,,0.71268,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40594,SRR3228698,SRX1634598,SRS1345861,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input 2,GSM2088163,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input 2,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:2|genotype:WT|treatment:n1,GSM2088163,GSM2088163: input 2; Danio rerio; RIP Seq,GSM2088163,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088163,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_2h.input.fastq.gz,fastq,703375200.0,14067504.0,GSM2088163 r1,0:50,A:125686246;C:228251341;G:193846290;T:155577830;N:13493,50,,,,125686246,228251341,193846290,155577830,13493,SRX1634598,SRS1345861,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.98596,,0.35619,,0.88521,,0.80927,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
40595,SRR3228697,SRX1634597,SRS1345862,SRP071818,PRJNA315314,The functions of m6A and Ythdf2 during zebrafish early development,GSE79213,Other,We report the m6A methylation maps of zebrafish embryos during early development  and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish   MZT  highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0  2  4  6  8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0  2  4  6  8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6  8  12  24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx  36  48 h.p.f. Replicate of each seq is also included.,,pubmed:28192787,,input 0,GSM2088162,,tissue:whole zebrafish embryo|genotype:WT|treatment:n1,input 0,Data analysis for each experiment: 1 for m6A seq  reads were aligned to the reference genome danRer10 using Tophat v2.0.14  ref with parameter  g 1   library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates  in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks  the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform  windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene  the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a  median reads count of the IP sample in all 100 bp windows on the current mRNA b  reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a×d/b×c. 2 for m6A CLIP seq  post removing the adapter sequence  the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly  mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq  Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.,whole zebrafish embryo,,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,embryos were collected and cultured in medium at 28.5 °C  and then harvested at each time point into TRIzol.,development time h.p.f.:0|genotype:WT|treatment:n1,GSM2088162,GSM2088162: input 0; Danio rerio; RIP Seq,GSM2088162,,1,total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples  mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems  202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.,GEO Accession:GSM2088162,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP071818,,,m6A_0h.input.fastq.gz,fastq,650787500.0,13015750.0,GSM2088162 r1,0:50,A:117902403;C:207274717;G:177773347;T:147824646;N:12387,50,,,,117902403,207274717,177773347,147824646,12387,SRX1634597,SRS1345862,SRA385720,GEO,"Chuan He Lab, Chemistry, University of Chicago",1,0.98268,,0.32108,,0.85669,,0.76239,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,trueseq,bulk,unknown,unknown,,United States,2016-03-14,Undetermined,Embryo,Whole Organism,All anatomical structures
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,,,,input shield rep2,GSM2390028,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,1785772532,1552902091,1571407685,1649464013,291713,SRX2345570,SRS1796136,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03627,,0.01,,0.96676,,0.66777,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,input shield rep1,GSM2390027,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,1002751444,902509483,908627718,951814220,170349,SRX2345569,SRS1796134,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03936,,0.01095,,0.96518,,0.68725,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,ip shield rep2,GSM2390026,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,ip_shield_rep2.fastq,fastq,3855863926.0,41019829.0,GSM2390026 r1,0:94,A:1044010018;C:931492803;G:952890289;T:926349254;N:1121562,94,,,,1044010018,931492803,952890289,926349254,1121562,SRX2345568,SRS1796132,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03311,,0.00481,,0.96337,,0.68612,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,ip shield rep1,GSM2390025,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,1087077899,996101257,1020588721,1002667943,1188682,SRX2345567,SRS1796131,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.01898,,0.00264,,0.97238,,0.59809,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,input sphere rep2,GSM2390024,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,991404019,883789087,892976599,916520929,165390,SRX2345566,SRS1796152,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03619,,0.00867,,0.96051,,0.63934,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,input sphere rep1,GSM2390023,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,1014569244,912257296,925742711,921776107,170216,SRX2345565,SRS1796139,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.04287,,0.00892,,0.95085,,0.50435,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,ip sphere rep2,GSM2390022,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,1037910962,957162730,963824694,966381238,1147000,SRX2345564,SRS1796133,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03492,,0.00427,,0.95026,,0.60529,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,ip sphere rep1,GSM2390021,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,1114959829,1018236207,1019156922,1032304051,1209991,SRX2345563,SRS1796143,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03035,,0.00288,,0.94757,,0.5787,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,input 64cell rep2,GSM2390020,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,953869445,864903757,875832539,903947732,228913,SRX2345562,SRS1796129,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.04289,,0.00757,,0.9418,,0.6078,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,input 64cell rep1,GSM2390019,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,916878511,870431252,873611680,877750503,226800,SRX2345561,SRS1796141,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03397,,0.00616,,0.95268,,0.62545,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,ip 64cell rep2,GSM2390018,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,966880666,841411144,858285224,862983808,1117134,SRX2345560,SRS1796153,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.04775,,0.00421,,0.92845,,0.5748,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,ip 64cell rep1,GSM2390017,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,1040276279,945311584,953598043,971589029,1228799,SRX2345559,SRS1796135,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03544,,0.00268,,0.93914,,0.53712,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,input 1cell rep2,GSM2390016,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,898920912,816234808,823428476,840956466,221348,SRX2345558,SRS1796155,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.04513,,0.00864,,0.95085,,0.51692,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,input 1cell rep1,GSM2390015,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,951411355,878458528,890250453,929968044,233266,SRX2345557,SRS1796128,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.03728,,0.00668,,0.94901,,0.60038,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,ip 1cell rep2,GSM2390014,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,953699047,835179152,846963064,848487912,1103405,SRX2345556,SRS1796127,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.02534,,0.00219,,0.95891,,0.5975,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,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,,,,ip 1cell rep1,GSM2390013,,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’end  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,,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® 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’pre 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±1°C 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 500µS/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 °C  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,,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® 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’pre 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,,SRP093295,,,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,,,,961438376,875781200,891055201,880749228,1143097,SRX2345555,SRS1796130,SRA492943,GEO,"Klungland Lab, Dept of microbiology, Oslo University Hospital",1,0.01939,,0.00159,,0.96457,,0.53652,,94,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Norway,2016-11-14,Zygote,Embryo,Embryo Imprecise,All anatomical structures
53427,SRR9854014,SRX6608456,SRS5172704,SRP216689,PRJNA557179,Role of the Exon Junction Complex in Danio rerio,GSE135019,Transcriptome Analysis,The exon  junction complex EJC is composed of three core proteins Rbm8a  Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq.  We find that  as in human cells  zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant  magoh mutant and wild type sibling embryos.  This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants,,,,RBM8A RIPSEQ Rep3,GSM3983830,,tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,RBM8A RIPSEQ Rep3,Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters  m 20   discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters  p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters  s  c  F 0.51  sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples,Whole embryo,None NA,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,All embryos were raised at 28.5C upto the required developmental timepoint.,developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,GSM3983830,GSM3983830: RBM8A RIPSEQ Rep3; Danio rerio; RIP Seq,GSM3983830,,1,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,GEO Accession:GSM3983830,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP216689,,loader:fastq load.py,ripseqB3.fastq.gz,fastq,1174462616.0,32753220.0,GSM3983830 r1,0:35.86,A:277856243;C:303697175;G:340240303;T:252574884;N:94011,35,,,,277856243,303697175,340240303,252574884,94011,SRX6608456,SRS5172704,SRA928193,GEO,"Guramrit Singh, Molecular Genetics, The Ohio State University",1,0.90426,,0.1746,,0.77341,,0.57553,,35,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-07-29,Pharyngula,Embryo,Whole Organism,All anatomical structures
53428,SRR9854013,SRX6608455,SRS5172702,SRP216689,PRJNA557179,Role of the Exon Junction Complex in Danio rerio,GSE135019,Transcriptome Analysis,The exon  junction complex EJC is composed of three core proteins Rbm8a  Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq.  We find that  as in human cells  zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant  magoh mutant and wild type sibling embryos.  This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants,,,,RBM8A RIPSEQ Rep2,GSM3983829,,tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,RBM8A RIPSEQ Rep2,Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters  m 20   discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters  p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters  s  c  F 0.51  sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples,Whole embryo,None NA,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,All embryos were raised at 28.5C upto the required developmental timepoint.,developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,GSM3983829,GSM3983829: RBM8A RIPSEQ Rep2; Danio rerio; RIP Seq,GSM3983829,,1,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,GEO Accession:GSM3983829,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP216689,,loader:fastq load.py,ripseqB2.fastq.gz,fastq,65641776.0,2466295.0,GSM3983829 r1,0:26.62,A:18933213;C:16060113;G:13492679;T:17151951;N:3820,26,,,,18933213,16060113,13492679,17151951,3820,SRX6608455,SRS5172702,SRA928193,GEO,"Guramrit Singh, Molecular Genetics, The Ohio State University",1,0.17621,,0.02351,,0.88069,,0.60622,,15,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-07-29,Pharyngula,Embryo,Whole Organism,All anatomical structures
53429,SRR9854012,SRX6608454,SRS5172701,SRP216689,PRJNA557179,Role of the Exon Junction Complex in Danio rerio,GSE135019,Transcriptome Analysis,The exon  junction complex EJC is composed of three core proteins Rbm8a  Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq.  We find that  as in human cells  zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant  magoh mutant and wild type sibling embryos.  This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants,,,,RBM8A RIPSEQ Rep1,GSM3983828,,tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,RBM8A RIPSEQ Rep1,Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters  m 20   discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters  p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters  s  c  F 0.51  sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples,Whole embryo,None NA,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,All embryos were raised at 28.5C upto the required developmental timepoint.,developmental stage:24 hpf|rip antibody:Human Y14 Sigma  cat# Y1253|genotype/variation:RBM8A,GSM3983828,GSM3983828: RBM8A RIPSEQ Rep1; Danio rerio; RIP Seq,GSM3983828,,1,RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al.  Methods Mol Biol. 2018;1680:1 28. Briefly  a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product  which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.,GEO Accession:GSM3983828,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP216689,,loader:fastq load.py,ripseqB1.fastq.gz,fastq,403183413.0,11908151.0,GSM3983828 r1,0:33.86,A:80085450;C:111343041;G:140916198;T:70619085;N:219639,33,,,,80085450,111343041,140916198,70619085,219639,SRX6608454,SRS5172701,SRA928193,GEO,"Guramrit Singh, Molecular Genetics, The Ohio State University",1,0.862,,0.1026,,0.95359,,0.79372,,33,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2019-07-29,Pharyngula,Embryo,Whole Organism,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,,rip 4h WT rep1,GSM5179333,,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 ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein,control 4h RIP seq rep1,,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.,,tissue:zebrafish embryos|genotype:wild type|age:4 hpf,GSM5179333,GSM5179333: rip 4h WT rep1; Danio rerio; RIP Seq,GSM5179333,,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,,SRP311218,,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,,,,3779410126,2709781787,3301583942,2175291644,854801,SRX10375447,SRS8490053,SRA1207702,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.30752,,0.13393,,0.90575,,0.74028,,150,,B,,usable mapping rate,illumina,novaseq_era,full_length,other,smarter,bulk,unknown,unknown,,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,,rip 2h WT rep2,GSM5179332,,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 ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein,control 2h RIP seq rep2,,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.,,tissue:zebrafish embryos|genotype:wild type|age:2 hpf,GSM5179332,GSM5179332: rip 2h WT rep2; Danio rerio; RIP Seq,GSM5179332,,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,,SRP311218,,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,,,,3686415626,2826613772,3732955088,2073945227,875287,SRX10375446,SRS8490052,SRA1207702,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.1848,,0.11194,,0.9669,,0.82171,,150,,B,,usable mapping rate,illumina,novaseq_era,full_length,other,smarter,bulk,unknown,unknown,,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,,rip 2h WT rep1,GSM5179331,,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 ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein,control 2h RIP seq rep1,,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.,,tissue:zebrafish embryos|genotype:wild type|age:2 hpf,GSM5179331,GSM5179331: rip 2h WT rep1; Danio rerio; RIP Seq,GSM5179331,,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,,SRP311218,,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,,,,2671043775,2046825976,2545406298,1524056303,626448,SRX10375445,SRS8490051,SRA1207702,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.30731,,0.17665,,0.94117,,0.79653,,150,,B,,usable mapping rate,illumina,novaseq_era,full_length,other,smarter,bulk,unknown,unknown,,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,,rip 4h WT rep2,GSM5179334,,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 ‘‘–bowtie1’’. The target binding regions of Ddx3xb were identified using MACS2 software version 2.0.10 with options ‘–nomodel’   keep dup and   gsize=1.4e9  and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Genome build: Zv9 Supplementary files format and content: binding peaks for Ddx3xb protein,control 4h RIP seq rep2,,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.,,tissue:zebrafish embryos|genotype:wild type|age:4 hpf,GSM5179334,GSM5179334: rip 4h WT rep2; Danio rerio; RIP Seq,GSM5179334,,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,,SRP311218,,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,,,,4325573323,3059456045,4094407908,2464843410,989664,SRX10375444,SRS8490050,SRA1207702,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),1,0.19992,,0.08953,,0.93046,,0.71052,,150,,B,,usable mapping rate,illumina,novaseq_era,full_length,other,smarter,bulk,unknown,unknown,,China,2021-03-18,Blastula,Embryo,Embryo Imprecise,All anatomical structures
66086,SRR15900240,SRX12190888,SRS10168725,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM+CH 2,,strain:AB|isolate:CH2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab CH2,tchenlab CH2,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_CH_5.8.IP_R1.fastq.gz EOM_CH_5.8.IP_R2.fastq.gz EOM_CH_5.8.Input_R1.fastq.gz EOM_CH_5.8.Input_R2.fastq.gz,fastq fastq fastq fastq,13391108400.0,44637028.0,EOM CH 5.8.IP R1.fastq.gz,0:150 1:150,A:2721241817;C:3886076819;G:4096587749;T:2611313908;N:75888107,150,150,,,2721241817,3886076819,4096587749,2611313908,75888107,SRX12190888,SRS10168725,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.8442,0.59467,0.17491,0.14724,0.86147,0.89112,0.7593,0.63363,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66087,SRR15900241,SRX12190887,SRS10168724,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM+CH 1,,strain:AB|isolate:CH1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab CH1,tchenlab CH1,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_CH_4.16.IP_R1.fastq.gz EOM_CH_4.16.IP_R2.fastq.gz EOM_CH_4.16.Input_R1.fastq.gz EOM_CH_4.16.Input_R2.fastq.gz,fastq fastq fastq fastq,12428976000.0,41429920.0,EOM CH 4.16.IP R1.fastq.gz,0:150 1:150,A:2486344612;C:3648199763;G:3865825828;T:2365039093;N:63566704,150,150,,,2486344612,3648199763,3865825828,2365039093,63566704,SRX12190887,SRS10168724,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.91763,0.6223,0.18817,0.15102,0.84891,0.87957,0.74757,0.64429,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66088,SRR15900242,SRX12190886,SRS10168723,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM 3,,strain:AB|isolate:T3|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab T3,tchenlab T3,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_5.9.IP_R1.fastq.gz EOM_5.9.IP_R2.fastq.gz EOM_5.9.Input_R1.fastq.gz EOM_5.9.Input_R2.fastq.gz,fastq fastq fastq fastq,12301780200.0,41005934.0,EOM 5.9.IP R1.fastq.gz,0:150 1:150,A:2415542475;C:3651603114;G:3847935468;T:2318868176;N:67830967,150,150,,,2415542475,3651603114,3847935468,2318868176,67830967,SRX12190886,SRS10168723,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.87516,0.65874,0.18282,0.16547,0.85561,0.87657,0.72193,0.61862,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66089,SRR15900243,SRX12190885,SRS10168722,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM 2,,strain:AB|isolate:T2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab T2,tchenlab T2,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_5.8.IP_R1.fastq.gz EOM_5.8.IP_R2.fastq.gz EOM_5.8.Input_R1.fastq.gz EOM_5.8.Input_R2.fastq.gz,fastq fastq fastq fastq,12373139700.0,41243799.0,EOM 5.8.IP R1.fastq.gz,0:150 1:150,A:2429212483;C:3679585650;G:3865741937;T:2330164654;N:68434976,150,150,,,2429212483,3679585650,3865741937,2330164654,68434976,SRX12190885,SRS10168722,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.88644,0.67829,0.18408,0.16867,0.84652,0.8704,0.76376,0.64158,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66090,SRR15900244,SRX12190884,SRS10168721,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,EOM 1,,strain:AB|isolate:T1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab T1,tchenlab T1,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,EOM_4.16.IP_R1.fastq.gz EOM_4.16.IP_R2.fastq.gz EOM_4.16.Input_R1.fastq.gz EOM_4.16.Input_R2.fastq.gz,fastq fastq fastq fastq,13638730800.0,45462436.0,EOM 4.16.IP R1.fastq.gz,0:150 1:150,A:2673949221;C:4057121296;G:4266457677;T:2562131972;N:79070634,150,150,,,2673949221,4057121296,4266457677,2562131972,79070634,SRX12190884,SRS10168721,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.87634,0.65649,0.18403,0.16375,0.85486,0.87913,0.69253,0.6405,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66091,SRR15900245,SRX12190883,SRS10168720,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,DMSO 3,,strain:AB|isolate:C3|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab C3,tchenlab C3,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,DMSO_5.9.IP_R1.fastq.gz DMSO_5.9.IP_R2.fastq.gz DMSO_5.9.Input_R1.fastq.gz DMSO_5.9.Input_R2.fastq.gz,fastq fastq fastq fastq,12477964200.0,41593214.0,DMSO 5.9.IP R1.fastq.gz,0:150 1:150,A:2462053397;C:3697418372;G:3878832850;T:2368512335;N:71147246,150,150,,,2462053397,3697418372,3878832850,2368512335,71147246,SRX12190883,SRS10168720,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.94535,0.75289,0.20051,0.18779,0.84139,0.8646,0.74818,0.65269,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66092,SRR15900246,SRX12190882,SRS10168719,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,DMSO 2,,strain:AB|isolate:C2|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab C2,tchenlab C2,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,DMSO_5.8.IP_R1.fastq.gz DMSO_5.8.IP_R2.fastq.gz DMSO_5.8.Input_R1.fastq.gz DMSO_5.8.Input_R2.fastq.gz,fastq fastq fastq fastq,12272849400.0,40909498.0,DMSO 5.8.IP R1.fastq.gz,0:150 1:150,A:2381041881;C:3673513092;G:3850518138;T:2295835815;N:71940474,150,150,,,2381041881,3673513092,3850518138,2295835815,71940474,SRX12190882,SRS10168719,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.88711,0.71046,0.18073,0.17436,0.84654,0.8674,0.76218,0.63257,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
66093,SRR15900247,SRX12190881,SRS10168718,SRP337081,PRJNA763243,m6A RNA methylation regulated by AHR contributes to the cardiac developmental toxicity of PM2.5 in zebrafish embryos,PRJNA763243,Other,This study aims to investigate the roles of m6A RNA methylation regulated by AHR in the heart developmental toxicity of PM2.5 in zebrafish embryos.EOM downregulates the expression levels of methyltransferase METTL14  which can be restored by AHR inhibitor CH or AHR knockdown. In addition  EOM increased ROS levels and cell apoptosis in the heart region of zebrafish embryos  and these can be attenuated by enforced METTL14 overexpression. In conclusion  AHR activated by PM2.5 significantly inhibits METTL14 expression  which in turn disrupts heart development via oxidative stress and apoptosis  resulting in heart defects in zebrafish embryos.,,,,,DMSO 1,,strain:AB|isolate:C1|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72 hpf organism or animal,,,,,,,,,RNA m6A methylation of zebrafish,tchenlab C1,tchenlab C1,M6A RNA immunoprecipitation was performed using GenSeqTM m6A RNA IP kit GenSeq.NEBNextUltra II Directional RNA Library Prep kit was used to construct RNA sequencing libraries for Input RNA samples without xxx and IP RNA samples post immunoprecipitation.Library inspection is performed using the BioAnalyzer 2100 analyzer Agilent.High throughput sequencing was performed using a 150 bp dual terminal mode on Illumina NovaSeq 6000 sequencer.,,,RIP-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP337081,,loader:fastq load.py,DMSO_4.16.IP_R1.fastq.gz DMSO_4.16.IP_R2.fastq.gz DMSO_4.16.Input_R1.fastq.gz DMSO_4.16.Input_R2.fastq.gz,fastq fastq fastq fastq,12900597000.0,43001990.0,DMSO 4.16.IP R1.fastq.gz,0:150 1:150,A:2517062962;C:3854768074;G:4032734290;T:2426295392;N:69736282,150,150,,,2517062962,3854768074,4032734290,2426295392,69736282,SRX12190881,SRS10168718,SRA1294636,"Soochow University|Department of Toxicology, School of Public Health",Soochow University,2,0.75605,0.5734,0.16268,0.14503,0.8714,0.89422,0.72976,0.64046,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,Unknown,2021-09-15,Larval,Larval,Undetermined,Undetermined
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,,,,m6A Embryos 5hpf,m6A Embryos 5hpf,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal,,,,,,,,,MeRIP Seq of Embryo 5hpf Gentanicin,2,2,Embryo 5hpf Gentanicin,,,RIP-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP439912,,,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,,,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,,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,,,,m6A Embryos 5hpf,m6A Embryos 5hpf,,strain:AB|breed:Egg water|age:5hpf|dev stage:5hpf|sex:not applicable|tissue:Embryos|BioSampleModel:Model organism or animal,,,,,,,,,MeRIP Seq of WT Embryo 5hpf,1,1,WT Embryo 5hpf,,,RIP-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP439912,,,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,,,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,,China,2023-05-27,Blastula,Embryo,Embryo Imprecise,All anatomical structures