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
33123,SRR29672615,SRX25176099,SRS21866000,SRP517393,PRJNA1130538,ac4C transcriptomes of Zebrafish and Worm,GSE271258,Other,ac4C modification appears in mutilple model organisms including Zebrafish and Worm Overall design: To investigate whether ac4C modification is involved in evolution  we performed ac4C RIP seq on Zebrafish and Worm.,,,,Zebrafish ac4C,GSM8372406,,tissue:Animal organ cells|cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C Abcam catalog No. ab252215|geo loc name:missing|collection date:missing,Zebrafish ac4C,The raw ac4C RIP seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for ac4C modification peak calling and the significant methylation was identified by exomepeak2   and the ac4C peak calling can be visualized by IGV software. The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the ac4C peaks contained the consensus of ac4C motif sequences. For mRNA seq  the mRNA expression level was analyzed by StringTie  and differentially expressed mRNAs were calculated by DEseq. The substrates of ac4C regulators were obtained from starBase v2.0. The statistical enrichment analysis of Gene Ontology GO and Kyoto Encyclopedia of Genes and Genomes KEGG pathway for differentially expressed genes DEGs and differentially methylated mRNAs were applied by DAVID. Assembly: danRer10 or WBcel235 Supplementary files format and content: The processed data files is in CSV format  containing the expression levels and ac4C status changes for each gene.,Animal organ cells,,Total RNA was extracted according to manufacturer’s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps  by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched,,cell type:Animal organ cells|genotype:Wild type|rip antibody:anti ac4C  Abcam  catalog No. ab252215,GSM8372406,GSM8372406: Zebrafish ac4C; Danio rerio; RIP Seq,GSM8372406 r1,GSM8372406,1,Total RNA was extracted according to manufacturer's instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina® Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer's instruction. The kit eliminates duplication bias in PCR and sequencing steps  by using unique molecular identifier UMI of 8 random bases to label the pre amplified cDNA molecules. The library products corresponding to 200 500 bps were enriched,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP517393,,,Fish_IP.clean.R2.fastq.gz Fish_IP.clean.R1.fastq.gz,fastq fastq,816231517.0,3830403.0,GSM8372406 r1,0:102.34 1:110.76,A:199381841;C:207571478;G:205740791;T:203535549;N:1858,102,110,,,199381841,207571478,205740791,203535549,1858,SRX25176099,SRS21866000,SRA1914369,Fujian Medical University,Fujian Medical University,2,0.60415,0.60545,0.08824,0.08794,0.78796,0.78733,0.43432,0.43842,126,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-07-01,Undetermined,Undetermined,Undetermined,Undetermined
34614,SRR32137213,SRX27483377,SRS23906281,SRP560121,PRJNA1216205,rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation,GSE288109,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish  we performed RIP seq analysis using rbm24a GFP knock in samples  with IgG serving as the control.,,,,Zebrafish  RIP seq  Rbm24a Knock in2 IP2,GSM8759069,,source name:whole embryo|tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in2 IP2,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in,GSM8759069,GSM8759069: Zebrafish  RIP seq  Rbm24a Knock in2 IP2; Danio rerio; RIP Seq,GSM8759069 r1,GSM8759069,1,Total RNAs were extracted from Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP560121,,,RIP_IP2.R1.fq.gz RIP_IP2.R2.fq.gz,fastq fastq,18215080774.0,60314837.0,GSM8759069 r1,0:151 1:151,A:3824315591;C:5035112770;G:5644328190;T:3707941000;N:3383223,151,151,,,3824315591,5035112770,5644328190,3707941000,3383223,SRX27483377,SRS23906281,SRA2061743,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",,,,,,,,,,,,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-01-27,Multi-stage,Embryo,Whole Organism,All anatomical structures
34615,SRR32137214,SRX27483376,SRS23906280,SRP560121,PRJNA1216205,rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation,GSE288109,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish  we performed RIP seq analysis using rbm24a GFP knock in samples  with IgG serving as the control.,,,,Zebrafish  RIP seq  Rbm24a Knock in1 IP1,GSM8759068,,source name:whole embryo|tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in1 IP1,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in,GSM8759068,GSM8759068: Zebrafish  RIP seq  Rbm24a Knock in1 IP1; Danio rerio; RIP Seq,GSM8759068 r1,GSM8759068,1,Total RNAs were extracted from Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP560121,,,RIP_IP1.R1.fq.gz RIP_IP1.R2.fq.gz,fastq fastq,22190472874.0,73478387.0,GSM8759068 r1,0:151 1:151,A:4585155428;C:6233832602;G:6882198251;T:4484977909;N:4308684,151,151,,,4585155428,6233832602,6882198251,4484977909,4308684,SRX27483376,SRS23906280,SRA2061743,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",,,,,,,,,,,,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-01-27,Multi-stage,Embryo,Whole Organism,All anatomical structures
34616,SRR32137215,SRX27483375,SRS23906279,SRP560121,PRJNA1216205,rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation,GSE288109,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish  we performed RIP seq analysis using rbm24a GFP knock in samples  with IgG serving as the control.,,,,Zebrafish  RIP seq  Rbm24a Knock in2 IgG2,GSM8759067,,source name:whole embryo|tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in2 IgG2,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in,GSM8759067,GSM8759067: Zebrafish  RIP seq  Rbm24a Knock in2 IgG2; Danio rerio; RIP Seq,GSM8759067 r1,GSM8759067,1,Total RNAs were extracted from Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP560121,,,RIP_IgG2.R1.fq.gz RIP_IgG2.R2.fq.gz,fastq fastq,18588838088.0,61552444.0,GSM8759067 r1,0:151 1:151,A:3864885070;C:5250483318;G:5713729791;T:3756127723;N:3612186,151,151,,,3864885070,5250483318,5713729791,3756127723,3612186,SRX27483375,SRS23906279,SRA2061743,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",,,,,,,,,,,,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-01-27,Multi-stage,Embryo,Whole Organism,All anatomical structures
34617,SRR32137216,SRX27483374,SRS23906278,SRP560121,PRJNA1216205,rbm24a is an organizer component of germ plasm to determine germ cell fate 202409 validation,GSE288109,Other,The  formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants  but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs  which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows  where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs  resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm  highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To comprehensively characterize the RNA binding landscape of Rbm24a in zebrafish  we performed RIP seq analysis using rbm24a GFP knock in samples  with IgG serving as the control.,,,,Zebrafish  RIP seq  Rbm24a Knock in1 IgG1,GSM8759066,,source name:whole embryo|tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in1 IgG1,Each library was amplified by a 15 cycle PCR  and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample,whole embryo,,Total RNAs were extracted from Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|cell line:4 cell stage|cell type:embryonic cell|genotype:knock in,GSM8759066,GSM8759066: Zebrafish  RIP seq  Rbm24a Knock in1 IgG1; Danio rerio; RIP Seq,GSM8759066 r1,GSM8759066,1,Total RNAs were extracted from Mrbm24a embryos at 4 cell sphere 24 hpf stage  using TRIzol reagent Invitrogen  and were precipitated by cold isopropanol 50%  v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg of immunoprecipitated RNA was utilized for library construction. Ribosomal RNA depletion was performed using RNase H based probes followed by magnetic bead purification. RNA fragmentation was achieved through magnesium catalyzed hydrolysis under elevated temperature 94°C for 6 min. First strand cDNA synthesis was initiated with random hexamer primers and reverse transcriptase  followed by second strand synthesis using DNA polymerase I with dUTP incorporation for strand marking. Double stranded cDNA fragments underwent end repair and three prime adenylation using a single tube enzymatic reaction system. Illumina compatible adaptors with unique dual indexes were ligated to both ends of the DNA fragments. Size selection of adaptor ligated products 180 250 bp was performed using double sided SPRI bead purification. PCR amplification was conducted with P5/P7 primers for 12 cycles  followed by AMPure XP bead purification to remove primer dimers. Library quality was verified by Agilent 2100 Bioanalyzer DNA High Sensitivity chip analysis. Indexed libraries were pooled in equimolar ratios and subjected to paired end sequencing 2×150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP560121,,,RIP_IgG1.R1.fq.gz RIP_IgG1.R2.fq.gz,fastq fastq,18008086350.0,59629425.0,GSM8759066 r1,0:151 1:151,A:3736851298;C:5091099145;G:5529269310;T:3647429389;N:3437208,151,151,,,3736851298,5091099145,5529269310,3647429389,3437208,SRX27483374,SRS23906278,SRA2061743,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",,,,,,,,,,,,B,T,mate2 technical by mapping diff,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2025-01-27,Multi-stage,Embryo,Whole Organism,All anatomical structures
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
42000,SRR5379364,SRX2674572,SRS2073700,SRP102513,PRJNA380609,Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing,GSE97067,Other,DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development  we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.,,pubmed:29636379,,ddx39a 24hpf RIPseq,GSM2550918,,source name:embryos|genotype:ddx39a mutant|tissue:embryo|developmental stage:24hpf,ddx39a 24hpf RIPseq,Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample,embryos,,Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.,,genotype:ddx39a mutant|tissue:embryo|developmental stage:24hpf,GSM2550918,GSM2550918: ddx39a 24hpf RIPseq; Danio rerio; RIP Seq,GSM2550918,,1,Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.,GEO Accession:GSM2550918,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP102513,,,RDWHDANwwwCAABRAAPEI-206_1.fq.gz RDWHDANwwwCAABRAAPEI-206_2.fq.gz,fastq fastq,3819239400.0,19096197.0,GSM2550918 r1,0:100 1:100,A:751858949;C:1169790479;G:1139713624;T:756987876;N:888472,100,100,,,751858949,1169790479,1139713624,756987876,888472,SRX2674572,SRS2073700,SRA549449,GEO,"Xin Lou Lab, Medical School, Nanjing University",2,0.98659,0.98572,0.28836,0.28975,0.89422,0.89558,0.75396,0.78553,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2017-03-27,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
42001,SRR5379363,SRX2674571,SRS2073697,SRP102513,PRJNA380609,Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing,GSE97067,Other,DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development  we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.,,pubmed:29636379,,WT 24hpf RIPseq,GSM2550917,,source name:embryos|genotype:wild type|tissue:embryo|developmental stage:24hpf,WT 24hpf RIPseq,Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample,embryos,,Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.,,genotype:wild type|tissue:embryo|developmental stage:24hpf,GSM2550917,GSM2550917: WT 24hpf RIPseq; Danio rerio; RIP Seq,GSM2550917,,1,Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymeraseΙ. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer’s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.,GEO Accession:GSM2550917,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP102513,,,RDWHDANwwwCAAARAAPEI-205_2.fq.gz RDWHDANwwwCAAARAAPEI-205_1.fq.gz,fastq fastq,3802882200.0,19014411.0,GSM2550917 r1,0:100 1:100,A:733911232;C:1178365174;G:1154031422;T:735690235;N:884137,100,100,,,733911232,1178365174,1154031422,735690235,884137,SRX2674571,SRS2073697,SRA549449,GEO,"Xin Lou Lab, Medical School, Nanjing University",2,0.9866,0.98469,0.30567,0.30486,0.90796,0.90928,0.82926,0.83029,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,China,2017-03-27,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
43454,SRR7169686,SRX4087616,SRS3304345,SRP115900,PRJNA399133,RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN,GSE102861,Transcriptome Analysis,We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.,,pubmed:29765956,,IN wholefishtranscriptome RNAseq rep4,GSM3143177,,source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:whole fish|antibody:n1,IN wholefishtranscriptome RNAseq rep4,Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample,Tgmyo6b:GFP 2A rpl10a 3xHA,Untreated,RNA was isolated from the immunoprecipitated and input samples using the Qiagen RNeasy Plus Micro kit Cat#74034.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,embryos were grown at 28 degrees C in E3 media until 5dpf,developmental stage:5dpf|tissue:whole fish|antibody:n1,GSM3143177,GSM3143177: IN wholefishtranscriptome RNAseq rep4; Danio rerio; RIP Seq,GSM3143177,,1,RNA was isolated from the immunoprecipitated and input samples using the Qiagen RNeasy Plus Micro kit Cat#74034.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer's instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM3143177,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP115900,,,RiboZF_IN3_R1.fastq.gz RiboZF_IN3_R2.fastq.gz,fastq fastq,9065897639.0,60495321.0,GSM3143177 r1,0:74.96 1:74.90,A:2375136682;C:2190164060;G:2113095817;T:2385734886;N:1766194,74,74,,,2375136682,2190164060,2113095817,2385734886,1766194,SRX4087616,SRS3304345,SRA601675,GEO,"Department: Institute for Genome Sciences, University of Maryland in Baltimore",2,0.92807,0.92373,0.0842,0.08335,0.71754,0.72305,0.45254,0.46074,75,75,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2018-05-16,Larval,Larval,Whole Organism,All anatomical structures
43455,SRR5952030,SRX3110524,SRS2445617,SRP115900,PRJNA399133,RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN,GSE102861,Transcriptome Analysis,We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.,,pubmed:29765956,,IN wholefishtranscriptome RNAseq rep3,GSM2747297,,source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:whole fish|antibody:n1,IN wholefishtranscriptome RNAseq rep3,Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample,Tgmyo6b:GFP 2A rpl10a 3xHA,Untreated,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,embryos were grown at 28 degrees C in E3 media until 5dpf,developmental stage:5dpf|tissue:whole fish|antibody:n1,GSM2747297,GSM2747297: IN wholefishtranscriptome RNAseq rep3; Danio rerio; RIP Seq,GSM2747297,,1,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2747297,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP115900,,,RiboZF_IN4_R1.fastq.gz RiboZF_IN4_R2.fastq.gz,fastq fastq,8796307376.0,58697576.0,GSM2747297 r1,0:74.96 1:74.90,A:2326140676;C:2104630190;G:2033251376;T:2330582425;N:1702709,74,74,,,2326140676,2104630190,2033251376,2330582425,1702709,SRX3110524,SRS2445617,SRA601675,GEO,"Department: Institute for Genome Sciences, University of Maryland in Baltimore",2,0.94186,0.93847,0.08006,0.08004,0.70169,0.70778,0.46714,0.45678,75,75,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2017-08-21,Larval,Larval,Whole Organism,All anatomical structures
43456,SRR5952029,SRX3110523,SRS2445616,SRP115900,PRJNA399133,RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN,GSE102861,Transcriptome Analysis,We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.,,pubmed:29765956,,IN wholefishtranscriptome RNAseq rep2,GSM2747296,,source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:whole fish|antibody:n1,IN wholefishtranscriptome RNAseq rep2,Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample,Tgmyo6b:GFP 2A rpl10a 3xHA,Untreated,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,embryos were grown at 28 degrees C in E3 media until 5dpf,developmental stage:5dpf|tissue:whole fish|antibody:n1,GSM2747296,GSM2747296: IN wholefishtranscriptome RNAseq rep2; Danio rerio; RIP Seq,GSM2747296,,1,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2747296,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP115900,,,RiboZF_IN2_R1.fastq.gz RiboZF_IN2_R2.fastq.gz,fastq fastq,7407816750.0,49385445.0,GSM2747296 r1,0:75 1:75,A:1965588922;C:1772589081;G:1716538525;T:1951670484;N:1429738,75,75,,,1965588922,1772589081,1716538525,1951670484,1429738,SRX3110523,SRS2445616,SRA601675,GEO,"Department: Institute for Genome Sciences, University of Maryland in Baltimore",2,0.93743,0.9347,0.07981,0.07938,0.69721,0.70246,0.46381,0.46767,75,75,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2017-08-21,Larval,Larval,Whole Organism,All anatomical structures
43457,SRR5952028,SRX3110522,SRS2445615,SRP115900,PRJNA399133,RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN,GSE102861,Transcriptome Analysis,We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.,,pubmed:29765956,,IN wholefishtranscriptome RNAseq rep1,GSM2747295,,source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:whole fish|antibody:n1,IN wholefishtranscriptome RNAseq rep1,Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample,Tgmyo6b:GFP 2A rpl10a 3xHA,Untreated,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,embryos were grown at 28 degrees C in E3 media until 5dpf,developmental stage:5dpf|tissue:whole fish|antibody:n1,GSM2747295,GSM2747295: IN wholefishtranscriptome RNAseq rep1; Danio rerio; RIP Seq,GSM2747295,,1,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2747295,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP115900,,,RiboZF_IN1_R1.fastq.gz RiboZF_IN1_R2.fastq.gz,fastq fastq,4971869342.0,33177517.0,GSM2747295 r1,0:74.96 1:74.90,A:1277896624;C:1224383725;G:1184225816;T:1284401610;N:961567,74,74,,,1277896624,1224383725,1184225816,1284401610,961567,SRX3110522,SRS2445615,SRA601675,GEO,"Department: Institute for Genome Sciences, University of Maryland in Baltimore",2,0.94557,0.94195,0.09264,0.0931,0.69785,0.70337,0.48067,0.48526,75,74,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2017-08-21,Larval,Larval,Whole Organism,All anatomical structures
43458,SRR5952027,SRX3110521,SRS2445614,SRP115900,PRJNA399133,RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN,GSE102861,Transcriptome Analysis,We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.,,pubmed:29765956,,IP HCtranslatome RNAseq rep3,GSM2747294,,source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA,IP HCtranslatome RNAseq rep3,Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample,Tgmyo6b:GFP 2A rpl10a 3xHA,Untreated,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,embryos were grown at 28 degrees C in E3 media until 5dpf,developmental stage:5dpf|tissue:hair cells enriched|antibody:HA,GSM2747294,GSM2747294: IP HCtranslatome RNAseq rep3; Danio rerio; RIP Seq,GSM2747294,,1,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2747294,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP115900,,,RiboZF_IP4_R1.fastq.gz RiboZF_IP4_R2.fastq.gz,fastq fastq,4994833580.0,33330363.0,GSM2747294 r1,0:74.96 1:74.90,A:1202677579;C:1288784412;G:1278463604;T:1223941397;N:966588,74,74,,,1202677579,1288784412,1278463604,1223941397,966588,SRX3110521,SRS2445614,SRA601675,GEO,"Department: Institute for Genome Sciences, University of Maryland in Baltimore",2,0.61854,0.6151,0.20328,0.19651,0.83599,0.84104,0.60632,0.59954,75,75,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2017-08-21,Larval,Larval,Embryo Imprecise,All anatomical structures
43459,SRR5952026,SRX3110520,SRS2445613,SRP115900,PRJNA399133,RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN,GSE102861,Transcriptome Analysis,We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.,,pubmed:29765956,,IP HCtranslatome RNAseq rep2,GSM2747293,,source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA,IP HCtranslatome RNAseq rep2,Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample,Tgmyo6b:GFP 2A rpl10a 3xHA,Untreated,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,embryos were grown at 28 degrees C in E3 media until 5dpf,developmental stage:5dpf|tissue:hair cells enriched|antibody:HA,GSM2747293,GSM2747293: IP HCtranslatome RNAseq rep2; Danio rerio; RIP Seq,GSM2747293,,1,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2747293,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP115900,,,RiboZF_IP2_R1.fastq.gz RiboZF_IP2_R2.fastq.gz,fastq fastq,4530855300.0,30205702.0,GSM2747293 r1,0:75 1:75,A:1112381418;C:1153277132;G:1147183468;T:1117133915;N:879367,75,75,,,1112381418,1153277132,1147183468,1117133915,879367,SRX3110520,SRS2445613,SRA601675,GEO,"Department: Institute for Genome Sciences, University of Maryland in Baltimore",2,0.64948,0.64878,0.15967,0.15683,0.80756,0.81288,0.56438,0.56275,75,75,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2017-08-21,Larval,Larval,Embryo Imprecise,All anatomical structures
43460,SRR5952025,SRX3110519,SRS2445612,SRP115900,PRJNA399133,RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN,GSE102861,Transcriptome Analysis,We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.,,pubmed:29765956,,IP HCtranslatome RNAseq rep1,GSM2747292,,source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA,IP HCtranslatome RNAseq rep1,Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample,Tgmyo6b:GFP 2A rpl10a 3xHA,Untreated,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,embryos were grown at 28 degrees C in E3 media until 5dpf,developmental stage:5dpf|tissue:hair cells enriched|antibody:HA,GSM2747292,GSM2747292: IP HCtranslatome RNAseq rep1; Danio rerio; RIP Seq,GSM2747292,,1,RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer’s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM2747292,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP115900,,,RiboZF_IP1_R1.fastq.gz RiboZF_IP1_R2.fastq.gz,fastq fastq,5261113350.0,35074089.0,GSM2747292 r1,0:75 1:75,A:1356848229;C:1276483567;G:1260001700;T:1366757927;N:1021927,75,75,,,1356848229,1276483567,1260001700,1366757927,1021927,SRX3110519,SRS2445612,SRA601675,GEO,"Department: Institute for Genome Sciences, University of Maryland in Baltimore",2,0.66363,0.6599,0.15644,0.15316,0.76808,0.7725,0.48538,0.48933,75,75,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,trueseq,bulk,unknown,unknown,,United States,2017-08-21,Larval,Larval,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
54307,SRR10129555,SRX6857975,SRS5395856,SRP221863,PRJNA565584,The functions of igf2bp3 during zebrafish early development,PRJNA565584,Whole Genome Sequencing,RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.,,,,Model organism or animal sample from Danio rerio,RIP seq zebrafish embryo HA rabbit,,strain:AB|dev stage:embryo|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,RIP seq zebrafish embryo sphere HA,HA sphere,HA sphere,RIP seq,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP221863,,,IP2_R1.fq.gz IP2_R2.fq.gz,fastq fastq,7528561800.0,25095206.0,IP2 R1.fq.gz,0:150 1:150,A:1638987252;C:1830922014;G:2628590112;T:1430016657;N:45765,150,150,,,1638987252,1830922014,2628590112,1430016657,45765,SRX6857975,SRS5395856,SRA962995,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.92316,0.96332,0.32571,0.34771,0.89173,0.88962,0.89557,0.89793,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-09-17,Blastula,Embryo,Embryo Imprecise,All anatomical structures
54308,SRR10129346,SRX6857766,SRS5395649,SRP221863,PRJNA565584,The functions of igf2bp3 during zebrafish early development,PRJNA565584,Whole Genome Sequencing,RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.,,,,Model organism or animal sample from Danio rerio,RIP seq zebrafish embryo IgG rabbit,,strain:AB|dev stage:embryo|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal,,,,,,,,,RIP seq zebrafish embryo sphere IgG,IgG sphere,IgG sphere,RIP seq,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP221863,,,IgG1_R1.fq.gz IgG1_R2.fq.gz,fastq fastq,2647374600.0,8824582.0,IgG1 R1.fq.gz,0:150 1:150,A:565620765;C:650153559;G:936592543;T:494992101;N:15632,150,150,,,565620765,650153559,936592543,494992101,15632,SRX6857766,SRS5395649,SRA962944,Huazhong Agricultural University|College of Fisheries,Huazhong Agricultural University,2,0.95349,0.96423,0.33504,0.34458,0.93748,0.93726,0.85176,0.91118,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2019-09-17,Blastula,Embryo,Embryo Imprecise,All anatomical structures
60021,SRR12103084,SRX8627422,SRS6915731,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,SCI IP,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI IP|BioSampleModel:Model organism or animal,,,,,,,,,IP library sequencing data of treated sample,SCIIP BKDL192540807 1a,SCIIP BKDL192540807 1a,IP library sequencing data of treated sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,SCIIP_BKDL192540807-1a_1.fq.gz SCIIP_BKDL192540807-1a_2.fq.gz,fastq fastq,7110503700.0,23701679.0,SCIIP BKDL192540807 1a 1.fq.gz,0:150 1:150,A:1520693228;C:1953670419;G:2215620460;T:1420407690;N:111903,150,150,,,1520693228,1953670419,2215620460,1420407690,111903,SRX8627422,SRS6915731,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.9115,0.9147,0.19936,0.2033,0.81864,0.81919,0.66838,0.6677,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60022,SRR12103085,SRX8627421,SRS6915730,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,SCI Input,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI Input|BioSampleModel:Model organism or animal,,,,,,,,,Input library sequencing data of treated sample,SCIIN BKDL192540809 1a,SCIIN BKDL192540809 1a,Input library sequencing data of treated sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,SCIIN_BKDL192540809-1a_2.fq.gz SCIIN_BKDL192540809-1a_1.fq.gz,fastq fastq,7774587300.0,25915291.0,SCIIN BKDL192540809 1a 1.fq.gz,0:150 1:150,A:1595151855;C:2243828590;G:2397611978;T:1537918306;N:76571,150,150,,,1595151855,2243828590,2397611978,1537918306,76571,SRX8627421,SRS6915730,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.96018,0.96291,0.23754,0.23744,0.84904,0.85245,0.74661,0.74738,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60023,SRR12103086,SRX8627420,SRS6915729,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,Control IP,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control IP|BioSampleModel:Model organism or animal,,,,,,,,,IP library sequencing data of control sample,controlIP BKDL192540808 1a,controlIP BKDL192540808 1a,IP library sequencing data of control sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,controlIP_BKDL192540808-1a_2.fq.gz controlIP_BKDL192540808-1a_1.fq.gz,fastq fastq,7359972600.0,24533242.0,controlIP BKDL192540808 1a 1.fq.gz,0:150 1:150,A:1569051886;C:2002692591;G:2333418000;T:1454676484;N:133639,150,150,,,1569051886,2002692591,2333418000,1454676484,133639,SRX8627420,SRS6915729,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.92004,0.92293,0.20272,0.20739,0.83254,0.83291,0.68471,0.65224,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60024,SRR12103087,SRX8627419,SRS6915728,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,Control Input,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control Input|BioSampleModel:Model organism or animal,,,,,,,,,Input library sequencing data of control sample,controlIN BKDL192540810 1a,controlIN BKDL192540810 1a,Input library sequencing data of control sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,controlIN_BKDL192540810-1a_1.fq.gz controlIN_BKDL192540810-1a_2.fq.gz,fastq fastq,7830123600.0,26100412.0,controlIN BKDL192540810 1a 1.fq.gz,0:150 1:150,A:1589371287;C:2296547915;G:2409439612;T:1534684151;N:80635,150,150,,,1589371287,2296547915,2409439612,1534684151,80635,SRX8627419,SRS6915728,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.97501,0.97626,0.23177,0.23578,0.89497,0.8971,0.78501,0.77674,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60025,SRR12103783,SRX8627954,SRS6916259,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,PCB4 IP,GSM4644253,,tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217,PCB4 IP,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217,GSM4644253,GSM4644253: PCB4 IP; Danio rerio; RIP Seq,GSM4644253,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644253,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,P4_m6A-IP_S16_R1_001.fastq.gz P4_m6A-IP_S16_R2_001.fastq.gz,fastq fastq,2309150560.0,15191780.0,GSM4644253 r1,0:76 1:76,A:490672579;C:656568819;G:666651729;T:495020365;N:237068,76,76,,,490672579,656568819,666651729,495020365,237068,SRX8627954,SRS6916259,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.94474,0.944,0.18094,0.18203,0.7515,0.75554,0.60771,0.6152,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60026,SRR12103782,SRX8627953,SRS6916258,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,PCB3 IP,GSM4644252,,tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216,PCB3 IP,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216,GSM4644252,GSM4644252: PCB3 IP; Danio rerio; RIP Seq,GSM4644252,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644252,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,P3_m6A-IP_S15_R2_001.fastq.gz P3_m6A-IP_S15_R1_001.fastq.gz,fastq fastq,2965972504.0,19512977.0,GSM4644252 r1,0:76 1:76,A:620624207;C:853765538;G:874990332;T:616281897;N:310530,76,76,,,620624207,853765538,874990332,616281897,310530,SRX8627953,SRS6916258,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.93433,0.93213,0.16543,0.16208,0.75043,0.753,0.62186,0.64359,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60027,SRR12103781,SRX8627952,SRS6916257,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,PCB2 IP,GSM4644251,,tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215,PCB2 IP,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215,GSM4644251,GSM4644251: PCB2 IP; Danio rerio; RIP Seq,GSM4644251,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644251,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,P2_m6A-IP_S14_R2_001.fastq.gz P2_m6A-IP_S14_R1_001.fastq.gz,fastq fastq,2687973472.0,17684036.0,GSM4644251 r1,0:76 1:76,A:585901626;C:744255122;G:756993274;T:600539454;N:283996,76,76,,,585901626,744255122,756993274,600539454,283996,SRX8627952,SRS6916257,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.9445,0.94466,0.16876,0.17035,0.74728,0.75022,0.57878,0.57933,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60028,SRR12103780,SRX8627951,SRS6916256,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,PCB1 IP,GSM4644250,,tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214,PCB1 IP,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214,GSM4644250,GSM4644250: PCB1 IP; Danio rerio; RIP Seq,GSM4644250,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644250,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,P1_m6A-IP_S13_R1_001.fastq.gz P1_m6A-IP_S13_R2_001.fastq.gz,fastq fastq,2596174288.0,17080094.0,GSM4644250 r1,0:76 1:76,A:564523297;C:723443207;G:735894528;T:572044392;N:268864,76,76,,,564523297,723443207,735894528,572044392,268864,SRX8627951,SRS6916256,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.93494,0.93528,0.17469,0.17518,0.746,0.74803,0.60114,0.60005,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60029,SRR12103779,SRX8627950,SRS6916255,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,PCB4 Input,GSM4644249,,tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1,PCB4 Input,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:PCB126|strain:AB|fraction:input control|antibody:n1,GSM4644249,GSM4644249: PCB4 Input; Danio rerio; RIP Seq,GSM4644249,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644249,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,P4_INPUT_S8_R1_001.fastq.gz P4_INPUT_S8_R2_001.fastq.gz,fastq fastq,3655473384.0,24049167.0,GSM4644249 r1,0:76 1:76,A:680110064;C:1145409769;G:1179103219;T:650470372;N:379960,76,76,,,680110064,1145409769,1179103219,650470372,379960,SRX8627950,SRS6916255,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.93037,0.96319,0.21668,0.22563,0.86338,0.86385,0.77257,0.70059,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60030,SRR12103778,SRX8627949,SRS6916254,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,PCB3 Input,GSM4644248,,tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1,PCB3 Input,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:PCB126|strain:AB|fraction:input control|antibody:n1,GSM4644248,GSM4644248: PCB3 Input; Danio rerio; RIP Seq,GSM4644248,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644248,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,P3_INPUT_S7_R1_001.fastq.gz P3_INPUT_S7_R2_001.fastq.gz,fastq fastq,4926238376.0,32409463.0,GSM4644248 r1,0:76 1:76,A:929043061;C:1530175131;G:1577898210;T:888604850;N:517124,76,76,,,929043061,1530175131,1577898210,888604850,517124,SRX8627949,SRS6916254,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.92875,0.95698,0.21539,0.22073,0.85253,0.85431,0.76235,0.68659,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60031,SRR12103777,SRX8627948,SRS6916253,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,PCB2 Input,GSM4644247,,tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1,PCB2 Input,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:PCB126|strain:AB|fraction:input control|antibody:n1,GSM4644247,GSM4644247: PCB2 Input; Danio rerio; RIP Seq,GSM4644247,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644247,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,P2_INPUT_S6_R1_001.fastq.gz P2_INPUT_S6_R2_001.fastq.gz,fastq fastq,5669611400.0,37300075.0,GSM4644247 r1,0:76 1:76,A:1050955836;C:1780355588;G:1829450728;T:1008257255;N:591993,76,76,,,1050955836,1780355588,1829450728,1008257255,591993,SRX8627948,SRS6916253,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.93297,0.93791,0.21298,0.21667,0.85902,0.86302,0.7387,0.69759,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60032,SRR12103776,SRX8627947,SRS6916252,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,PCB1 Input,GSM4644246,,tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1,PCB1 Input,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:PCB126|strain:AB|fraction:input control|antibody:n1,GSM4644246,GSM4644246: PCB1 Input; Danio rerio; RIP Seq,GSM4644246,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644246,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,P1_INPUT_S5_R1_001.fastq.gz P1_INPUT_S5_R2_001.fastq.gz,fastq fastq,4154972744.0,27335347.0,GSM4644246 r1,0:76 1:76,A:764769282;C:1310937656;G:1344287240;T:734545457;N:433109,76,76,,,764769282,1310937656,1344287240,734545457,433109,SRX8627947,SRS6916252,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.92033,0.95428,0.21666,0.2245,0.86571,0.8678,0.74089,0.68247,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60033,SRR12103775,SRX8627946,SRS6916251,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,DMSO4 IP,GSM4644245,,tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217,DMSO4 IP,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217,GSM4644245,GSM4644245: DMSO4 IP; Danio rerio; RIP Seq,GSM4644245,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644245,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,D4_m6A-IP_S12_R1_001.fastq.gz D4_m6A-IP_S12_R2_001.fastq.gz,fastq fastq,2415539920.0,15891710.0,GSM4644245 r1,0:76 1:76,A:519904759;C:674887600;G:688106098;T:532387711;N:253752,76,76,,,519904759,674887600,688106098,532387711,253752,SRX8627946,SRS6916251,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.94931,0.94824,0.16515,0.16656,0.74858,0.7497,0.57724,0.58102,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60034,SRR12103774,SRX8627945,SRS6916250,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,DMSO3 IP,GSM4644244,,tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216,DMSO3 IP,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216,GSM4644244,GSM4644244: DMSO3 IP; Danio rerio; RIP Seq,GSM4644244,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644244,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,D3_m6A-IP_S11_R1_001.fastq.gz D3_m6A-IP_S11_R2_001.fastq.gz,fastq fastq,2419255408.0,15916154.0,GSM4644244 r1,0:76 1:76,A:524637988;C:675158080;G:687344217;T:531861650;N:253473,76,76,,,524637988,675158080,687344217,531861650,253473,SRX8627945,SRS6916250,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.93623,0.93621,0.18212,0.18165,0.74308,0.74426,0.60527,0.60757,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60035,SRR12103773,SRX8627944,SRS6916249,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,DMSO2 IP,GSM4644243,,tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215,DMSO2 IP,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215,GSM4644243,GSM4644243: DMSO2 IP; Danio rerio; RIP Seq,GSM4644243,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644243,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,D2_m6A-IP_S10_R1_001.fastq.gz D2_m6A-IP_S10_R2_001.fastq.gz,fastq fastq,2698406448.0,17752674.0,GSM4644243 r1,0:76 1:76,A:578126060;C:760791571;G:775423382;T:583783650;N:281785,76,76,,,578126060,760791571,775423382,583783650,281785,SRX8627944,SRS6916249,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.9433,0.94318,0.17976,0.1816,0.74992,0.75215,0.58844,0.61497,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60036,SRR12103772,SRX8627943,SRS6916248,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,DMSO1 IP,GSM4644242,,tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214,DMSO1 IP,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214,GSM4644242,GSM4644242: DMSO1 IP; Danio rerio; RIP Seq,GSM4644242,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644242,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,D1_m6A-IP_S9_R1_001.fastq.gz D1_m6A-IP_S9_R2_001.fastq.gz,fastq fastq,2588221344.0,17027772.0,GSM4644242 r1,0:76 1:76,A:552076254;C:730948542;G:744135059;T:560788856;N:272633,76,76,,,552076254,730948542,744135059,560788856,272633,SRX8627943,SRS6916248,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.93871,0.9398,0.17681,0.17588,0.74688,0.74915,0.59376,0.61045,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60037,SRR12103771,SRX8627942,SRS6916247,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,DMSO4 Input,GSM4644241,,tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1,DMSO4 Input,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:DMSO control|strain:AB|fraction:input control|antibody:n1,GSM4644241,GSM4644241: DMSO4 Input; Danio rerio; RIP Seq,GSM4644241,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644241,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,D4_INPUT_S4_R1_001.fastq.gz D4_INPUT_S4_R2_001.fastq.gz,fastq fastq,4085824752.0,26880426.0,GSM4644241 r1,0:76 1:76,A:734095239;C:1307425224;G:1339970208;T:703907493;N:426588,76,76,,,734095239,1307425224,1339970208,703907493,426588,SRX8627942,SRS6916247,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.94341,0.94693,0.21035,0.21294,0.86306,0.86571,0.66228,0.69648,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60038,SRR12103770,SRX8627941,SRS6916246,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,DMSO3 Input,GSM4644240,,tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1,DMSO3 Input,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:DMSO control|strain:AB|fraction:input control|antibody:n1,GSM4644240,GSM4644240: DMSO3 Input; Danio rerio; RIP Seq,GSM4644240,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644240,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,D3_INPUT_S3_R1_001.fastq.gz D3_INPUT_S3_R2_001.fastq.gz,fastq fastq,3627749800.0,23866775.0,GSM4644240 r1,0:76 1:76,A:677883991;C:1133504965;G:1166401920;T:649582074;N:376850,76,76,,,677883991,1133504965,1166401920,649582074,376850,SRX8627941,SRS6916246,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.92028,0.96282,0.2164,0.22913,0.86517,0.8661,0.73802,0.70578,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60039,SRR12103769,SRX8627940,SRS6916245,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,DMSO2 Input,GSM4644239,,tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1,DMSO2 Input,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:DMSO control|strain:AB|fraction:input control|antibody:n1,GSM4644239,GSM4644239: DMSO2 Input; Danio rerio; RIP Seq,GSM4644239,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644239,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,D2_INPUT_S2_R2_001.fastq.gz D2_INPUT_S2_R1_001.fastq.gz,fastq fastq,2991355592.0,19679971.0,GSM4644239 r1,0:76 1:76,A:555548434;C:937287598;G:965607991;T:532600162;N:311407,76,76,,,555548434,937287598,965607991,532600162,311407,SRX8627940,SRS6916245,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.92966,0.96538,0.21752,0.22835,0.86137,0.86701,0.71065,0.70316,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
60040,SRR12103768,SRX8627939,SRS6916244,SRP269097,PRJNA642647,PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos,GSE153436,Other,Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,pubmed:33064826,,DMSO1 Input,GSM4644238,,tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1,DMSO1 Input,Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf,78 hpf embryos,,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,,agent:DMSO control|strain:AB|fraction:input control|antibody:n1,GSM4644238,GSM4644238: DMSO1 Input; Danio rerio; RIP Seq,GSM4644238,,1,AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28±0.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.,GEO Accession:GSM4644238,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP269097,,,D1_INPUT_S1_R1_001.fastq.gz D1_INPUT_S1_R2_001.fastq.gz,fastq fastq,3551567552.0,23365576.0,GSM4644238 r1,0:76 1:76,A:659305531;C:1112775748;G:1146213503;T:632894453;N:378317,76,76,,,659305531,1112775748,1146213503,632894453,378317,SRX8627939,SRS6916244,SRA1091999,GEO,"Aluru Lab, Biology, Woods Hole Oceanographic Institution",2,0.92942,0.96366,0.21295,0.2231,0.8574,0.85934,0.75989,0.75855,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2020-06-28,Larval,Larval,Embryo Imprecise,All anatomical structures
63731,SRR13998081,SRX10375447,SRS8490053,SRP311218,PRJNA715461,RIP seq for Ddx3xb in zebrafish embryos,GSE169161,Other,We show that liquid liquid phase separation LLPS mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N terminal intrinsically disordered regions IDRs  and the gradually increased ATP concentration post fertilization promotes its aggregation capability. Ddx3xb deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation  further leading to developmental defect. The phenotype in Ddx3xb deficiency embryos can be efficiently rescued by condensed Ddx3xb  but not the Ddx3xb without xxx ability. Mechanistically  the condensation of Ddx3xb is vital for its RNA helicase activity  which is critical for involved in promoting translation efficiency of maternal mRNAs through opening five prime UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT  highlighting the critical role of protein phase separation in translational control and animal early development.    Overall design: RIP seq of 4 samples from Ddx3xb mRNA injected zebrafish embryos at xxx and 4 hpf including two biological replicates,parent bioproject:PRJNA715459,pubmed:35661831,,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
70712,SRR20077343,SRX16115141,SRS13777745,SRP385866,PRJNA857663,RIP seq for Cpeb1b in zebrafish embryos,GSE207904,Transcriptome Analysis,Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates,parent bioproject:PRJNA857656,,,Flag Cpeb1b replicate 2,GSM6322839,,source name:Flag Cpeb1b replicate 2|tissue:zebrafish embryos|genotype:wild type|age:16 hpf,Flag Cpeb1b replicate 2,The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with ‘‘–bowtie1’’. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples,Flag Cpeb1b replicate 2,,Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.,,tissue:zebrafish embryos|genotype:wild type|age:16 hpf,GSM6322839,GSM6322839: Flag Cpeb1b replicate 2; Danio rerio; RIP Seq,GSM6322839 r1,GSM6322839,1,Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385866,,loader:fastq load.py,Flag_Cpeb1b_replicate_2.R1.fq.gz Flag_Cpeb1b_replicate_2.R2.fq.gz,fastq fastq,14733801000.0,49112670.0,GSM6322839 r1,0:150 1:150,A:4141614412;C:3363207101;G:3881752054;T:3344596903;N:2630530,150,150,,,4141614412,3363207101,3881752054,3344596903,2630530,SRX16115141,SRS13777745,SRA1452503,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.05175,0.02071,0.01394,0.00703,0.99383,0.99758,0.80854,0.85616,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,full_length,other,smarter,bulk,unknown,unknown,,China,2022-07-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
70713,SRR20077344,SRX16115140,SRS13777744,SRP385866,PRJNA857663,RIP seq for Cpeb1b in zebrafish embryos,GSE207904,Transcriptome Analysis,Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates,parent bioproject:PRJNA857656,,,Flag Cpeb1b replicate 1,GSM6322838,,source name:Flag Cpeb1b replicate 1|tissue:zebrafish embryos|genotype:wild type|age:16 hpf,Flag Cpeb1b replicate 1,The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with ‘‘–bowtie1’’. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools’ intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples,Flag Cpeb1b replicate 1,,Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.,,tissue:zebrafish embryos|genotype:wild type|age:16 hpf,GSM6322838,GSM6322838: Flag Cpeb1b replicate 1; Danio rerio; RIP Seq,GSM6322838 r1,GSM6322838,1,Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 °C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP385866,,loader:fastq load.py,Flag_Cpeb1b_replicate_1.R1.fq.gz Flag_Cpeb1b_replicate_1.R2.fq.gz,fastq fastq,15482669700.0,51608899.0,GSM6322838 r1,0:150 1:150,A:4303443264;C:3570990345;G:4030059369;T:3575508224;N:2668498,150,150,,,4303443264,3570990345,4030059369,3575508224,2668498,SRX16115140,SRS13777744,SRA1452503,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.03751,0.01773,0.01056,0.00621,0.99346,0.99736,0.89693,0.8036,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,full_length,other,smarter,bulk,unknown,unknown,,China,2022-07-11,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
72695,SRR23071963,SRX19025119,SRS16444168,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,fac input rep2,GSM6932553,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing,fac input rep2,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf,GSM6932553,GSM6932553: fac input rep2; Danio rerio; RIP Seq,GSM6932553 r1,GSM6932553,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,fac_input_rep2.r1.fastq.gz fac_input_rep2.r2.fastq.gz,fastq fastq,2715443520.0,22628696.0,GSM6932553 r1,0:60 1:60,A:568252635;C:811004878;G:879629678;T:456548654;N:7675,60,60,,,568252635,811004878,879629678,456548654,7675,SRX19025119,SRS16444168,SRA1573941,University of Chicago,University of Chicago,2,0.76709,0.75848,0.06636,0.06594,0.96465,0.96617,0.79957,0.75254,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72696,SRR23071964,SRX19025118,SRS16444167,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,fac input rep1,GSM6932552,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing,fac input rep1,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf,GSM6932552,GSM6932552: fac input rep1; Danio rerio; RIP Seq,GSM6932552 r1,GSM6932552,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,fac_input_rep1.r1.fastq.gz fac_input_rep1.r2.fastq.gz,fastq fastq,2788666560.0,23238888.0,GSM6932552 r1,0:60 1:60,A:597611112;C:824776004;G:894293861;T:471977509;N:8074,60,60,,,597611112,824776004,894293861,471977509,8074,SRX19025118,SRS16444167,SRA1573941,University of Chicago,University of Chicago,2,0.75557,0.74928,0.06802,0.06744,0.96364,0.96508,0.80265,0.73963,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72697,SRR23071965,SRX19025117,SRS16444166,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,fac clip rep2,GSM6932551,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing,fac clip rep2,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf,GSM6932551,GSM6932551: fac clip rep2; Danio rerio; RIP Seq,GSM6932551 r1,GSM6932551,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,fac_clip_rep2.r1.fastq.gz fac_clip_rep2.r2.fastq.gz,fastq fastq,3636207480.0,30301729.0,GSM6932551 r1,0:60 1:60,A:856114407;C:984704325;G:1019721588;T:775657296;N:9864,60,60,,,856114407,984704325,1019721588,775657296,9864,SRX19025117,SRS16444166,SRA1573941,University of Chicago,University of Chicago,2,0.95337,0.93978,0.20127,0.22016,0.90295,0.90893,0.69108,0.66666,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72698,SRR23071966,SRX19025116,SRS16444165,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,fac clip rep1,GSM6932550,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing,fac clip rep1,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf,GSM6932550,GSM6932550: fac clip rep1; Danio rerio; RIP Seq,GSM6932550 r1,GSM6932550,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,fac_clip_rep1.r1.fastq.gz fac_clip_rep1.r2.fastq.gz,fastq fastq,4241534520.0,35346121.0,GSM6932550 r1,0:60 1:60,A:1001822053;C:1148816744;G:1187189848;T:903693863;N:12012,60,60,,,1001822053,1148816744,1187189848,903693863,12012,SRX19025116,SRS16444165,SRA1573941,University of Chicago,University of Chicago,2,0.9489,0.9407,0.19979,0.22138,0.90161,0.90741,0.67794,0.66231,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72699,SRR23071967,SRX19025115,SRS16444164,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,dfo input rep2,GSM6932549,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing,dfo input rep2,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf,GSM6932549,GSM6932549: dfo input rep2; Danio rerio; RIP Seq,GSM6932549 r1,GSM6932549,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,dfo_input_rep2.r1.fastq.gz dfo_input_rep2.r2.fastq.gz,fastq fastq,2472387240.0,20603227.0,GSM6932549 r1,0:60 1:60,A:522247513;C:735343841;G:798068271;T:416720603;N:7012,60,60,,,522247513,735343841,798068271,416720603,7012,SRX19025115,SRS16444164,SRA1573941,University of Chicago,University of Chicago,2,0.7577,0.75837,0.06797,0.06744,0.96437,0.96627,0.80292,0.74592,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72700,SRR23071968,SRX19025114,SRS16444163,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,dfo input rep1,GSM6932548,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing,dfo input rep1,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf,GSM6932548,GSM6932548: dfo input rep1; Danio rerio; RIP Seq,GSM6932548 r1,GSM6932548,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,dfo_input_rep1.fastq.gz dfo_input_rep1.r2.fastq.gz,fastq fastq,2546588760.0,21221573.0,GSM6932548 r1,0:60 1:60,A:536450815;C:753080253;G:819027741;T:438022880;N:7071,60,60,,,536450815,753080253,819027741,438022880,7071,SRX19025114,SRS16444163,SRA1573941,University of Chicago,University of Chicago,2,0.75957,0.75514,0.06963,0.06896,0.96345,0.96526,0.80322,0.73584,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72701,SRR23071969,SRX19025113,SRS16444162,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,dfo clip rep2,GSM6932547,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing,dfo clip rep2,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf,GSM6932547,GSM6932547: dfo clip rep2; Danio rerio; RIP Seq,GSM6932547 r1,GSM6932547,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,dfo_clip_rep2.r1.fastq.gz dfo_clip_rep2.r2.fastq.gz,fastq fastq,4151061480.0,34592179.0,GSM6932547 r1,0:60 1:60,A:968004394;C:1130874104;G:1164829960;T:887341478;N:11544,60,60,,,968004394,1130874104,1164829960,887341478,11544,SRX19025113,SRS16444162,SRA1573941,University of Chicago,University of Chicago,2,0.92425,0.93056,0.20043,0.2242,0.8966,0.901,0.68964,0.62588,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72702,SRR23071970,SRX19025112,SRS16444161,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,dfo clip rep1,GSM6932546,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing,dfo clip rep1,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf,GSM6932546,GSM6932546: dfo clip rep1; Danio rerio; RIP Seq,GSM6932546 r1,GSM6932546,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,dfo_clip_rep1.r1.fastq.gz dfo_clip_rep1.r2.fastq.gz,fastq fastq,3549376560.0,29578138.0,GSM6932546 r1,0:60 1:60,A:829453498;C:966398146;G:998787767;T:754727094;N:10055,60,60,,,829453498,966398146,998787767,754727094,10055,SRX19025112,SRS16444161,SRA1573941,University of Chicago,University of Chicago,2,0.94985,0.93128,0.20616,0.22409,0.89548,0.90055,0.67094,0.65117,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72703,SRR23071971,SRX19025111,SRS16444160,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,ctrl input rep2,GSM6932545,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment|geo loc name:missing|collection date:missing,ctrl input rep2,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment,GSM6932545,GSM6932545: ctrl input rep2; Danio rerio; RIP Seq,GSM6932545 r1,GSM6932545,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,ctrl_input_rep2.r1.fastq.gz ctrl_input_rep2.r2.fastq.gz,fastq fastq,2305351440.0,19211262.0,GSM6932545 r1,0:60 1:60,A:494731676;C:683635423;G:735706555;T:391271420;N:6366,60,60,,,494731676,683635423,735706555,391271420,6366,SRX19025111,SRS16444160,SRA1573941,University of Chicago,University of Chicago,2,0.75012,0.76494,0.06496,0.06503,0.9696,0.97023,0.80848,0.76006,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72704,SRR23071972,SRX19025110,SRS16444159,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,ctrl input rep1,GSM6932544,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment|geo loc name:missing|collection date:missing,ctrl input rep1,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment,GSM6932544,GSM6932544: ctrl input rep1; Danio rerio; RIP Seq,GSM6932544 r1,GSM6932544,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,ctrl_input_rep1.r1.fastq.gz ctrl_input_rep1.r2.fastq.gz,fastq fastq,2870115000.0,23917625.0,GSM6932544 r1,0:60 1:60,A:616586993;C:849261640;G:916690149;T:487568187;N:8031,60,60,,,616586993,849261640,916690149,487568187,8031,SRX19025110,SRS16444159,SRA1573941,University of Chicago,University of Chicago,2,0.76321,0.76237,0.06602,0.06566,0.97064,0.96903,0.68553,0.75314,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72705,SRR23071973,SRX19025109,SRS16444158,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,ctrl clip rep2,GSM6932543,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment|geo loc name:missing|collection date:missing,ctrl clip rep2,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment,GSM6932543,GSM6932543: ctrl clip rep2; Danio rerio; RIP Seq,GSM6932543 r1,GSM6932543,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,ctrl_clip_rep2.r1.fastq.gz ctrl_clip_rep2.r2.fastq.gz,fastq fastq,3309978960.0,27583158.0,GSM6932543 r1,0:60 1:60,A:774105538;C:895792317;G:931799487;T:708272623;N:8995,60,60,,,774105538,895792317,931799487,708272623,8995,SRX19025109,SRS16444158,SRA1573941,University of Chicago,University of Chicago,2,0.94553,0.92262,0.21092,0.22735,0.90985,0.91407,0.67372,0.67171,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
72706,SRR23071974,SRX19025108,SRS16444157,SRP417272,PRJNA923391,MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function,GSE222803,Other,Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC,,pubmed:38366571,,ctrl clip rep1,GSM6932542,,source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment|geo loc name:missing|collection date:missing,ctrl clip rep1,Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm,whole embryo,For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4°C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20°C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.,tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment,GSM6932542,GSM6932542: ctrl clip rep1; Danio rerio; RIP Seq,GSM6932542 r1,GSM6932542,1,For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 °C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 °C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 °C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 × Halt™ Protease and Phosphatase Inhibitor Cocktail  1 × RNaseOUT Recombinant Ribonuclease Inhibitor at 4 °C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/μL RNase T1 Thermo Scientific at 22 °C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP417272,,loader:fastq load.py,ctrl_clip_rep1.r1.fastq.gz ctrl_clip_rep1.r2.fastq.gz,fastq fastq,3392768880.0,28273074.0,GSM6932542 r1,0:60 1:60,A:795387316;C:918606802;G:949982957;T:728782720;N:9085,60,60,,,795387316,918606802,949982957,728782720,9085,SRX19025108,SRS16444157,SRA1573941,University of Chicago,University of Chicago,2,0.92844,0.92193,0.20693,0.22683,0.90826,0.91297,0.68754,0.67062,60,60,B,B,biological fallback assumption,illumina,novaseq_era,full_length,small_rna,smarter,bulk,unknown,unknown,,United States,2023-01-12,Multi-stage,Multi-stage,Whole Organism,All anatomical structures
74097,SRR23433707,SRX19347585,SRS16745103,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,mt input rep2,GSM7039976,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing,mt input rep2,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1,GSM7039976,GSM7039976: mt input rep2; Danio rerio; RIP Seq,GSM7039976 r1,GSM7039976,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,mt2_input_R1.fastq.gz mt2_input_R2.fastq.gz,fastq fastq,11987520719.0,46102921.0,GSM7039976 r1,0:129.98 1:130.04,A:2818961833;C:3185310727;G:3125514774;T:2857679978;N:53407,129,130,,,2818961833,3185310727,3125514774,2857679978,53407,SRX19347585,SRS16745103,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.92498,0.92723,0.26901,0.26318,0.72691,0.72646,0.55297,0.56674,103,103,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74098,SRR23433708,SRX19347584,SRS16745102,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,mt IP  rep2,GSM7039975,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing,mt IP  rep2,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A,GSM7039975,GSM7039975: mt IP  rep2; Danio rerio; RIP Seq,GSM7039975 r1,GSM7039975,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,mt2_IP_R1.fastq.gz mt2_IP_R2.fastq.gz,fastq fastq,10153956215.0,38248544.0,GSM7039975 r1,0:132.74 1:132.73,A:2745473943;C:2337991849;G:2337827470;T:2732618213;N:44740,132,132,,,2745473943,2337991849,2337827470,2732618213,44740,SRX19347584,SRS16745102,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.91716,0.92124,0.17169,0.17213,0.69057,0.69092,0.45478,0.4582,133,133,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74099,SRR23433709,SRX19347583,SRS16745101,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,mt input rep1,GSM7039974,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing,mt input rep1,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1,GSM7039974,GSM7039974: mt input rep1; Danio rerio; RIP Seq,GSM7039974 r1,GSM7039974,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,mt1_input_R1.fastq.gz mt1_input_R2.fastq.gz,fastq fastq,11979139891.0,42665152.0,GSM7039974 r1,0:140.37 1:140.40,A:3143624979;C:2854874515;G:2775482425;T:3204809556;N:348416,140,140,,,3143624979,2854874515,2775482425,3204809556,348416,SRX19347583,SRS16745101,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.89189,0.90001,0.35263,0.34917,0.71058,0.70907,0.54777,0.55293,125,125,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74100,SRR23433710,SRX19347582,SRS16745100,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,mt IP  rep1,GSM7039973,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing,mt IP  rep1,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A,GSM7039973,GSM7039973: mt IP  rep1; Danio rerio; RIP Seq,GSM7039973 r1,GSM7039973,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,mt1_IP_R1.fastq.gz mt1_IP_R2.fastq.gz,fastq fastq,12145897814.0,43352862.0,GSM7039973 r1,0:140.09 1:140.07,A:3459248498;C:2615706052;G:2628261332;T:3442334843;N:347089,140,140,,,3459248498,2615706052,2628261332,3442334843,347089,SRX19347582,SRS16745100,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.86681,0.87664,0.304,0.305,0.68012,0.67831,0.44055,0.4418,142,142,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74101,SRR23433711,SRX19347581,SRS16745099,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,sibling input rep2,GSM7039972,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing,sibling input rep2,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1,GSM7039972,GSM7039972: sibling input rep2; Danio rerio; RIP Seq,GSM7039972 r1,GSM7039972,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,sibling2_input_R1.fastq.gz sibling2_input_R2.fastq.gz,fastq fastq,12272791017.0,47579480.0,GSM7039972 r1,0:128.94 1:129.00,A:2905993856;C:3237323144;G:3186607999;T:2942811604;N:54414,128,129,,,2905993856,3237323144,3186607999,2942811604,54414,SRX19347581,SRS16745099,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.92733,0.92947,0.27234,0.26711,0.72391,0.72409,0.52625,0.55052,126,126,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74102,SRR23433712,SRX19347580,SRS16745098,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,sibling IP  rep2,GSM7039971,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing,sibling IP  rep2,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A,GSM7039971,GSM7039971: sibling IP  rep2; Danio rerio; RIP Seq,GSM7039971 r1,GSM7039971,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,sibling2_IP_R1.fastq.gz sibling2_IP_R2.fastq.gz,fastq fastq,10402768351.0,39113148.0,GSM7039971 r1,0:132.99 1:132.98,A:2806053427;C:2400476074;G:2403977422;T:2792214821;N:46607,132,132,,,2806053427,2400476074,2403977422,2792214821,46607,SRX19347580,SRS16745098,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.90198,0.9063,0.18008,0.18091,0.69428,0.69396,0.44811,0.42925,147,147,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74103,SRR23433713,SRX19347579,SRS16745097,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,sibling input rep1,GSM7039970,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing,sibling input rep1,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1,GSM7039970,GSM7039970: sibling input rep1; Danio rerio; RIP Seq,GSM7039970 r1,GSM7039970,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,sibling1_input_R1.fastq.gz sibling1_input_R2.fastq.gz,fastq fastq,13094981449.0,46647417.0,GSM7039970 r1,0:140.35 1:140.37,A:3434495131;C:3120669719;G:3036482303;T:3502963330;N:370966,140,140,,,3434495131,3120669719,3036482303,3502963330,370966,SRX19347579,SRS16745097,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.89276,0.90193,0.352,0.3489,0.70905,0.70719,0.52165,0.52427,142,142,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure