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
32033,SRR28976522,SRX24505963,SRS21254128,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,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 elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  Rbm24a Knock in IP,GSM8259538,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in IP,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 WT and 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 total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:GFP,GSM8259538,GSM8259538: Zebrafish  RIP seq  Rbm24a Knock in IP; Danio rerio; RIP Seq,GSM8259538 r1,GSM8259538,1,Total RNAs were extracted from WT and 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 total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_KI_IP_R2.fq.gz RIP_KI_IP_R1.fq.gz,fastq fastq,6457893104.0,21383752.0,GSM8259538 r1,0:151 1:151,A:975588225;C:2019180290;G:2469634919;T:992947702;N:541968,151,151,,,975588225,2019180290,2469634919,992947702,541968,SRX24505963,SRS21254128,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.90304,0.86018,0.20083,0.20471,0.96382,0.96743,0.96102,0.98876,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32034,SRR28976523,SRX24505962,SRS21254127,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,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 elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  wild type IP,GSM8259537,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  wild type IP,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 WT and 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 total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:GFP,GSM8259537,GSM8259537: Zebrafish  RIP seq  wild type IP; Danio rerio; RIP Seq,GSM8259537 r1,GSM8259537,1,Total RNAs were extracted from WT and 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 total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_WT_IP_R2.fq.gz RIP_WT_IP_R1.fq.gz,fastq fastq,4501412680.0,14905340.0,GSM8259537 r1,0:151 1:151,A:651609366;C:1285679784;G:1901211768;T:662533141;N:378621,151,151,,,651609366,1285679784,1901211768,662533141,378621,SRX24505962,SRS21254127,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.96426,0.81361,0.26579,0.2253,0.97784,0.97806,0.8699,0.93379,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32035,SRR28976524,SRX24505961,SRS21254126,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,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 elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  Rbm24a Knock in input,GSM8259536,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  Rbm24a Knock in input,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 WT and 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 total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:Rbm24a Knock in|antibody:input,GSM8259536,GSM8259536: Zebrafish  RIP seq  Rbm24a Knock in input; Danio rerio; RIP Seq,GSM8259536 r1,GSM8259536,1,Total RNAs were extracted from WT and 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 total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_KI_Input_R2.fq.gz RIP_KI_Input_R1.fq.gz,fastq fastq,9539398726.0,31587413.0,GSM8259536 r1,0:151 1:151,A:2233069830;C:2078359171;G:3009942870;T:2217201959;N:824896,151,151,,,2233069830,2078359171,3009942870,2217201959,824896,SRX24505961,SRS21254126,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.90112,0.81448,0.02415,0.01993,0.79287,0.79807,0.47884,0.48186,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
32036,SRR28976525,SRX24505960,SRS21254125,SRP506702,PRJNA1109723,rbm24a is an organizer component of germ plasm to determine germ cell fate,GSE267086,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 elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish  we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.,,,,Zebrafish  RIP seq  wild type input,GSM8259535,,source name:whole embryo|tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input|geo loc name:missing|collection date:missing,Zebrafish  RIP seq  wild type input,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 WT and 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 total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer’s instructions.,Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C,tissue:whole embryo|developmental stage:4 cell stage|cell type:embryonic cell|genotype:wild type|antibody:input,GSM8259535,GSM8259535: Zebrafish  RIP seq  wild type input; Danio rerio; RIP Seq,GSM8259535 r1,GSM8259535,1,Total RNAs were extracted from WT and 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 total RNA was used for following library preparation. The polyA mRNA isolation was performed  using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high  temperature. Priming was performed using Random Primers. First strand cDNA and the second strand  cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and  add a dA tailing in one reaction  followed by a T A ligation to add adaptors to both ends. Size selection of  Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by  PCR using P5 and P7 primers and the PCR products were validated.  Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to  manufacturer's instructions.,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP506702,,,RIP_WT_Input_R2.fq.gz RIP_WT_Input_R1.fq.gz,fastq fastq,14180410302.0,46955001.0,GSM8259535 r1,0:151 1:151,A:3380011534;C:2883841476;G:4593876270;T:3321465622;N:1215400,151,151,,,3380011534,2883841476,4593876270,3321465622,1215400,SRX24505960,SRS21254125,SRA1863578,"Ang Li, College of Life Sciences, shandong university","Ang Li, College of Life Sciences, shandong university",2,0.86497,0.64685,0.04432,0.02854,0.79324,0.8031,0.52927,0.53304,151,151,B,B,mate2-mate1 similar by mapping diff,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,China,2024-05-09,Cleavage,Embryo,Whole Organism,All anatomical structures
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
40701,SRR3231363,SRX1637111,SRS1342926,SRP071849,PRJNA315400,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq],GSE79161,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.,parent bioproject:PRJNA315403,pubmed:30086300,,Input 3,GSM2087141,,tissue:Zebrafish Zygotes|fraction:Input,Input 3,Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.,Zebrafish Zygotes,,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,Zebrafish were maintained under standard conditions.,fraction:Input,GSM2087141,GSM2087141: Input 3; Danio rerio; RIP Seq,GSM2087141,,1,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,GEO Accession:GSM2087141,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP071849,,,WT_Input_3.fastq.gz,fastq,1902296226.0,37299926.0,GSM2087141 r1,0:51,A:466290166;C:465344039;G:486942278;T:483240280;N:479463,51,,,,466290166,465344039,486942278,483240280,479463,SRX1637111,SRS1342926,SRA385813,GEO,"Rene Ketting, RNA silencing, IMB",1,0.85793,,0.14814,,0.79941,,0.55214,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2016-03-13,Zygote,Embryo,Oocyte,Reproductive System
40702,SRR3231362,SRX1637110,SRS1342927,SRP071849,PRJNA315400,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq],GSE79161,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.,parent bioproject:PRJNA315403,pubmed:30086300,,Input 2,GSM2087140,,tissue:Zebrafish Zygotes|fraction:Input,Input 2,Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.,Zebrafish Zygotes,,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,Zebrafish were maintained under standard conditions.,fraction:Input,GSM2087140,GSM2087140: Input 2; Danio rerio; RIP Seq,GSM2087140,,1,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,GEO Accession:GSM2087140,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP071849,,,WT_Input_2.fastq.gz,fastq,1540737999.0,30210549.0,GSM2087140 r1,0:51,A:380481772;C:379741192;G:395453141;T:384675313;N:386581,51,,,,380481772,379741192,395453141,384675313,386581,SRX1637110,SRS1342927,SRA385813,GEO,"Rene Ketting, RNA silencing, IMB",1,0.8787,,0.14935,,0.79202,,0.54381,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2016-03-13,Zygote,Embryo,Oocyte,Reproductive System
40703,SRR3231361,SRX1637109,SRS1342928,SRP071849,PRJNA315400,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq],GSE79161,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.,parent bioproject:PRJNA315403,pubmed:30086300,,Input 1,GSM2087139,,tissue:Zebrafish Zygotes|fraction:Input,Input 1,Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.,Zebrafish Zygotes,,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,Zebrafish were maintained under standard conditions.,fraction:Input,GSM2087139,GSM2087139: Input 1; Danio rerio; RIP Seq,GSM2087139,,1,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,GEO Accession:GSM2087139,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP071849,,,WT_Input_1.fastq.gz,fastq,1109818905.0,21761155.0,GSM2087139 r1,,,,,,,,,,,,SRX1637109,SRS1342928,SRA385813,GEO,"Rene Ketting, RNA silencing, IMB",1,0.87467,,0.18794,,0.79411,,0.63378,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2016-03-13,Zygote,Embryo,Oocyte,Reproductive System
40704,SRR3231360,SRX1637108,SRS1342929,SRP071849,PRJNA315400,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq],GSE79161,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.,parent bioproject:PRJNA315403,pubmed:30086300,,Tdrd6a IP 3,GSM2087138,,tissue:Zebrafish Zygotes|fraction:Tdrd6a IP,Tdrd6a IP 3,Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.,Zebrafish Zygotes,,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,Zebrafish were maintained under standard conditions.,fraction:Tdrd6a IP,GSM2087138,GSM2087138: Tdrd6a IP 3; Danio rerio; RIP Seq,GSM2087138,,1,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,GEO Accession:GSM2087138,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP071849,,,WT_Tdrd6a_IP_3.fastq.gz,fastq,843641439.0,16541989.0,GSM2087138 r1,0:51,A:216465581;C:196892096;G:207722567;T:222361382;N:199813,51,,,,216465581,196892096,207722567,222361382,199813,SRX1637108,SRS1342929,SRA385813,GEO,"Rene Ketting, RNA silencing, IMB",1,0.84615,,0.08957,,0.78768,,0.50612,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2016-03-13,Zygote,Embryo,Oocyte,Reproductive System
40705,SRR3231359,SRX1637107,SRS1342930,SRP071849,PRJNA315400,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq],GSE79161,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.,parent bioproject:PRJNA315403,pubmed:30086300,,Tdrd6a IP 2,GSM2087137,,tissue:Zebrafish Zygotes|fraction:Tdrd6a IP,Tdrd6a IP 2,Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.,Zebrafish Zygotes,,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,Zebrafish were maintained under standard conditions.,fraction:Tdrd6a IP,GSM2087137,GSM2087137: Tdrd6a IP 2; Danio rerio; RIP Seq,GSM2087137,,1,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,GEO Accession:GSM2087137,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP071849,,,WT_Tdrd6a_IP_2.fastq.gz,fastq,391198050.0,7670550.0,GSM2087137 r1,0:51,A:99015594;C:91525929;G:97155710;T:103371571;N:129246,51,,,,99015594,91525929,97155710,103371571,129246,SRX1637107,SRS1342930,SRA385813,GEO,"Rene Ketting, RNA silencing, IMB",1,0.85778,,0.12015,,0.80515,,0.47541,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2016-03-13,Zygote,Embryo,Oocyte,Reproductive System
40706,SRR3231358,SRX1637106,SRS1342931,SRP071849,PRJNA315400,Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq],GSE79161,Transcriptome Analysis,Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.,parent bioproject:PRJNA315403,pubmed:30086300,,Tdrd6a IP 1,GSM2087136,,tissue:Zebrafish Zygotes|fraction:Tdrd6a IP,Tdrd6a IP 1,Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.,Zebrafish Zygotes,,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,Zebrafish were maintained under standard conditions.,fraction:Tdrd6a IP,GSM2087136,GSM2087136: Tdrd6a IP 1; Danio rerio; RIP Seq,GSM2087136,,1,mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.,GEO Accession:GSM2087136,RIP-Seq,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP071849,,,WT_Tdrd6a_IP_1.fastq.gz,fastq,1927415052.0,37792452.0,GSM2087136 r1,0:51,A:498125298;C:444860381;G:468826607;T:515142356;N:460410,51,,,,498125298,444860381,468826607,515142356,460410,SRX1637106,SRS1342931,SRA385813,GEO,"Rene Ketting, RNA silencing, IMB",1,0.86194,,0.09753,,0.80146,,0.47808,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,other,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,Germany,2016-03-13,Zygote,Embryo,Oocyte,Reproductive System
41511,SRR5004963,SRX2336797,SRS1790193,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,zebrafish embryos ythdf2 RIP rep2,GSM2386192,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,zebrafish embryos ythdf2 RIP rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software,zebrafish embryos,,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,GSM2386192,GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq,GSM2386192,,1,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386192,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz,fastq fastq,4007024510.0,19836755.0,GSM2386192 r1,0:101 1:101,A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309,101,101,,,769487104,1245093129,1251328145,740377823,738309,SRX2336797,SRS1790193,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.97768,0.97802,0.22786,0.21743,0.89885,0.89968,0.77584,0.83808,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41512,SRR5004962,SRX2336796,SRS1790194,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,zebrafish embryos ythdf2 RIP rep1,GSM2386191,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,zebrafish embryos ythdf2 RIP rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software,zebrafish embryos,,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,GSM2386191,GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq,GSM2386191,,1,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386191,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP092907,,,ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz,fastq fastq,6144583662.0,30418731.0,GSM2386191 r1,0:101 1:101,A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305,101,101,,,1227614258,1869131844,1825793436,1220118819,1925305,SRX2336796,SRS1790194,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.96857,0.96917,0.23397,0.22377,0.89832,0.90147,0.78619,0.8258,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
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
49539,SRR8937005,SRX5717518,SRS4655938,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP INPUT 2hpf rep2,GSM3732425,,source name:RIP INPUT 2hpf|strain:AB strain|age:2 hpf|tissue:whole embryo,RIP INPUT 2hpf rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP INPUT 2hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:2 hpf|tissue:whole embryo,GSM3732425,GSM3732425: RIP INPUT 2hpf rep2; Danio rerio; RIP Seq,GSM3732425,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732425,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP-INPUT_2hpf_rep2_R1.fastq.gz RIP-INPUT_2hpf_rep2_R2.fastq.gz,fastq fastq,16388119500.0,54627065.0,GSM3732425 r1,0:150 1:150,A:3232127065;C:4976385987;G:5052844082;T:3122288663;N:4473703,150,150,,,3232127065,4976385987,5052844082,3122288663,4473703,SRX5717518,SRS4655938,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.98209,0.9812,0.33332,0.33565,0.93811,0.94186,0.95153,0.95984,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Cleavage,Embryo,Whole Organism,All anatomical structures
49540,SRR8937004,SRX5717517,SRS4655937,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP INPUT 2hpf rep1,GSM3732424,,source name:RIP INPUT 2hpf|strain:AB strain|age:2 hpf|tissue:whole embryo,RIP INPUT 2hpf rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP INPUT 2hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:2 hpf|tissue:whole embryo,GSM3732424,GSM3732424: RIP INPUT 2hpf rep1; Danio rerio; RIP Seq,GSM3732424,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732424,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP-INPUT_2hpf_rep1_R1.fastq.gz RIP-INPUT_2hpf_rep1_R2.fastq.gz,fastq fastq,18857336400.0,62857788.0,GSM3732424 r1,0:150 1:150,A:3116761123;C:6239715125;G:6450542871;T:3049605751;N:711530,150,150,,,3116761123,6239715125,6450542871,3049605751,711530,SRX5717517,SRS4655937,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.97874,0.96891,0.03494,0.03355,0.92693,0.93456,0.9502,0.94986,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Cleavage,Embryo,Whole Organism,All anatomical structures
49541,SRR8937003,SRX5717516,SRS4655936,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP INPUT 0hpf rep2,GSM3732423,,source name:RIP INPUT 0hpf|strain:AB strain|age:0 hpf|tissue:whole embryo,RIP INPUT 0hpf rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP INPUT 0hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:0 hpf|tissue:whole embryo,GSM3732423,GSM3732423: RIP INPUT 0hpf rep2; Danio rerio; RIP Seq,GSM3732423,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732423,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP-INPUT_0hpf_rep2_R1.fastq.gz RIP-INPUT_0hpf_rep2_R2.fastq.gz,fastq fastq,17402218800.0,58007396.0,GSM3732423 r1,0:150 1:150,A:3416144403;C:5315174821;G:5345201218;T:3320906221;N:4792137,150,150,,,3416144403,5315174821,5345201218,3320906221,4792137,SRX5717516,SRS4655936,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.9819,0.9814,0.33605,0.34016,0.93458,0.93963,0.90172,0.91272,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Zygote,Embryo,Whole Organism,All anatomical structures
49542,SRR8937002,SRX5717515,SRS4655935,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP INPUT 0hpf rep1,GSM3732422,,source name:RIP INPUT 0hpf|strain:AB strain|age:0 hpf|tissue:whole embryo,RIP INPUT 0hpf rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP INPUT 0hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:0 hpf|tissue:whole embryo,GSM3732422,GSM3732422: RIP INPUT 0hpf rep1; Danio rerio; RIP Seq,GSM3732422,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732422,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP-INPUT_0hpf_rep1_R1.fastq.gz RIP-INPUT_0hpf_rep1_R2.fastq.gz,fastq fastq,16615204800.0,55384016.0,GSM3732422 r1,0:150 1:150,A:2869477028;C:5392959051;G:5575878422;T:2776252538;N:637761,150,150,,,2869477028,5392959051,5575878422,2776252538,637761,SRX5717515,SRS4655935,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.97584,0.96561,0.04007,0.03832,0.9262,0.933,0.94642,0.94376,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Zygote,Embryo,Whole Organism,All anatomical structures
49543,SRR8937001,SRX5717514,SRS4655934,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP 2hpf rep2,GSM3732421,,source name:RIP 2hpf|strain:AB strain|age:2 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,RIP 2hpf rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP 2hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:2 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,GSM3732421,GSM3732421: RIP 2hpf rep2; Danio rerio; RIP Seq,GSM3732421,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732421,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP_2hpf_rep2_R1.fastq.gz RIP_2hpf_rep2_R2.fastq.gz,fastq fastq,17557024800.0,58523416.0,GSM3732421 r1,0:150 1:150,A:4454737772;C:4407385601;G:4364085079;T:4328962997;N:1853351,150,150,,,4454737772,4407385601,4364085079,4328962997,1853351,SRX5717514,SRS4655934,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.96216,0.96226,0.08174,0.08009,0.76907,0.77693,0.68824,0.65939,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Cleavage,Embryo,Whole Organism,All anatomical structures
49544,SRR8937000,SRX5717513,SRS4655933,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP 2hpf rep1,GSM3732420,,source name:RIP 2hpf|strain:AB strain|age:2 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,RIP 2hpf rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP 2hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:2 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,GSM3732420,GSM3732420: RIP 2hpf rep1; Danio rerio; RIP Seq,GSM3732420,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732420,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP_2hpf_rep1_R1.fastq.gz RIP_2hpf_rep1_R2.fastq.gz,fastq fastq,5656083600.0,18853612.0,GSM3732420 r1,0:150 1:150,A:1244757394;C:1581273853;G:1666307178;T:1162885398;N:859777,150,150,,,1244757394,1581273853,1666307178,1162885398,859777,SRX5717513,SRS4655933,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.80705,0.80575,0.2454,0.24923,0.85478,0.85644,0.83319,0.80065,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Cleavage,Embryo,Whole Organism,All anatomical structures
49545,SRR8936999,SRX5717512,SRS4655932,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP 0hpf rep2,GSM3732419,,source name:RIP 0hpf|strain:AB strain|age:0 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,RIP 0hpf rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP 0hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:0 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,GSM3732419,GSM3732419: RIP 0hpf rep2; Danio rerio; RIP Seq,GSM3732419,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732419,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP_0hpf_rep2_R1.fastq.gz RIP_0hpf_rep2_R2.fastq.gz,fastq fastq,14319153300.0,47730511.0,GSM3732419 r1,0:150 1:150,A:3633266473;C:3581763715;G:3602109377;T:3500497801;N:1515934,150,150,,,3633266473,3581763715,3602109377,3500497801,1515934,SRX5717512,SRS4655932,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.96309,0.96299,0.09978,0.09922,0.80012,0.80635,0.7641,0.76535,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Zygote,Embryo,Whole Organism,All anatomical structures
49546,SRR8936998,SRX5717511,SRS4655931,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP 0hpf rep1,GSM3732418,,source name:RIP 0hpf|strain:AB strain|age:0 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,RIP 0hpf rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.1.1. MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,RIP 0hpf,,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|age:0 hpf|tissue:whole embryo|rip antibody:rabbit polyclonal anti Ybx1 antibody,GSM3732418,GSM3732418: RIP 0hpf rep1; Danio rerio; RIP Seq,GSM3732418,,1,Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol® Reagent Ambion. mRNA was extracted with using Dynabeads® mRNA Purification Kit Ambion and subjected to TURBO™ DNase Invitrogen treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA BisSeq library construction. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3732418,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP_0hpf_rep1_R1.fastq.gz RIP_0hpf_rep1_R2.fastq.gz,fastq fastq,7807878000.0,26026260.0,GSM3732418 r1,0:150 1:150,A:1698013251;C:2200605244;G:2305251364;T:1602824248;N:1183893,150,150,,,1698013251,2200605244,2305251364,1602824248,1183893,SRX5717511,SRS4655931,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.89154,0.89105,0.26373,0.26886,0.82477,0.827,0.79125,0.77711,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2019-04-22,Zygote,Embryo,Whole Organism,All anatomical structures
49549,SRR7942636,SRX4776901,SRS3857441,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP 4hpf rep2,GSM3406902,,source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo,RIP 4hpf rep2,RIP seq and iCLIP seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10  respectively. RIP seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. iCLIP: To identify the Ybx1 targets’ locus  the mode of truncation calling was performed. For each truncation position  the coverages of unique tag k and truncations m were determined by CIMS.pl program CLIP Tool Kit  CTK. The sites were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,Zebrafish embryo,,RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo,GSM3406902,GSM3406902: RIP 4hpf rep2; Danio rerio; RIP Seq,GSM3406902,,1,RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3406902,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP_4hpf_rep2_R1.fastq.gz RIP_4hpf_rep2_R2.fastq.gz,fastq fastq,22888305600.0,76294352.0,GSM3406902 r1,0:150 1:150,A:5927520807;C:4846894836;G:4996844576;T:7111789925;N:5255456,150,150,,,5927520807,4846894836,4996844576,7111789925,5255456,SRX4776901,SRS3857441,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.2704,0.17205,0.06114,0.06961,0.95879,0.9698,0.94515,0.83252,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2018-09-28,Blastula,Embryo,Whole Organism,All anatomical structures
49550,SRR7942635,SRX4776900,SRS3857440,SRP162876,PRJNA493828,Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.,GSE120646,Other,The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBOâ„¢ DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90°C in 10× RNA Fragmentation Reagent Ambion  then stopped by 10× RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 µl bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 µM hydroquinone Sigma and subjected to heat incubation at 75°C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 °C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 µl of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.,parent bioproject:PRJNA534030,,,RIP 4hpf rep1,GSM3406901,,source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo,RIP 4hpf rep1,RIP seq and iCLIP seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10  respectively. RIP seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools’ intersectBed. iCLIP: To identify the Ybx1 targets’ locus  the mode of truncation calling was performed. For each truncation position  the coverages of unique tag k and truncations m were determined by CIMS.pl program CLIP Tool Kit  CTK. The sites were annotated by applying BEDTools’ intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.,Zebrafish embryo,,RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,,strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo,GSM3406901,GSM3406901: RIP 4hpf rep1; Danio rerio; RIP Seq,GSM3406901,,1,RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/μl RNasin by rotating at 4°C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4°C for 1 h. 50 μl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 μl Protein A Dynabeads for 4 h at 4°C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/µl RNasin for eight times and once with 1ml ice cold 1× PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55°C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO™ DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.,GEO Accession:GSM3406901,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP162876,,,RIP_4hpf_rep1_R1.fastq.gz RIP_4hpf_rep1_R2.fastq.gz,fastq fastq,19929300600.0,66431002.0,GSM3406901 r1,0:150 1:150,A:5076575451;C:4235012507;G:4442151234;T:6170975339;N:4586069,150,150,,,5076575451,4235012507,4442151234,6170975339,4586069,SRX4776900,SRS3857440,SRA786939,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.27932,0.16557,0.06585,0.06178,0.95692,0.96844,0.94238,0.84334,150,150,B,B,mate2-mate1 similar by mapping diff,illumina,hiseq_era,full_length,random_priming,smarter,bulk,clip,iclip,,China,2018-09-28,Blastula,Embryo,Whole Organism,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