{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\" and experiment.library_strategy = \"RIP-Seq\"", "rows": [[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.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in IP", "GSM8259538", null, "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", null, "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 \u00b5g/each sample. 1 \u03bcg 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\u2019s 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 \u00b5g/each sample. 1 \u03bcg 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506702", null, null, "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, null, null, 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", null, "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.", null, null, null, "Zebrafish  RIP seq  wild type IP", "GSM8259537", null, "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", null, "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 \u00b5g/each sample. 1 \u03bcg 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\u2019s 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 \u00b5g/each sample. 1 \u03bcg 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506702", null, null, "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, null, null, 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", null, "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.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in input", "GSM8259536", null, "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", null, "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 \u00b5g/each sample. 1 \u03bcg 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\u2019s 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 \u00b5g/each sample. 1 \u03bcg 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506702", null, null, "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, null, null, 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", null, "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.", null, null, null, "Zebrafish  RIP seq  wild type input", "GSM8259535", null, "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", null, "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 \u00b5g/each sample. 1 \u03bcg 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\u2019s 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 \u00b5g/each sample. 1 \u03bcg 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.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP506702", null, null, "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, null, null, 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", null, "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.", null, null, null, "Zebrafish ac4C", "GSM8372406", null, "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", null, "Total RNA was extracted according to manufacturer\u2019s instruction. The stranded RNA sequencing library was constructed by KC DigitalTM Stranded mRNA Library Prep Kit for Illumina\u00ae Catalog NO. DR08502  Wuhan Seqhealth Co.  Ltd. China following the manufacturer\u2019s 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", null, "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\u00ae 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", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP517393", null, null, "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, null, null, 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", null, "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.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in2 IP2", "GSM8759069", null, "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", null, "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 \u00b5g/each sample. 1 \u03bcg 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\u00b0C 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\u00d7150 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 \u00b5g/each sample. 1 \u03bcg 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\u00b0C 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\u00d7150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP560121", null, null, "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, null, null, 3824315591, 5035112770, 5644328190, 3707941000, 3383223, "SRX27483377", "SRS23906281", "SRA2061743", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in1 IP1", "GSM8759068", null, "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", null, "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 \u00b5g/each sample. 1 \u03bcg 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\u00b0C 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\u00d7150 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 \u00b5g/each sample. 1 \u03bcg 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\u00b0C 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\u00d7150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP560121", null, null, "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, null, null, 4585155428, 6233832602, 6882198251, 4484977909, 4308684, "SRX27483376", "SRS23906280", "SRA2061743", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in2 IgG2", "GSM8759067", null, "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", null, "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 \u00b5g/each sample. 1 \u03bcg 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\u00b0C 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\u00d7150 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 \u00b5g/each sample. 1 \u03bcg 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\u00b0C 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\u00d7150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP560121", null, null, "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, null, null, 3864885070, 5250483318, 5713729791, 3756127723, 3612186, "SRX27483375", "SRS23906279", "SRA2061743", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "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.", null, null, null, "Zebrafish  RIP seq  Rbm24a Knock in1 IgG1", "GSM8759066", null, "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", null, "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 \u00b5g/each sample. 1 \u03bcg 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\u00b0C 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\u00d7150 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 \u00b5g/each sample. 1 \u03bcg 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\u00b0C 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\u00d7150 bp on an Illumina NovaSeq 6000 platform following the manufacturer's standardized workflow.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP560121", null, null, "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, null, null, 3736851298, 5091099145, 5529269310, 3647429389, 3437208, "SRX27483374", "SRS23906278", "SRA2061743", "Ang Li, College of Life Sciences, shandong university", "Ang Li, College of Life Sciences, shandong university", null, null, null, null, null, null, null, null, null, null, null, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-01-27", "Multi-stage", "Embryo", "Whole Organism", "All anatomical structures"], [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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "zebrafish embryos ythdf2 RIP rep2", "GSM2386192", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386192", "GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq", "GSM2386192", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "pubmed:28869969", null, "zebrafish embryos ythdf2 RIP rep1", "GSM2386191", null, "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", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386191", "GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq", "GSM2386191", null, "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 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s 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", null, "SRP092907", null, null, "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, null, null, 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", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [42000, "SRR5379364", "SRX2674572", "SRS2073700", "SRP102513", "PRJNA380609", "Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing", "GSE97067", "Other", "DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development  we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.", null, "pubmed:29636379", null, "ddx39a 24hpf RIPseq", "GSM2550918", null, "source name:embryos|genotype:ddx39a mutant|tissue:embryo|developmental stage:24hpf", "ddx39a 24hpf RIPseq", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "embryos", null, "Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "genotype:ddx39a mutant|tissue:embryo|developmental stage:24hpf", "GSM2550918", "GSM2550918: ddx39a 24hpf RIPseq; Danio rerio; RIP Seq", "GSM2550918", null, "1", "Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2550918", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP102513", null, null, "RDWHDANwwwCAABRAAPEI-206_1.fq.gz RDWHDANwwwCAABRAAPEI-206_2.fq.gz", "fastq fastq", 3819239400.0, 19096197.0, "GSM2550918 r1", "0:100 1:100", "A:751858949;C:1169790479;G:1139713624;T:756987876;N:888472", 100, 100, null, null, 751858949, 1169790479, 1139713624, 756987876, 888472, "SRX2674572", "SRS2073700", "SRA549449", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.98659, 0.98572, 0.28836, 0.28975, 0.89422, 0.89558, 0.75396, 0.78553, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-03-27", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [42001, "SRR5379363", "SRX2674571", "SRS2073697", "SRP102513", "PRJNA380609", "Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing", "GSE97067", "Other", "DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development  we pursued transcriptome analysis RNA Seq on wild type and ddx39a mutant zebrafish embryos at 24 hpf And by using RIP seq to identify targeted RNA which were DDX39A binded. Overall design: Using RNA seq to identify the changes in the transcriptomic landscape in ddx39a mutants. Using RIP seq to identify DDX39A binding RNAs.", null, "pubmed:29636379", null, "WT 24hpf RIPseq", "GSM2550917", null, "source name:embryos|genotype:wild type|tissue:embryo|developmental stage:24hpf", "WT 24hpf RIPseq", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "embryos", null, "Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "genotype:wild type|tissue:embryo|developmental stage:24hpf", "GSM2550917", "GSM2550917: WT 24hpf RIPseq; Danio rerio; RIP Seq", "GSM2550917", null, "1", "Microinjection ddx39a Flag mRNA in ddx39a mutant embryos at one cell stage. Lysates were clarified from 24hpf embryos were isolated with anti Flag beads. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2550917", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP102513", null, null, "RDWHDANwwwCAAARAAPEI-205_2.fq.gz RDWHDANwwwCAAARAAPEI-205_1.fq.gz", "fastq fastq", 3802882200.0, 19014411.0, "GSM2550917 r1", "0:100 1:100", "A:733911232;C:1178365174;G:1154031422;T:735690235;N:884137", 100, 100, null, null, 733911232, 1178365174, 1154031422, 735690235, 884137, "SRX2674571", "SRS2073697", "SRA549449", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.9866, 0.98469, 0.30567, 0.30486, 0.90796, 0.90928, 0.82926, 0.83029, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-03-27", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:29765956", null, "IN wholefishtranscriptome RNAseq rep4", "GSM3143177", null, "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\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:whole fish|antibody:n1", "GSM3143177", "GSM3143177: IN wholefishtranscriptome RNAseq rep4; Danio rerio; RIP Seq", "GSM3143177", null, "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", null, "SRP115900", null, null, "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, null, null, 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", null, "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.", null, "pubmed:29765956", null, "IN wholefishtranscriptome RNAseq rep3", "GSM2747297", null, "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\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:whole fish|antibody:n1", "GSM2747297", "GSM2747297: IN wholefishtranscriptome RNAseq rep3; Danio rerio; RIP Seq", "GSM2747297", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747297", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "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, null, null, 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", null, "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.", null, "pubmed:29765956", null, "IN wholefishtranscriptome RNAseq rep2", "GSM2747296", null, "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\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:whole fish|antibody:n1", "GSM2747296", "GSM2747296: IN wholefishtranscriptome RNAseq rep2; Danio rerio; RIP Seq", "GSM2747296", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747296", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "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, null, null, 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", null, "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.", null, "pubmed:29765956", null, "IN wholefishtranscriptome RNAseq rep1", "GSM2747295", null, "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\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:whole fish|antibody:n1", "GSM2747295", "GSM2747295: IN wholefishtranscriptome RNAseq rep1; Danio rerio; RIP Seq", "GSM2747295", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747295", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "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, null, null, 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", null, "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.", null, "pubmed:29765956", null, "IP HCtranslatome RNAseq rep3", "GSM2747294", null, "source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "IP HCtranslatome RNAseq rep3", "Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample", "Tgmyo6b:GFP 2A rpl10a 3xHA", "Untreated", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "GSM2747294", "GSM2747294: IP HCtranslatome RNAseq rep3; Danio rerio; RIP Seq", "GSM2747294", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747294", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "RiboZF_IP4_R1.fastq.gz RiboZF_IP4_R2.fastq.gz", "fastq fastq", 4994833580.0, 33330363.0, "GSM2747294 r1", "0:74.96 1:74.90", "A:1202677579;C:1288784412;G:1278463604;T:1223941397;N:966588", 74, 74, null, null, 1202677579, 1288784412, 1278463604, 1223941397, 966588, "SRX3110521", "SRS2445614", "SRA601675", "GEO", "Department: Institute for Genome Sciences, University of Maryland in Baltimore", 2, 0.61854, 0.6151, 0.20328, 0.19651, 0.83599, 0.84104, 0.60632, 0.59954, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-21", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [43459, "SRR5952026", "SRX3110520", "SRS2445613", "SRP115900", "PRJNA399133", "RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN", "GSE102861", "Transcriptome Analysis", "We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.", null, "pubmed:29765956", null, "IP HCtranslatome RNAseq rep2", "GSM2747293", null, "source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "IP HCtranslatome RNAseq rep2", "Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample", "Tgmyo6b:GFP 2A rpl10a 3xHA", "Untreated", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "GSM2747293", "GSM2747293: IP HCtranslatome RNAseq rep2; Danio rerio; RIP Seq", "GSM2747293", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747293", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "RiboZF_IP2_R1.fastq.gz RiboZF_IP2_R2.fastq.gz", "fastq fastq", 4530855300.0, 30205702.0, "GSM2747293 r1", "0:75 1:75", "A:1112381418;C:1153277132;G:1147183468;T:1117133915;N:879367", 75, 75, null, null, 1112381418, 1153277132, 1147183468, 1117133915, 879367, "SRX3110520", "SRS2445613", "SRA601675", "GEO", "Department: Institute for Genome Sciences, University of Maryland in Baltimore", 2, 0.64948, 0.64878, 0.15967, 0.15683, 0.80756, 0.81288, 0.56438, 0.56275, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-21", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [43460, "SRR5952025", "SRX3110519", "SRS2445612", "SRP115900", "PRJNA399133", "RNA seq profiling of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish hair cell IP vs. whole fish IN", "GSE102861", "Transcriptome Analysis", "We have developed and tested the efficiency of the Tgmyo6b:GFP 2A rpl10a 3xHA zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells IP compared to the whole fish transcriptome IN.  We show through RNA seq that HA tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts. Overall design: Tgmyo6b:GFP 2A rpl10a 3xHA were homogenized at 5dpf and the hair cell translatome was enriched for by HA tagged ribosome immunoprecipitation  followed by RNA extraction. IP samples were compared to input RNA controls IN in independent biological triplicates.", null, "pubmed:29765956", null, "IP HCtranslatome RNAseq rep1", "GSM2747292", null, "source name:Tgmyo6b:GFP 2A rpl10a 3xHA|developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "IP HCtranslatome RNAseq rep1", "Base calls were performed using the built in Illumina basecaller Sequenced reads were trimmed for adaptor sequence  and then mapped to Mouse GRCm38 reference using the TopHat splice aware aligner Reads Per Kilobase of gene per Million mapped reads RPKM were calculated for each sample. Differential expression of genes were computed between infected and uninfected samples Genome build: Danio rerioGRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each sample", "Tgmyo6b:GFP 2A rpl10a 3xHA", "Untreated", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "embryos were grown at 28 degrees C in E3 media until 5dpf", "developmental stage:5dpf|tissue:hair cells enriched|antibody:HA", "GSM2747292", "GSM2747292: IP HCtranslatome RNAseq rep1; Danio rerio; RIP Seq", "GSM2747292", null, "1", "RNA was isolated from the infected mouse tissues using the Qiagen Rneasy mini kit Cat#74104.HC translatome was enriched for by ribosome immunoprecipitation using an HA antibody see manuscript for full protocol Libraries were prepared from 25ng of RNA using the TruSeq RNA Sample Prep kit Illumina per manufacturer\u2019s instructions  with an additional PCR cycle.RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2747292", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP115900", null, null, "RiboZF_IP1_R1.fastq.gz RiboZF_IP1_R2.fastq.gz", "fastq fastq", 5261113350.0, 35074089.0, "GSM2747292 r1", "0:75 1:75", "A:1356848229;C:1276483567;G:1260001700;T:1366757927;N:1021927", 75, 75, null, null, 1356848229, 1276483567, 1260001700, 1366757927, 1021927, "SRX3110519", "SRS2445612", "SRA601675", "GEO", "Department: Institute for Genome Sciences, University of Maryland in Baltimore", 2, 0.66363, 0.6599, 0.15644, 0.15316, 0.76808, 0.7725, 0.48538, 0.48933, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-21", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP INPUT 2hpf rep2", "GSM3732425", null, "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\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "RIP INPUT 2hpf", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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.", null, "strain:AB strain|age:2 hpf|tissue:whole embryo", "GSM3732425", "GSM3732425: RIP INPUT 2hpf rep2; Danio rerio; RIP Seq", "GSM3732425", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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", null, "SRP162876", null, null, "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, null, null, 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", null, "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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP INPUT 2hpf rep1", "GSM3732424", null, "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\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "RIP INPUT 2hpf", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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.", null, "strain:AB strain|age:2 hpf|tissue:whole embryo", "GSM3732424", "GSM3732424: RIP INPUT 2hpf rep1; Danio rerio; RIP Seq", "GSM3732424", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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", null, "SRP162876", null, null, "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, null, null, 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", null, "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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP INPUT 0hpf rep2", "GSM3732423", null, "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\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "RIP INPUT 0hpf", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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.", null, "strain:AB strain|age:0 hpf|tissue:whole embryo", "GSM3732423", "GSM3732423: RIP INPUT 0hpf rep2; Danio rerio; RIP Seq", "GSM3732423", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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", null, "SRP162876", null, null, "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, null, null, 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", null, "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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP INPUT 0hpf rep1", "GSM3732422", null, "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\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "RIP INPUT 0hpf", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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.", null, "strain:AB strain|age:0 hpf|tissue:whole embryo", "GSM3732422", "GSM3732422: RIP INPUT 0hpf rep1; Danio rerio; RIP Seq", "GSM3732422", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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", null, "SRP162876", null, null, "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, null, null, 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", null, "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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP 2hpf rep2", "GSM3732421", null, "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\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "RIP 2hpf", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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.", null, "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", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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", null, "SRP162876", null, null, "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, null, null, 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", null, "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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP 2hpf rep1", "GSM3732420", null, "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\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "RIP 2hpf", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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.", null, "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", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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", null, "SRP162876", null, null, "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, null, null, 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", null, "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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP 0hpf rep2", "GSM3732419", null, "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\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "RIP 0hpf", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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.", null, "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", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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", null, "SRP162876", null, null, "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, null, null, 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", null, "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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP 0hpf rep1", "GSM3732418", null, "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\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "RIP 0hpf", null, "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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.", null, "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", null, "1", "Total RNA was isolated from zebrafish embryos harvested at different stages using TRIzol\u00ae Reagent Ambion. mRNA was extracted with using Dynabeads\u00ae mRNA Purification Kit Ambion and subjected to TURBO\u2122 DNase Invitrogen treatment at 37\u00b0C 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", null, "SRP162876", null, null, "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, null, null, 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", null, "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/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP 4hpf rep2", "GSM3406902", null, "source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo", "RIP 4hpf rep2", "RIP seq and iCLIP seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10  respectively. RIP seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools\u2019 intersectBed. iCLIP: To identify the Ybx1 targets\u2019 locus  the mode of truncation calling was performed. For each truncation position  the coverages of unique tag k and truncations m were determined by CIMS.pl program CLIP Tool Kit  CTK. The sites were annotated by applying BEDTools\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "Zebrafish embryo", null, "RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u03bcl RNasin by rotating at 4\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00b0C for 1 h. 50 \u03bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u03bcl Protein A Dynabeads for 4 h at 4\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00d7 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u2122 DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.", null, "strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo", "GSM3406902", "GSM3406902: RIP 4hpf rep2; Danio rerio; RIP Seq", "GSM3406902", null, "1", "RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u03bcl RNasin by rotating at 4\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00b0C for 1 h. 50 \u03bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u03bcl Protein A Dynabeads for 4 h at 4\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00d7 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u2122 DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.", "GEO Accession:GSM3406902", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162876", null, null, "RIP_4hpf_rep2_R1.fastq.gz RIP_4hpf_rep2_R2.fastq.gz", "fastq fastq", 22888305600.0, 76294352.0, "GSM3406902 r1", "0:150 1:150", "A:5927520807;C:4846894836;G:4996844576;T:7111789925;N:5255456", 150, 150, null, null, 5927520807, 4846894836, 4996844576, 7111789925, 5255456, "SRX4776901", "SRS3857441", "SRA786939", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.2704, 0.17205, 0.06114, 0.06961, 0.95879, 0.9698, 0.94515, 0.83252, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "hiseq_era", "full_length", "random_priming", "smarter", "bulk", "clip", "iclip", null, "China", "2018-09-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [49550, "SRR7942635", "SRX4776900", "SRS3857440", "SRP162876", "PRJNA493828", "Ybx1 binding sites and Ybx1 binding m5C sites in zebrafish embryo sample.", "GSE120646", "Other", "The maternal to zygotic transition MZT is a conserved and fundamental process during which the embryo undergoes dramatic reprogramming to convert maternal environment to embryonic driven programing. However  how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein  through genome wide profiling of RNA 5 methylcytosine m5C in zebrafish early embryos  we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify that the Y box binding protein 1 Ybx1 prefers to recognizing m5C modified mRNAs through p p interaction with a key residue Trp45 in its cold shock domain CSD  which plays essential roles in maternal mRNA stability and early embryogenesis of zebrafish. Cooperated with an mRNA stabilizer Pabpc1a  Ybx1 promotes the stability of its target mRNAs in an m5C dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation regulated maternal mRNA stability during zebrafish MZT  highlighting the critical role of m5C mRNA methylation in early development. Overall design: Examination of Ybx1 binding sites  and Ybx1 binding m5C sites in zebrafish embryo. RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u00e2\u201e\u00a2 DNase Invitrogen  AM2238. iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp. RNA RIP BisSeq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u00ce\u00bcl RNasin by rotating at 4\u00c2\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00c2\u00b0C for 1 h. 50 \u00ce\u00bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u00ce\u00bcl Protein A Dynabeads for 4 h at 4\u00c2\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00c2\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00c3\u2014 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00c2\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The purified mRNA was used for RNA BisSeq library construction. Around 200 ng mRNA premixed with the in vitro transcribed Dhfr mRNA at a ratio of 300:1 Dhfr mRNA serves as methylation conversion control was fragmented to 100 nt fragments for 1 min at 90\u00b0C in 10\u00d7 RNA Fragmentation Reagent Ambion  then stopped by 10\u00d7 RNA stop solution Ambion  and precipitated with 100% ethanol. The RNA pellet was resuspended in 100 \u00b5l bisulfite solution pH 5.1  which is a 100:1 mixture of 40% sodium bisulfite Sigma and 600 \u00b5M hydroquinone Sigma and subjected to heat incubation at 75\u00b0C for 4.5 h. The reaction mixture was desalted by passing through Nanosep with 3K Omega 500/pk columns PALL Corporation with centrifugation. post washed with nuclease free water and centrifuged for five times  the RNA was finally disolved in 75 ?l nuclease free water and then desulfonated by incubation with an equal volume of 1 M Tris HCl pH 9.0 at 75 \u00b0C for 1 h. post ethanol precipitation  the RNA was resuspended in 11 \u00b5l of RNase free water and subjected to library construction. Reverse transcription was carried out with superscript II Reverse Transcriptase Invitrogen and ACT random hexamers. The following procedures were performed with the KAPA Stranded mRNA Seq Kit KAPA according to the manufacturer?s instructions.Libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 125 bp.", "parent bioproject:PRJNA534030", null, null, "RIP 4hpf rep1", "GSM3406901", null, "source name:Zebrafish embryo|strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo", "RIP 4hpf rep1", "RIP seq and iCLIP seq reads were aligned to the zv9 genome assembly using TopHat v2.1.1 and BWA v0.7.10  respectively. RIP seq: MACS2 v2.1.1 were used for the peak calling and peaks were annotated by applying BEDTools\u2019 intersectBed. iCLIP: To identify the Ybx1 targets\u2019 locus  the mode of truncation calling was performed. For each truncation position  the coverages of unique tag k and truncations m were determined by CIMS.pl program CLIP Tool Kit  CTK. The sites were annotated by applying BEDTools\u2019 intersectBed. Genome build: zv9 Supplementary files format and content: Ybx1 binding sites in two biological replicates.", "Zebrafish embryo", null, "RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u03bcl RNasin by rotating at 4\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00b0C for 1 h. 50 \u03bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u03bcl Protein A Dynabeads for 4 h at 4\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00d7 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u2122 DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.", null, "strain:AB strain|cell type:Zebrafish embryo|age:4 hpf|tissue:whole embryo", "GSM3406901", "GSM3406901: RIP 4hpf rep1; Danio rerio; RIP Seq", "GSM3406901", null, "1", "RIP seq: Briefly  500 zebrafish embryos at shield stage 4 hpf were resuspended with 2 ml lysis buffer 150 mM KCl  10 mM HEPES pH 7.6  2 mM EDTA  0.5% NP 40  0.5 mM DTT  1:100 protease inhibitor cocktail  0.4 U/\u03bcl RNasin by rotating at 4\u00b0C for 30 min and centrifuged at 15 000 g for 15 min. The supernatant was collected and pre cleared with protein A Dynabeads by rotation at 4\u00b0C for 1 h. 50 \u03bcl pre cleared embryo lysate was saved as Input and the left were incubated with affinity purified rabbit polyclonal anti Ybx1 antibody prepared by AbMax  China and 30 \u03bcl Protein A Dynabeads for 4 h at 4\u00b0C or overnight. post washing with1 ml ice cold NT2 buffer 200 mM NaCl  50 mM HEPES pH 7.6  2 mM EDTA  0.05% NP 40  0.5 mM DTT  0.4U/\u00b5l RNasin for eight times and once with 1ml ice cold 1\u00d7 PK buffer 100 mM Tris HCl pH 7.4  50 mM NaCl  10 mM EDTA   0.2% SDS  the beads was treated in 200 ul PK buffer containing 20 ul proteinase K Roche  0311582001 for 1 h at 55\u00b0C. The solution was collected and subjected to RNA extraction with Acid Phenol: ChCl3 pH4.34.7 and ethanol precipitation. The Input RNA was extracted by using TRIzol reagent. Both the Input and IP RNA were treated by TURBO\u2122 DNase Invitrogen  AM2238.  iCLIP seq: 1000 zebrafish embryos at 4 hpf were irradiated twice with 0.8 J/cm2 Stratalinker 2400  Stratagene  lysed and subjected to mild fragmentation. Crosslinked RNA protein complexes were immunoprecipated using polyclonal Ybx1 antibody Abmax and protein A dynabeads. RNA was extracted and subjected to library construction using Smarter smRNA Seq kit Takara. All the libraries were sequenced using HiSeq2500 Illumina in paired read mode  creating reads with a length of 150 bp.", "GEO Accession:GSM3406901", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162876", null, null, "RIP_4hpf_rep1_R1.fastq.gz RIP_4hpf_rep1_R2.fastq.gz", "fastq fastq", 19929300600.0, 66431002.0, "GSM3406901 r1", "0:150 1:150", "A:5076575451;C:4235012507;G:4442151234;T:6170975339;N:4586069", 150, 150, null, null, 5076575451, 4235012507, 4442151234, 6170975339, 4586069, "SRX4776900", "SRS3857440", "SRA786939", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.27932, 0.16557, 0.06585, 0.06178, 0.95692, 0.96844, 0.94238, 0.84334, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "hiseq_era", "full_length", "random_priming", "smarter", "bulk", "clip", "iclip", null, "China", "2018-09-28", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [54307, "SRR10129555", "SRX6857975", "SRS5395856", "SRP221863", "PRJNA565584", "The functions of igf2bp3 during zebrafish early development", "PRJNA565584", "Whole Genome Sequencing", "RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.", null, null, null, "Model organism or animal sample from Danio rerio", "RIP seq zebrafish embryo HA rabbit", null, "strain:AB|dev stage:embryo|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RIP seq zebrafish embryo sphere HA", "HA sphere", "HA sphere", "RIP seq", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP221863", null, null, "IP2_R1.fq.gz IP2_R2.fq.gz", "fastq fastq", 7528561800.0, 25095206.0, "IP2 R1.fq.gz", "0:150 1:150", "A:1638987252;C:1830922014;G:2628590112;T:1430016657;N:45765", 150, 150, null, null, 1638987252, 1830922014, 2628590112, 1430016657, 45765, "SRX6857975", "SRS5395856", "SRA962995", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", 2, 0.92316, 0.96332, 0.32571, 0.34771, 0.89173, 0.88962, 0.89557, 0.89793, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-17", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [54308, "SRR10129346", "SRX6857766", "SRS5395649", "SRP221863", "PRJNA565584", "The functions of igf2bp3 during zebrafish early development", "PRJNA565584", "Whole Genome Sequencing", "RNA seq and RIP seq data of wild type and maternal igf2bp3 mutant embryos at different stages.", null, null, null, "Model organism or animal sample from Danio rerio", "RIP seq zebrafish embryo IgG rabbit", null, "strain:AB|dev stage:embryo|sex:not applicable|tissue:embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RIP seq zebrafish embryo sphere IgG", "IgG sphere", "IgG sphere", "RIP seq", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP221863", null, null, "IgG1_R1.fq.gz IgG1_R2.fq.gz", "fastq fastq", 2647374600.0, 8824582.0, "IgG1 R1.fq.gz", "0:150 1:150", "A:565620765;C:650153559;G:936592543;T:494992101;N:15632", 150, 150, null, null, 565620765, 650153559, 936592543, 494992101, 15632, "SRX6857766", "SRS5395649", "SRA962944", "Huazhong Agricultural University|College of Fisheries", "Huazhong Agricultural University", 2, 0.95349, 0.96423, 0.33504, 0.34458, 0.93748, 0.93726, 0.85176, 0.91118, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-09-17", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, null, null, null, "SCI IP", null, "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", null, null, null, null, null, null, null, null, "IP library sequencing data of treated sample", "SCIIP BKDL192540807 1a", "SCIIP BKDL192540807 1a", "IP library sequencing data of treated sample", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP269070", null, null, "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, null, null, 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", null, "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", null, null, null, null, "SCI Input", null, "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", null, null, null, null, null, null, null, null, "Input library sequencing data of treated sample", "SCIIN BKDL192540809 1a", "SCIIN BKDL192540809 1a", "Input library sequencing data of treated sample", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP269070", null, null, "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, null, null, 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", null, "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", null, null, null, null, "Control IP", null, "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", null, null, null, null, null, null, null, null, "IP library sequencing data of control sample", "controlIP BKDL192540808 1a", "controlIP BKDL192540808 1a", "IP library sequencing data of control sample", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP269070", null, null, "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, null, null, 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", null, "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", null, null, null, null, "Control Input", null, "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", null, null, null, null, null, null, null, null, "Input library sequencing data of control sample", "controlIN BKDL192540810 1a", "controlIN BKDL192540810 1a", "Input library sequencing data of control sample", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP269070", null, null, "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, null, null, 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", null, "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\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB4 IP", "GSM4644253", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217", "PCB4 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217", "GSM4644253", "GSM4644253: PCB4 IP; Danio rerio; RIP Seq", "GSM4644253", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644253", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P4_m6A-IP_S16_R1_001.fastq.gz P4_m6A-IP_S16_R2_001.fastq.gz", "fastq fastq", 2309150560.0, 15191780.0, "GSM4644253 r1", "0:76 1:76", "A:490672579;C:656568819;G:666651729;T:495020365;N:237068", 76, 76, null, null, 490672579, 656568819, 666651729, 495020365, 237068, "SRX8627954", "SRS6916259", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94474, 0.944, 0.18094, 0.18203, 0.7515, 0.75554, 0.60771, 0.6152, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60026, "SRR12103782", "SRX8627953", "SRS6916258", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB3 IP", "GSM4644252", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216", "PCB3 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216", "GSM4644252", "GSM4644252: PCB3 IP; Danio rerio; RIP Seq", "GSM4644252", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644252", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P3_m6A-IP_S15_R2_001.fastq.gz P3_m6A-IP_S15_R1_001.fastq.gz", "fastq fastq", 2965972504.0, 19512977.0, "GSM4644252 r1", "0:76 1:76", "A:620624207;C:853765538;G:874990332;T:616281897;N:310530", 76, 76, null, null, 620624207, 853765538, 874990332, 616281897, 310530, "SRX8627953", "SRS6916258", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93433, 0.93213, 0.16543, 0.16208, 0.75043, 0.753, 0.62186, 0.64359, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60027, "SRR12103781", "SRX8627952", "SRS6916257", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB2 IP", "GSM4644251", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215", "PCB2 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215", "GSM4644251", "GSM4644251: PCB2 IP; Danio rerio; RIP Seq", "GSM4644251", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644251", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P2_m6A-IP_S14_R2_001.fastq.gz P2_m6A-IP_S14_R1_001.fastq.gz", "fastq fastq", 2687973472.0, 17684036.0, "GSM4644251 r1", "0:76 1:76", "A:585901626;C:744255122;G:756993274;T:600539454;N:283996", 76, 76, null, null, 585901626, 744255122, 756993274, 600539454, 283996, "SRX8627952", "SRS6916257", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.9445, 0.94466, 0.16876, 0.17035, 0.74728, 0.75022, 0.57878, 0.57933, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60028, "SRR12103780", "SRX8627951", "SRS6916256", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB1 IP", "GSM4644250", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214", "PCB1 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214", "GSM4644250", "GSM4644250: PCB1 IP; Danio rerio; RIP Seq", "GSM4644250", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644250", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P1_m6A-IP_S13_R1_001.fastq.gz P1_m6A-IP_S13_R2_001.fastq.gz", "fastq fastq", 2596174288.0, 17080094.0, "GSM4644250 r1", "0:76 1:76", "A:564523297;C:723443207;G:735894528;T:572044392;N:268864", 76, 76, null, null, 564523297, 723443207, 735894528, 572044392, 268864, "SRX8627951", "SRS6916256", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93494, 0.93528, 0.17469, 0.17518, 0.746, 0.74803, 0.60114, 0.60005, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60029, "SRR12103779", "SRX8627950", "SRS6916255", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB4 Input", "GSM4644249", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1", "PCB4 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:input control|antibody:n1", "GSM4644249", "GSM4644249: PCB4 Input; Danio rerio; RIP Seq", "GSM4644249", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644249", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P4_INPUT_S8_R1_001.fastq.gz P4_INPUT_S8_R2_001.fastq.gz", "fastq fastq", 3655473384.0, 24049167.0, "GSM4644249 r1", "0:76 1:76", "A:680110064;C:1145409769;G:1179103219;T:650470372;N:379960", 76, 76, null, null, 680110064, 1145409769, 1179103219, 650470372, 379960, "SRX8627950", "SRS6916255", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93037, 0.96319, 0.21668, 0.22563, 0.86338, 0.86385, 0.77257, 0.70059, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60030, "SRR12103778", "SRX8627949", "SRS6916254", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB3 Input", "GSM4644248", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1", "PCB3 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:input control|antibody:n1", "GSM4644248", "GSM4644248: PCB3 Input; Danio rerio; RIP Seq", "GSM4644248", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644248", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P3_INPUT_S7_R1_001.fastq.gz P3_INPUT_S7_R2_001.fastq.gz", "fastq fastq", 4926238376.0, 32409463.0, "GSM4644248 r1", "0:76 1:76", "A:929043061;C:1530175131;G:1577898210;T:888604850;N:517124", 76, 76, null, null, 929043061, 1530175131, 1577898210, 888604850, 517124, "SRX8627949", "SRS6916254", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92875, 0.95698, 0.21539, 0.22073, 0.85253, 0.85431, 0.76235, 0.68659, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60031, "SRR12103777", "SRX8627948", "SRS6916253", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB2 Input", "GSM4644247", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1", "PCB2 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:input control|antibody:n1", "GSM4644247", "GSM4644247: PCB2 Input; Danio rerio; RIP Seq", "GSM4644247", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644247", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P2_INPUT_S6_R1_001.fastq.gz P2_INPUT_S6_R2_001.fastq.gz", "fastq fastq", 5669611400.0, 37300075.0, "GSM4644247 r1", "0:76 1:76", "A:1050955836;C:1780355588;G:1829450728;T:1008257255;N:591993", 76, 76, null, null, 1050955836, 1780355588, 1829450728, 1008257255, 591993, "SRX8627948", "SRS6916253", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93297, 0.93791, 0.21298, 0.21667, 0.85902, 0.86302, 0.7387, 0.69759, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60032, "SRR12103776", "SRX8627947", "SRS6916252", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "PCB1 Input", "GSM4644246", null, "tissue:78 hpf embryos|agent:PCB126|strain:AB|fraction:input control|antibody:n1", "PCB1 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:PCB126|strain:AB|fraction:input control|antibody:n1", "GSM4644246", "GSM4644246: PCB1 Input; Danio rerio; RIP Seq", "GSM4644246", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644246", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "P1_INPUT_S5_R1_001.fastq.gz P1_INPUT_S5_R2_001.fastq.gz", "fastq fastq", 4154972744.0, 27335347.0, "GSM4644246 r1", "0:76 1:76", "A:764769282;C:1310937656;G:1344287240;T:734545457;N:433109", 76, 76, null, null, 764769282, 1310937656, 1344287240, 734545457, 433109, "SRX8627947", "SRS6916252", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92033, 0.95428, 0.21666, 0.2245, 0.86571, 0.8678, 0.74089, 0.68247, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60033, "SRR12103775", "SRX8627946", "SRS6916251", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO4 IP", "GSM4644245", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217", "DMSO4 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279217", "GSM4644245", "GSM4644245: DMSO4 IP; Danio rerio; RIP Seq", "GSM4644245", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644245", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D4_m6A-IP_S12_R1_001.fastq.gz D4_m6A-IP_S12_R2_001.fastq.gz", "fastq fastq", 2415539920.0, 15891710.0, "GSM4644245 r1", "0:76 1:76", "A:519904759;C:674887600;G:688106098;T:532387711;N:253752", 76, 76, null, null, 519904759, 674887600, 688106098, 532387711, 253752, "SRX8627946", "SRS6916251", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94931, 0.94824, 0.16515, 0.16656, 0.74858, 0.7497, 0.57724, 0.58102, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60034, "SRR12103774", "SRX8627945", "SRS6916250", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO3 IP", "GSM4644244", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216", "DMSO3 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279216", "GSM4644244", "GSM4644244: DMSO3 IP; Danio rerio; RIP Seq", "GSM4644244", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644244", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D3_m6A-IP_S11_R1_001.fastq.gz D3_m6A-IP_S11_R2_001.fastq.gz", "fastq fastq", 2419255408.0, 15916154.0, "GSM4644244 r1", "0:76 1:76", "A:524637988;C:675158080;G:687344217;T:531861650;N:253473", 76, 76, null, null, 524637988, 675158080, 687344217, 531861650, 253473, "SRX8627945", "SRS6916250", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93623, 0.93621, 0.18212, 0.18165, 0.74308, 0.74426, 0.60527, 0.60757, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60035, "SRR12103773", "SRX8627944", "SRS6916249", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO2 IP", "GSM4644243", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215", "DMSO2 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279215", "GSM4644243", "GSM4644243: DMSO2 IP; Danio rerio; RIP Seq", "GSM4644243", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644243", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D2_m6A-IP_S10_R1_001.fastq.gz D2_m6A-IP_S10_R2_001.fastq.gz", "fastq fastq", 2698406448.0, 17752674.0, "GSM4644243 r1", "0:76 1:76", "A:578126060;C:760791571;G:775423382;T:583783650;N:281785", 76, 76, null, null, 578126060, 760791571, 775423382, 583783650, 281785, "SRX8627944", "SRS6916249", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.9433, 0.94318, 0.17976, 0.1816, 0.74992, 0.75215, 0.58844, 0.61497, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60036, "SRR12103772", "SRX8627943", "SRS6916248", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO1 IP", "GSM4644242", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214", "DMSO1 IP", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:m6A immunoprecipitated sample|antibody:m6A antibody   Synaptic Systems  catalog#202 003; RRID: AB 2279214", "GSM4644242", "GSM4644242: DMSO1 IP; Danio rerio; RIP Seq", "GSM4644242", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644242", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D1_m6A-IP_S9_R1_001.fastq.gz D1_m6A-IP_S9_R2_001.fastq.gz", "fastq fastq", 2588221344.0, 17027772.0, "GSM4644242 r1", "0:76 1:76", "A:552076254;C:730948542;G:744135059;T:560788856;N:272633", 76, 76, null, null, 552076254, 730948542, 744135059, 560788856, 272633, "SRX8627943", "SRS6916248", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.93871, 0.9398, 0.17681, 0.17588, 0.74688, 0.74915, 0.59376, 0.61045, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60037, "SRR12103771", "SRX8627942", "SRS6916247", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO4 Input", "GSM4644241", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "DMSO4 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "GSM4644241", "GSM4644241: DMSO4 Input; Danio rerio; RIP Seq", "GSM4644241", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644241", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D4_INPUT_S4_R1_001.fastq.gz D4_INPUT_S4_R2_001.fastq.gz", "fastq fastq", 4085824752.0, 26880426.0, "GSM4644241 r1", "0:76 1:76", "A:734095239;C:1307425224;G:1339970208;T:703907493;N:426588", 76, 76, null, null, 734095239, 1307425224, 1339970208, 703907493, 426588, "SRX8627942", "SRS6916247", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.94341, 0.94693, 0.21035, 0.21294, 0.86306, 0.86571, 0.66228, 0.69648, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60038, "SRR12103770", "SRX8627941", "SRS6916246", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO3 Input", "GSM4644240", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "DMSO3 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "GSM4644240", "GSM4644240: DMSO3 Input; Danio rerio; RIP Seq", "GSM4644240", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644240", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D3_INPUT_S3_R1_001.fastq.gz D3_INPUT_S3_R2_001.fastq.gz", "fastq fastq", 3627749800.0, 23866775.0, "GSM4644240 r1", "0:76 1:76", "A:677883991;C:1133504965;G:1166401920;T:649582074;N:376850", 76, 76, null, null, 677883991, 1133504965, 1166401920, 649582074, 376850, "SRX8627941", "SRS6916246", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92028, 0.96282, 0.2164, 0.22913, 0.86517, 0.8661, 0.73802, 0.70578, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60039, "SRR12103769", "SRX8627940", "SRS6916245", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO2 Input", "GSM4644239", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "DMSO2 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "GSM4644239", "GSM4644239: DMSO2 Input; Danio rerio; RIP Seq", "GSM4644239", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644239", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D2_INPUT_S2_R2_001.fastq.gz D2_INPUT_S2_R1_001.fastq.gz", "fastq fastq", 2991355592.0, 19679971.0, "GSM4644239 r1", "0:76 1:76", "A:555548434;C:937287598;G:965607991;T:532600162;N:311407", 76, 76, null, null, 555548434, 937287598, 965607991, 532600162, 311407, "SRX8627940", "SRS6916245", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92966, 0.96538, 0.21752, 0.22835, 0.86137, 0.86701, 0.71065, 0.70316, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [60040, "SRR12103768", "SRX8627939", "SRS6916244", "SRP269097", "PRJNA642647", "PCB126 3 three prime 4 4' 5 Pentachlorobiphenyl induced alterations in m6A RNA modifications in zebrafish embryos", "GSE153436", "Other", "Chemical modifications of proteins  DNA and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests these RNA modifications epitranscriptomics have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6 methyladenosine m6A. In a subset of mammalian mRNAs  m6A sites are preferentially enriched near stop codons  in three prime UTRs  and within exons  suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes  it is important to understand the effects of exposure on this important layer of gene regulation. Hence  the objective of this study was to characterize the acute effects of developmental exposure to PCB126  an environmentally relevant dioxin like PCB  on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for xxx hours starting from xxx hpf and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing MeRIP seq  as well as assessing changes in mRNA splicing. We observed several hundreds of peaks that are differentially expressed in response to PCB126 exposure FDR 5%. The majority of the peaks are preferentially located around the three primeUTR and stop codons. Pathway analysis of m6A marked transcripts induced by PCB126 exposure revealed that these transcripts are associated with important developmental pathways MAPK  Hedgehog  Notch and Wnt. These results suggest that PCB126 could affect developmental gene expression patterns by altering m6A levels. Gene expression analysis revealed upregulation of classical aryl hydrocarbon receptor AHR target genes such as cytochrome P450s in response to PCB126 exposure. Interestingly  none of the AHR target genes overlapped with the m6A altered transcripts  suggesting that xenobiotic metabolism may not be under m6A regulation. Further studies are necessary to understand the functional consequences of exposure associated alterations in m6A levels. This work is supported by NIEHS ES024915. Overall design: AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "pubmed:33064826", null, "DMSO1 Input", "GSM4644238", null, "tissue:78 hpf embryos|agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "DMSO1 Input", "Pre processing using Trimmomatic Remving ribosomal reads using bbduk Mapping the reads using STAR aligner Peak calling using macs14 Gene expression analysis on Input samples; htseq count followed by edgeR statistical analysis Genome build: Danio rerio.GRCz11.96 Supplementary files format and content: tdf", "78 hpf embryos", null, "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", null, "agent:DMSO control|strain:AB|fraction:input control|antibody:n1", "GSM4644238", "GSM4644238: DMSO1 Input; Danio rerio; RIP Seq", "GSM4644238", null, "1", "AB strain of zebrafish embryos were exposed to 10 nM PCB126 3 three prime 4 4' 5 pentachlorobiphenyl  99.2% purity; UltraScientific  RI  USA or DMSO solvent control; 0.01% starting at 72 hpf for 6 hours. This duration of exposure was chosen based on previous studies that demonstrated differential gene expression post 6 hour exposure. In addition  short term exposure allows us to characterize primary changes in the m6A patterns. Each treatment consisted of four biological replicates with 48 embryos per replicate. Embryos were maintained in glass petri dishes at 28\u00b10.5oC at a density of 1 embryo per mL in 0.3X Danieau's solution pH 7.2. At the end of the exposure  embryos were thoroughly rinsed with 0.3X Danieau's solution and sampled for MeRIP sequencing.  Four biological replicates per treatment condition.", "GEO Accession:GSM4644238", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP269097", null, null, "D1_INPUT_S1_R1_001.fastq.gz D1_INPUT_S1_R2_001.fastq.gz", "fastq fastq", 3551567552.0, 23365576.0, "GSM4644238 r1", "0:76 1:76", "A:659305531;C:1112775748;G:1146213503;T:632894453;N:378317", 76, 76, null, null, 659305531, 1112775748, 1146213503, 632894453, 378317, "SRX8627939", "SRS6916244", "SRA1091999", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 2, 0.92942, 0.96366, 0.21295, 0.2231, 0.8574, 0.85934, 0.75989, 0.75855, 76, 76, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "other", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-06-28", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [66194, "SRR16096233", "SRX12382357", "SRS10353019", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep5", "GSM5599725", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep5", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599725", "GSM5599725: ZF zygote IP 1cell Rep5; Danio rerio; RIP Seq", "GSM5599725", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599725", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep5_R1.fastq.gz ZF_zygote_IP_1cell_Rep5_R2.fastq.gz", "fastq fastq", 3660517860.0, 35887430.0, "GSM5599725 r1", "0:51 1:51", "A:858138600;C:924733544;G:1002150083;T:875349961;N:145672", 51, 51, null, null, 858138600, 924733544, 1002150083, 875349961, 145672, "SRX12382357", "SRS10353019", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.83384, 0.82667, 0.09687, 0.11892, 0.79076, 0.79326, 0.63739, 0.60941, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66195, "SRR16096232", "SRX12382356", "SRS10353018", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep4", "GSM5599724", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep4", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599724", "GSM5599724: ZF zygote IP 1cell Rep4; Danio rerio; RIP Seq", "GSM5599724", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599724", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep4_R1.fastq.gz ZF_zygote_IP_1cell_Rep4_R2.fastq.gz", "fastq fastq", 3660205842.0, 35884371.0, "GSM5599724 r1", "0:51 1:51", "A:895738659;C:880838836;G:971118499;T:912364119;N:145729", 51, 51, null, null, 895738659, 880838836, 971118499, 912364119, 145729, "SRX12382356", "SRS10353018", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.87258, 0.86932, 0.06573, 0.07958, 0.78044, 0.78374, 0.55531, 0.5462, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66196, "SRR16096231", "SRX12382355", "SRS10353016", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep3", "GSM5599723", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599723", "GSM5599723: ZF zygote IP 1cell Rep3; Danio rerio; RIP Seq", "GSM5599723", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599723", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep3_R1.fastq.gz ZF_zygote_IP_1cell_Rep3_R2.fastq.gz", "fastq fastq", 2732409048.0, 26788324.0, "GSM5599723 r1", "0:51 1:51", "A:669345195;C:656715671;G:724415204;T:681825149;N:107829", 51, 51, null, null, 669345195, 656715671, 724415204, 681825149, 107829, "SRX12382355", "SRS10353016", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.85204, 0.83607, 0.06526, 0.08046, 0.78535, 0.78748, 0.60467, 0.50165, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66197, "SRR16096230", "SRX12382354", "SRS10353017", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep2", "GSM5599722", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599722", "GSM5599722: ZF zygote IP 1cell Rep2; Danio rerio; RIP Seq", "GSM5599722", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599722", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep2_R1.fastq.gz ZF_zygote_IP_1cell_Rep2_R2.fastq.gz", "fastq fastq", 2235668028.0, 21918314.0, "GSM5599722 r1", "0:51 1:51", "A:552522700;C:535947981;G:588168855;T:558939713;N:88779", 51, 51, null, null, 552522700, 535947981, 588168855, 558939713, 88779, "SRX12382354", "SRS10353017", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.85597, 0.85298, 0.06663, 0.07927, 0.79058, 0.79237, 0.57626, 0.56525, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66198, "SRR16096229", "SRX12382353", "SRS10353015", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep1", "GSM5599721", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599721", "GSM5599721: ZF zygote IP 1cell Rep1; Danio rerio; RIP Seq", "GSM5599721", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599721", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep1_R1.fastq.gz ZF_zygote_IP_1cell_Rep1_R2.fastq.gz", "fastq fastq", 1785761736.0, 17507468.0, "GSM5599721 r1", "0:51 1:51", "A:429081683;C:435813601;G:481376346;T:439419714;N:70392", 51, 51, null, null, 429081683, 435813601, 481376346, 439419714, 70392, "SRX12382353", "SRS10353015", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.75314, 0.75693, 0.0543, 0.06639, 0.79482, 0.79594, 0.57979, 0.56522, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66199, "SRR16096228", "SRX12382352", "SRS10353014", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep3", "GSM5599720", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599720", "GSM5599720: ZF zygote IP 5cell Rep3; Danio rerio; RIP Seq", "GSM5599720", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599720", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep3_R1.fastq.gz ZF_zygote_IP_5cell_Rep3_R2.fastq.gz", "fastq fastq", 2179659420.0, 21369210.0, "GSM5599720 r1", "0:51 1:51", "A:539092949;C:513857324;G:569620218;T:556940661;N:148268", 51, 51, null, null, 539092949, 513857324, 569620218, 556940661, 148268, "SRX12382352", "SRS10353014", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.92028, 0.90706, 0.03967, 0.05572, 0.78431, 0.78886, 0.49727, 0.48541, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66200, "SRR16096227", "SRX12382351", "SRS10353012", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep2", "GSM5599719", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599719", "GSM5599719: ZF zygote IP 5cell Rep2; Danio rerio; RIP Seq", "GSM5599719", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599719", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep2_R1.fastq.gz ZF_zygote_IP_5cell_Rep2_R2.fastq.gz", "fastq fastq", 2527184538.0, 24776319.0, "GSM5599719 r1", "0:51 1:51", "A:628307375;C:594702688;G:657847712;T:646151885;N:174878", 51, 51, null, null, 628307375, 594702688, 657847712, 646151885, 174878, "SRX12382351", "SRS10353012", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91811, 0.90487, 0.03919, 0.05376, 0.78315, 0.78729, 0.49414, 0.48564, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66201, "SRR16096226", "SRX12382350", "SRS10353011", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep1", "GSM5599718", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599718", "GSM5599718: ZF zygote IP 5cell Rep1; Danio rerio; RIP Seq", "GSM5599718", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599718", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep1_R1.fastq.gz ZF_zygote_IP_5cell_Rep1_R2.fastq.gz", "fastq fastq", 3481342518.0, 34130809.0, "GSM5599718 r1", "0:51 1:51", "A:865680250;C:823420389;G:907146965;T:884854199;N:240715", 51, 51, null, null, 865680250, 823420389, 907146965, 884854199, 240715, "SRX12382350", "SRS10353011", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91893, 0.90939, 0.04544, 0.06005, 0.78025, 0.78348, 0.50569, 0.49155, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66202, "SRR16096225", "SRX12382349", "SRS10353013", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep3", "GSM5599717", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599717", "GSM5599717: ZF zygote IP 10cell Rep3; Danio rerio; RIP Seq", "GSM5599717", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599717", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep3_R1.fastq.gz ZF_zygote_IP_10cell_Rep3_R2.fastq.gz", "fastq fastq", 2172362850.0, 21297675.0, "GSM5599717 r1", "0:51 1:51", "A:536043605;C:513512883;G:568368414;T:554284996;N:152952", 51, 51, null, null, 536043605, 513512883, 568368414, 554284996, 152952, "SRX12382349", "SRS10353013", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91859, 0.90522, 0.03736, 0.05214, 0.78715, 0.79129, 0.49736, 0.48681, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66203, "SRR16096224", "SRX12382348", "SRS10353010", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep2", "GSM5599716", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599716", "GSM5599716: ZF zygote IP 10cell Rep2; Danio rerio; RIP Seq", "GSM5599716", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599716", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep2_R1.fastq.gz ZF_zygote_IP_10cell_Rep2_R2.fastq.gz", "fastq fastq", 1840839492.0, 18047446.0, "GSM5599716 r1", "0:51 1:51", "A:454385290;C:437082102;G:482351138;T:466893642;N:127320", 51, 51, null, null, 454385290, 437082102, 482351138, 466893642, 127320, "SRX12382348", "SRS10353010", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.92217, 0.90956, 0.04012, 0.05483, 0.78819, 0.79318, 0.49756, 0.48256, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66204, "SRR16096223", "SRX12382347", "SRS10353009", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep1", "GSM5599715", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599715", "GSM5599715: ZF zygote IP 10cell Rep1; Danio rerio; RIP Seq", "GSM5599715", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599715", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep1_R1.fastq.gz ZF_zygote_IP_10cell_Rep1_R2.fastq.gz", "fastq fastq", 2400553680.0, 23534840.0, "GSM5599715 r1", "0:51 1:51", "A:594878203;C:567573525;G:625488388;T:612448386;N:165178", 51, 51, null, null, 594878203, 567573525, 625488388, 612448386, 165178, "SRX12382347", "SRS10353009", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91641, 0.908, 0.03979, 0.05394, 0.78455, 0.7892, 0.48862, 0.47478, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66205, "SRR16096222", "SRX12382346", "SRS10353008", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote Input 10cell Rep2", "GSM5599714", null, "tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote Input 10cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote Input 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599714", "GSM5599714: ZF zygote Input 10cell Rep2; Danio rerio; RIP Seq", "GSM5599714", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599714", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_Input_10cell_Rep2_R1.fastq.gz ZF_zygote_Input_10cell_Rep2_R2.fastq.gz", "fastq fastq", 3842772582.0, 37674241.0, "GSM5599714 r1", "0:51 1:51", "A:843564828;C:1054412690;G:1130769812;T:813758353;N:266899", 51, 51, null, null, 843564828, 1054412690, 1130769812, 813758353, 266899, "SRX12382346", "SRS10353008", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91511, 0.90868, 0.32791, 0.38048, 0.89457, 0.89441, 0.81532, 0.75274, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66206, "SRR16096221", "SRX12382345", "SRS10353007", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote Input 10cell Rep1", "GSM5599713", null, "tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote Input 10cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote Input 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599713", "GSM5599713: ZF zygote Input 10cell Rep1; Danio rerio; RIP Seq", "GSM5599713", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599713", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_Input_10cell_Rep1_R1.fastq.gz ZF_zygote_Input_10cell_Rep1_R2.fastq.gz", "fastq fastq", 4029368016.0, 39503608.0, "GSM5599713 r1", "0:51 1:51", "A:893562237;C:1096986475;G:1180690796;T:857849967;N:278541", 51, 51, null, null, 893562237, 1096986475, 1180690796, 857849967, 278541, "SRX12382345", "SRS10353007", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91491, 0.90807, 0.32799, 0.37836, 0.89292, 0.89282, 0.81006, 0.73354, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [70712, "SRR20077343", "SRX16115141", "SRS13777745", "SRP385866", "PRJNA857663", "RIP seq for Cpeb1b in zebrafish embryos", "GSE207904", "Transcriptome Analysis", "Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates", "parent bioproject:PRJNA857656", null, null, "Flag Cpeb1b replicate 2", "GSM6322839", null, "source name:Flag Cpeb1b replicate 2|tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "Flag Cpeb1b replicate 2", "The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples", "Flag Cpeb1b replicate 2", null, "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.", null, "tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "GSM6322839", "GSM6322839: Flag Cpeb1b replicate 2; Danio rerio; RIP Seq", "GSM6322839 r1", "GSM6322839", "1", "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP385866", null, "loader:fastq load.py", "Flag_Cpeb1b_replicate_2.R1.fq.gz Flag_Cpeb1b_replicate_2.R2.fq.gz", "fastq fastq", 14733801000.0, 49112670.0, "GSM6322839 r1", "0:150 1:150", "A:4141614412;C:3363207101;G:3881752054;T:3344596903;N:2630530", 150, 150, null, null, 4141614412, 3363207101, 3881752054, 3344596903, 2630530, "SRX16115141", "SRS13777745", "SRA1452503", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.05175, 0.02071, 0.01394, 0.00703, 0.99383, 0.99758, 0.80854, 0.85616, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2022-07-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [70713, "SRR20077344", "SRX16115140", "SRS13777744", "SRP385866", "PRJNA857663", "RIP seq for Cpeb1b in zebrafish embryos", "GSE207904", "Transcriptome Analysis", "Cpeb1b mediated cytoplasmic polyadenylation modulates hematopoietic stem and progenitor cell development via translational control Overall design: RIP seq of 2 samples from Flag cpeb1b mRNA injected zebrafish embryos at xxx hpf including two biological replicates", "parent bioproject:PRJNA857656", null, null, "Flag Cpeb1b replicate 1", "GSM6322838", null, "source name:Flag Cpeb1b replicate 1|tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "Flag Cpeb1b replicate 1", "The quality of raw sequencing reads was processed using FastQC and low quality bases were trimmed and filtered by cutadapt V 1.13 11 and Trimmomatic V 0.36 12. Processed reads were mapped to the zebrafish genome Zv9 using TopHat v2.1.1 18 with \u2018\u2018\u2013bowtie1\u2019\u2019. The target binding regions of Cpeb1b were identified using MACS2 software version 2.0.10. The target genes were annotated based on Ensembl release 79 gene annotation information by applying BEDTools\u2019 intersectBed version 2.16.2. Assembly: Zv9 Supplementary files format and content: rpkm for samples", "Flag Cpeb1b replicate 1", null, "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.", null, "tissue:zebrafish embryos|genotype:wild type|age:16 hpf", "GSM6322838", "GSM6322838: Flag Cpeb1b replicate 1; Danio rerio; RIP Seq", "GSM6322838 r1", "GSM6322838", "1", "Flag cpeb1b mRNA injected embryos were collected at xxx hpf and lysed in NETN lysis buffer 150 mM NaCl  0.5% NP 40  50 mM Tris HCl  pH 7.4  RNase inhibitor  Roche cocktail protease inhibitor. The lysate was incubated with anti FLAG M2 Magnetic Beads Merck for 4 h at 4 \u00b0C. Then  the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP seq assay  the bead bound RNA was extracted and then fragmented by RNA Fragmentation Reagent Ambion. The fragmented RNA was subjected to library construction using the SMARTer smRNA Seq kit Clontech.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP385866", null, "loader:fastq load.py", "Flag_Cpeb1b_replicate_1.R1.fq.gz Flag_Cpeb1b_replicate_1.R2.fq.gz", "fastq fastq", 15482669700.0, 51608899.0, "GSM6322838 r1", "0:150 1:150", "A:4303443264;C:3570990345;G:4030059369;T:3575508224;N:2668498", 150, 150, null, null, 4303443264, 3570990345, 4030059369, 3575508224, 2668498, "SRX16115140", "SRS13777744", "SRA1452503", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.03751, 0.01773, 0.01056, 0.00621, 0.99346, 0.99736, 0.89693, 0.8036, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "full_length", "other", "smarter", "bulk", "unknown", "unknown", null, "China", "2022-07-11", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [71624, "SRR21849078", "SRX17837652", "SRS15359804", "SRP401744", "PRJNA888821", "The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling", "PRJNA888821", "Other", "We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.", null, null, null, "33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 2", "Zebrafish 33 hpf.Bulk RIP seq.Flag hCsde1 2", null, "breed:Zebrafish|age:33 hpf|dev stage:HSPC generation|sex:pooled male and female|tissue:whole embryos|treatment:8|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 2", "Flag hCsde1 2", "Flag hCsde1 2", "RIP Seq", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP401744", null, null, "Flag-hCsde1-2_1.fq.gz Flag-hCsde1-2_2.fq.gz", "fastq fastq", 7253178600.0, 24177262.0, "Flag hCsde1 2 1.fq.gz", "0:150 1:150", "A:1490001899;C:2113749179;G:2152941566;T:1496406491;N:79465", 150, 150, null, null, 1490001899, 2113749179, 2152941566, 1496406491, 79465, "SRX17837652", "SRS15359804", "SRA1516844", "Institute of Hematology &amp; Blood Diseases Hospital|State Key Laboratory of Experimental Hematology", "Institute of Hematology & Blood Diseases Hospital", 2, 0.9907, 0.98973, 0.51575, 0.5119, 0.9459, 0.94631, 0.80609, 0.80353, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-10-09", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [71625, "SRR21849079", "SRX17837651", "SRS15359803", "SRP401744", "PRJNA888821", "The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling", "PRJNA888821", "Other", "We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.", null, null, null, "33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 1", "Zebrafish 33 hpf.Bulk RIP seq.Flag hCsde1 1", null, "breed:Zebrafish|age:33 hpf|dev stage:HSPC generation|sex:pooled male and female|tissue:whole embryos|treatment:7|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "33 hpf Zebrafish Bulk RIP seq.Flag hCsde1 1", "Flag hCsde1 1", "Flag hCsde1 1", "RIP Seq", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP401744", null, null, "Flag-hCsde1-1_1.fq.gz Flag-hCsde1-1_2.fq.gz", "fastq fastq", 5032252500.0, 16774175.0, "Flag hCsde1 1 1.fq.gz", "0:150 1:150", "A:1150344713;C:1135461821;G:1687878347;T:1058543429;N:24190", 150, 150, null, null, 1150344713, 1135461821, 1687878347, 1058543429, 24190, "SRX17837651", "SRS15359803", "SRA1516844", "Institute of Hematology &amp; Blood Diseases Hospital|State Key Laboratory of Experimental Hematology", "Institute of Hematology & Blood Diseases Hospital", 2, 0.22813, 0.23161, 0.06226, 0.06317, 0.92801, 0.92719, 0.73744, 0.71685, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-10-09", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [71626, "SRR21849080", "SRX17837650", "SRS15359801", "SRP401744", "PRJNA888821", "The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling", "PRJNA888821", "Other", "We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.", null, null, null, "33 hpf Zebrafish Bulk RIP seq.Control2", "Zebrafish 33 hpf.Bulk RIP seq.Control2", null, "breed:Zebrafish|age:33 hpf|dev stage:HSPC generation|sex:pooled male and female|tissue:whole embryos|treatment:6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "33 hpf Zebrafish Bulk RIP seq.Control2", "Control2", "Control2", "RIP Seq", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP401744", null, null, "Control2_1.fq.gz Control2_2.fq.gz", "fastq fastq", 7884108600.0, 26280362.0, "Control2 1.fq.gz", "0:150 1:150", "A:1586894082;C:2334065454;G:2372509011;T:1590552802;N:87251", 150, 150, null, null, 1586894082, 2334065454, 2372509011, 1590552802, 87251, "SRX17837650", "SRS15359801", "SRA1516844", "Institute of Hematology &amp; Blood Diseases Hospital|State Key Laboratory of Experimental Hematology", "Institute of Hematology & Blood Diseases Hospital", 2, 0.98745, 0.98691, 0.48401, 0.48011, 0.94095, 0.94113, 0.74796, 0.74138, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-10-09", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [71627, "SRR21849081", "SRX17837649", "SRS15359800", "SRP401744", "PRJNA888821", "The RNA binding protein CSDE1 promotes hematopoietic stem and progenitor cell generation via translational control of Wnt signaling", "PRJNA888821", "Other", "We identified RBP as an important post transcriptional regulator of HSPC generation and elucidated the underlying molecular mechanisms. The study also provides helpful insights into designing novel strategies for HSPC generation in vitro.", null, null, null, "33 hpf Zebrafish Bulk RIP seq.Control1", "Zebrafish 33 hpf.Bulk RIP seq.Control1", null, "breed:Zebrafish|age:33 hpf|dev stage:HSPC generation|sex:pooled male and female|tissue:whole embryos|treatment:5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "33 hpf Zebrafish Bulk RIP seq.Control1", "Control1", "Control1", "RIP Seq", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP401744", null, null, "Control1_1.fq.gz Control1_2.fq.gz", "fastq fastq", 6838591200.0, 22795304.0, "Control1 1.fq.gz", "0:150 1:150", "A:1483754703;C:1578056923;G:2412990846;T:1363739708;N:49020", 150, 150, null, null, 1483754703, 1578056923, 2412990846, 1363739708, 49020, "SRX17837649", "SRS15359800", "SRA1516844", "Institute of Hematology &amp; Blood Diseases Hospital|State Key Laboratory of 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"ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "ythdf2_MO_m6A_meRIP_replicate_2_R1.fastq.gz ythdf2_MO_m6A_meRIP_replicate_2_R2.fastq.gz", "fastq fastq", 7361721649.0, 26446542.0, "ythdf2 MO m6A meRIP replicate 2 R1.fastq.gz", "0:139.19 1:139.17", "A:1963471349;C:1716978769;G:1713549467;T:1967688429;N:33635", 139, 139, null, null, 1963471349, 1716978769, 1713549467, 1967688429, 33635, "SRX18764963", "SRS16199859", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.95246, 0.9547, 0.1386, 0.13796, 0.69757, 0.69593, 0.44772, 0.44911, 138, 138, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [72385, "SRR22805231", "SRX18764962", "SRS16199858", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "27", "27.ythdf2 MO m6A meRIP replicate 1", null, "strain:AB|isolate:27|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "27.ythdf2 MO m6A meRIP replicate 1", "27", "27", "27", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "ythdf2_MO_m6A_meRIP_replicate_1_R1.fastq.gz ythdf2_MO_m6A_meRIP_replicate_1_R2.fastq.gz", "fastq fastq", 7064658336.0, 25169165.0, "ythdf2 MO m6A meRIP replicate 1 R1.fastq.gz", "0:140.35 1:140.33", "A:1889792523;C:1642179006;G:1639348147;T:1893307582;N:31078", 140, 140, null, null, 1889792523, 1642179006, 1639348147, 1893307582, 31078, "SRX18764962", "SRS16199858", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.95312, 0.95495, 0.14782, 0.14808, 0.69856, 0.69656, 0.46053, 0.45683, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [72386, "SRR22805232", "SRX18764961", "SRS16199857", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "26", "26.Control knockdown m6A meRIP replicate 2", null, "strain:AB|isolate:26|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "26.Control knockdown m6A meRIP replicate 2", "26", "26", "26", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "Control_knockdown_m6A_meRIP_replicate_2_R1.fastq.gz Control_knockdown_m6A_meRIP_replicate_2_R2.fastq.gz", "fastq fastq", 6960835520.0, 25210812.0, "Control knockdown m6A meRIP replicate 2 R1.fastq.gz", "0:138.06 1:138.04", "A:1851748550;C:1628253635;G:1624430306;T:1856371475;N:31554", 138, 138, null, null, 1851748550, 1628253635, 1624430306, 1856371475, 31554, "SRX18764961", "SRS16199857", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.95077, 0.95337, 0.12974, 0.13019, 0.69846, 0.69737, 0.45561, 0.45724, 134, 134, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [72387, "SRR22805233", "SRX18764960", "SRS16199856", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "25", "25.Control knockdown m6A meRIP replicate 1", null, "strain:AB|isolate:25|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "25.Control knockdown m6A meRIP replicate 1", "25", "25", "25", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "Control_knockdown_m6A_meRIP_replicate_1_R1.fastq.gz Control_knockdown_m6A_meRIP_replicate_1_R2.fastq.gz", "fastq fastq", 7116588450.0, 25626978.0, "Control knockdown m6A meRIP replicate 1 R1.fastq.gz", "0:138.86 1:138.84", "A:1872021500;C:1685125220;G:1683152373;T:1876257768;N:31589", 138, 138, null, null, 1872021500, 1685125220, 1683152373, 1876257768, 31589, "SRX18764960", "SRS16199856", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.95363, 0.95468, 0.05483, 0.05373, 0.76777, 0.76648, 0.4523, 0.45215, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [72393, "SRR22805239", "SRX18764954", "SRS16199850", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "20", "20.BHbisPhenolF 10uM m6A meRIP replicate 2", null, "strain:AB|isolate:20|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "20.BHbisPhenolF 10uM m6A meRIP replicate 2", "20", "20", "20", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "BHPF_10uM_m6A_meRIP_replicate_2_R1.fastq.gz BHPF_10uM_m6A_meRIP_replicate_2_R2.fastq.gz", "fastq fastq", 7491317369.0, 26658666.0, "BHbisPhenolF 10uM m6A meRIP replicate 2 R1.fastq.gz", "0:140.51 1:140.49", "A:1978702731;C:1766538897;G:1763052208;T:1982989954;N:33579", 140, 140, null, null, 1978702731, 1766538897, 1763052208, 1982989954, 33579, "SRX18764954", "SRS16199850", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.9529, 0.95443, 0.08298, 0.08205, 0.68891, 0.68846, 0.47278, 0.47013, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [72394, "SRR22805240", "SRX18764953", "SRS16199849", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "19", "19.BHbisPhenolF 10uM m6A meRIP replicate 1", null, "strain:AB|isolate:19|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "19.BHbisPhenolF 10uM m6A meRIP replicate 1", "19", "19", "19", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "BHPF_10uM_m6A_meRIP_replicate_1_R1.fastq.gz BHPF_10uM_m6A_meRIP_replicate_1_R2.fastq.gz", "fastq fastq", 7103220388.0, 25558854.0, "BHbisPhenolF 10uM m6A meRIP replicate 1 R1.fastq.gz", "0:138.97 1:138.95", "A:1882505135;C:1667796740;G:1665421739;T:1887465071;N:31703", 138, 138, null, null, 1882505135, 1667796740, 1665421739, 1887465071, 31703, "SRX18764953", "SRS16199849", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.95261, 0.95474, 0.09233, 0.09094, 0.69794, 0.6966, 0.46269, 0.46455, 111, 111, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [72395, "SRR22805241", "SRX18764952", "SRS16199848", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "18", "18.DMSO control m6A meRIP replicate 2", null, "strain:AB|isolate:18|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "18.DMSO control m6A meRIP replicate 2", "18", "18", "18", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "DMSO_control_m6A_meRIP_replicate_2_R1.fastq.gz DMSO_control_m6A_meRIP_replicate_2_R2.fastq.gz", "fastq fastq", 7608584716.0, 27081562.0, "DMSO control m6A meRIP replicate 2 R1.fastq.gz", "0:140.48 1:140.47", "A:2016159583;C:1788089257;G:1783486901;T:2020815087;N:33888", 140, 140, null, null, 2016159583, 1788089257, 1783486901, 2020815087, 33888, "SRX18764952", "SRS16199848", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.9526, 0.95462, 0.08497, 0.08367, 0.69822, 0.69755, 0.46646, 0.4688, 114, 114, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [72396, "SRR22805242", "SRX18764951", "SRS16199847", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "17", "17.DMSO control m6A meRIP replicate 1", null, "strain:AB|isolate:17|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "17.DMSO control m6A meRIP replicate 1", "17", "17", "17", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "DMSO_control_m6A_meRIP_replicate_1_R1.fastq.gz DMSO_control_m6A_meRIP_replicate_1_R2.fastq.gz", "fastq fastq", 7394836277.0, 26199072.0, "DMSO control m6A meRIP replicate 1 R1.fastq.gz", "0:141.14 1:141.12", "A:1964011730;C:1732461692;G:1728237059;T:1970092128;N:33668", 141, 141, null, null, 1964011730, 1732461692, 1728237059, 1970092128, 33668, "SRX18764951", "SRS16199847", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.95315, 0.95536, 0.1083, 0.1071, 0.70694, 0.70587, 0.47144, 0.47082, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [72695, "SRR23071963", "SRX19025119", "SRS16444168", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "fac input rep2", "GSM6932553", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing", "fac input rep2", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf", "GSM6932553", "GSM6932553: fac input rep2; Danio rerio; RIP Seq", "GSM6932553 r1", "GSM6932553", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "fac_input_rep2.r1.fastq.gz fac_input_rep2.r2.fastq.gz", "fastq fastq", 2715443520.0, 22628696.0, "GSM6932553 r1", "0:60 1:60", "A:568252635;C:811004878;G:879629678;T:456548654;N:7675", 60, 60, null, null, 568252635, 811004878, 879629678, 456548654, 7675, "SRX19025119", "SRS16444168", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.76709, 0.75848, 0.06636, 0.06594, 0.96465, 0.96617, 0.79957, 0.75254, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72696, "SRR23071964", "SRX19025118", "SRS16444167", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "fac input rep1", "GSM6932552", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing", "fac input rep1", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf", "GSM6932552", "GSM6932552: fac input rep1; Danio rerio; RIP Seq", "GSM6932552 r1", "GSM6932552", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "fac_input_rep1.r1.fastq.gz fac_input_rep1.r2.fastq.gz", "fastq fastq", 2788666560.0, 23238888.0, "GSM6932552 r1", "0:60 1:60", "A:597611112;C:824776004;G:894293861;T:471977509;N:8074", 60, 60, null, null, 597611112, 824776004, 894293861, 471977509, 8074, "SRX19025118", "SRS16444167", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.75557, 0.74928, 0.06802, 0.06744, 0.96364, 0.96508, 0.80265, 0.73963, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72697, "SRR23071965", "SRX19025117", "SRS16444166", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "fac clip rep2", "GSM6932551", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing", "fac clip rep2", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf", "GSM6932551", "GSM6932551: fac clip rep2; Danio rerio; RIP Seq", "GSM6932551 r1", "GSM6932551", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "fac_clip_rep2.r1.fastq.gz fac_clip_rep2.r2.fastq.gz", "fastq fastq", 3636207480.0, 30301729.0, "GSM6932551 r1", "0:60 1:60", "A:856114407;C:984704325;G:1019721588;T:775657296;N:9864", 60, 60, null, null, 856114407, 984704325, 1019721588, 775657296, 9864, "SRX19025117", "SRS16444166", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.95337, 0.93978, 0.20127, 0.22016, 0.90295, 0.90893, 0.69108, 0.66666, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72698, "SRR23071966", "SRX19025116", "SRS16444165", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "fac clip rep1", "GSM6932550", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing", "fac clip rep1", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:1 mM FAC from 48 hpf to 78 hpf", "GSM6932550", "GSM6932550: fac clip rep1; Danio rerio; RIP Seq", "GSM6932550 r1", "GSM6932550", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "fac_clip_rep1.r1.fastq.gz fac_clip_rep1.r2.fastq.gz", "fastq fastq", 4241534520.0, 35346121.0, "GSM6932550 r1", "0:60 1:60", "A:1001822053;C:1148816744;G:1187189848;T:903693863;N:12012", 60, 60, null, null, 1001822053, 1148816744, 1187189848, 903693863, 12012, "SRX19025116", "SRS16444165", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.9489, 0.9407, 0.19979, 0.22138, 0.90161, 0.90741, 0.67794, 0.66231, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72699, "SRR23071967", "SRX19025115", "SRS16444164", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "dfo input rep2", "GSM6932549", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing", "dfo input rep2", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf", "GSM6932549", "GSM6932549: dfo input rep2; Danio rerio; RIP Seq", "GSM6932549 r1", "GSM6932549", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "dfo_input_rep2.r1.fastq.gz dfo_input_rep2.r2.fastq.gz", "fastq fastq", 2472387240.0, 20603227.0, "GSM6932549 r1", "0:60 1:60", "A:522247513;C:735343841;G:798068271;T:416720603;N:7012", 60, 60, null, null, 522247513, 735343841, 798068271, 416720603, 7012, "SRX19025115", "SRS16444164", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.7577, 0.75837, 0.06797, 0.06744, 0.96437, 0.96627, 0.80292, 0.74592, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72700, "SRR23071968", "SRX19025114", "SRS16444163", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "dfo input rep1", "GSM6932548", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing", "dfo input rep1", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf", "GSM6932548", "GSM6932548: dfo input rep1; Danio rerio; RIP Seq", "GSM6932548 r1", "GSM6932548", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "dfo_input_rep1.fastq.gz dfo_input_rep1.r2.fastq.gz", "fastq fastq", 2546588760.0, 21221573.0, "GSM6932548 r1", "0:60 1:60", "A:536450815;C:753080253;G:819027741;T:438022880;N:7071", 60, 60, null, null, 536450815, 753080253, 819027741, 438022880, 7071, "SRX19025114", "SRS16444163", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.75957, 0.75514, 0.06963, 0.06896, 0.96345, 0.96526, 0.80322, 0.73584, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72701, "SRR23071969", "SRX19025113", "SRS16444162", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "dfo clip rep2", "GSM6932547", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing", "dfo clip rep2", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf", "GSM6932547", "GSM6932547: dfo clip rep2; Danio rerio; RIP Seq", "GSM6932547 r1", "GSM6932547", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "dfo_clip_rep2.r1.fastq.gz dfo_clip_rep2.r2.fastq.gz", "fastq fastq", 4151061480.0, 34592179.0, "GSM6932547 r1", "0:60 1:60", "A:968004394;C:1130874104;G:1164829960;T:887341478;N:11544", 60, 60, null, null, 968004394, 1130874104, 1164829960, 887341478, 11544, "SRX19025113", "SRS16444162", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.92425, 0.93056, 0.20043, 0.2242, 0.8966, 0.901, 0.68964, 0.62588, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72702, "SRR23071970", "SRX19025112", "SRS16444161", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "dfo clip rep1", "GSM6932546", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf|geo loc name:missing|collection date:missing", "dfo clip rep1", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:0.5 mM DFO from 48 hpf to 78 hpf", "GSM6932546", "GSM6932546: dfo clip rep1; Danio rerio; RIP Seq", "GSM6932546 r1", "GSM6932546", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "dfo_clip_rep1.r1.fastq.gz dfo_clip_rep1.r2.fastq.gz", "fastq fastq", 3549376560.0, 29578138.0, "GSM6932546 r1", "0:60 1:60", "A:829453498;C:966398146;G:998787767;T:754727094;N:10055", 60, 60, null, null, 829453498, 966398146, 998787767, 754727094, 10055, "SRX19025112", "SRS16444161", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.94985, 0.93128, 0.20616, 0.22409, 0.89548, 0.90055, 0.67094, 0.65117, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72703, "SRR23071971", "SRX19025111", "SRS16444160", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "ctrl input rep2", "GSM6932545", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment|geo loc name:missing|collection date:missing", "ctrl input rep2", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment", "GSM6932545", "GSM6932545: ctrl input rep2; Danio rerio; RIP Seq", "GSM6932545 r1", "GSM6932545", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "ctrl_input_rep2.r1.fastq.gz ctrl_input_rep2.r2.fastq.gz", "fastq fastq", 2305351440.0, 19211262.0, "GSM6932545 r1", "0:60 1:60", "A:494731676;C:683635423;G:735706555;T:391271420;N:6366", 60, 60, null, null, 494731676, 683635423, 735706555, 391271420, 6366, "SRX19025111", "SRS16444160", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.75012, 0.76494, 0.06496, 0.06503, 0.9696, 0.97023, 0.80848, 0.76006, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72704, "SRR23071972", "SRX19025110", "SRS16444159", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "ctrl input rep1", "GSM6932544", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment|geo loc name:missing|collection date:missing", "ctrl input rep1", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment", "GSM6932544", "GSM6932544: ctrl input rep1; Danio rerio; RIP Seq", "GSM6932544 r1", "GSM6932544", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "ctrl_input_rep1.r1.fastq.gz ctrl_input_rep1.r2.fastq.gz", "fastq fastq", 2870115000.0, 23917625.0, "GSM6932544 r1", "0:60 1:60", "A:616586993;C:849261640;G:916690149;T:487568187;N:8031", 60, 60, null, null, 616586993, 849261640, 916690149, 487568187, 8031, "SRX19025110", "SRS16444159", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.76321, 0.76237, 0.06602, 0.06566, 0.97064, 0.96903, 0.68553, 0.75314, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72705, "SRR23071973", "SRX19025109", "SRS16444158", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "ctrl clip rep2", "GSM6932543", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment|geo loc name:missing|collection date:missing", "ctrl clip rep2", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment", "GSM6932543", "GSM6932543: ctrl clip rep2; Danio rerio; RIP Seq", "GSM6932543 r1", "GSM6932543", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "ctrl_clip_rep2.r1.fastq.gz ctrl_clip_rep2.r2.fastq.gz", "fastq fastq", 3309978960.0, 27583158.0, "GSM6932543 r1", "0:60 1:60", "A:774105538;C:895792317;G:931799487;T:708272623;N:8995", 60, 60, null, null, 774105538, 895792317, 931799487, 708272623, 8995, "SRX19025109", "SRS16444158", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.94553, 0.92262, 0.21092, 0.22735, 0.90985, 0.91407, 0.67372, 0.67171, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [72706, "SRR23071974", "SRX19025108", "SRS16444157", "SRP417272", "PRJNA923391", "MBD5  a m5C RNA reader  regulates histone ubiquitylation in development and function", "GSE222803", "Other", "Methyl CpG binding domain MBD containing proteins are readers of epigenetic information. The founding member  MeCP2  mutated in the Rett Syndrome  binds to methylated CpG DNAs.  MBD5 is an evolutionarily conserved MBD family member associated with epilepsy  autism spectrum disorders ASD  and early onset dementia. The mechanism of action of MBD5 remains unclear. Here we report that mbd5 regulates embryonic development  erythrocyte differentiation  iron metabolism  and behavior in zebrafish. MBD5 is essential to activate the expression of erythrocyte differentiation genes e.g.  hbae3  iron regulated genes e.g.  fth1  and ASD related genes e.g.  gabbr2  by binding to 5 methylcytosine m5C modified mRNAs  interacting with and stabilizing Additional Sex Combs Like 1 ASXL1  a component of the Polycomb Repressive Deubiquinase PR DUB complex  to facilitate removal of the repressive monoubiquitin mark at histone H2A H2A K119Ub  thereby facilitating gene activation. Together  these findings reveal MBD5 as a m5C RNA reader that links RNA methylation to histone modification in vivo. Overall design: [Dataset 1] 6 samples. Triplicates for ribo minus RNA Seq from 78 hpf zebrafish embryos treated with control or mbd5 morpholino [Dataset 2] 16 samples. Duplicates for CLIP seq experiments from 48 hpf 78 hpf zebrafish embryos treated with 0.5 mM DFO or 1 mM FAC", null, "pubmed:38366571", null, "ctrl clip rep1", "GSM6932542", null, "source name:whole embryo|tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment|geo loc name:missing|collection date:missing", "ctrl clip rep1", "Adapter trimming by Cutadapt Reads mapping by STAR to the transcriptome peak calling with pureCLIP or differential gene expression with DESeq2 Assembly: dr10 Supplementary files format and content: For [Dataset 1]  excel xlsx files  with differential expression by DESeq2. For [Dataset 2]  excel xlsx files  with CLIP seq peaks identified by pureCLIP algorithm", "whole embryo", "For [Dataset 1]  morpholino oligonucleotides are applied by microinjection. For [Dataset 2]  FAC F5879  Sigma Aldrich was dissolved in E3 medium at 50 mM and stored at 4\u00b0C. zebrafish were treated with 1 mM fresh FAC from 3 dpf 6 dpf every day prior to behavior analysis. DFO D9533  Sigma Aldrich was dissolved in E3 medium at 150 mM and stored at  20\u00b0C. Zebrafish were treated with 0.5 mM DFO from 3 dpf 6 dpf  replenished every day  prior to behavior analysis.", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", "Zebrafish embryos were treated with 0.003% 1 phenyl 2 thiourea PTU in E3 medium to prevent pigment formation. 3 month 9 month aged wild type or mbd5 mutant lines generated in this study were used for breeding or adult behavior analyses. Developmental stages were determined according to their morphology.", "tissue:whole embryo|genotype:Tg[zhsp70l:FLAGmbd5iso2 E2AGFP]|treatment:No treatment", "GSM6932542", "GSM6932542: ctrl clip rep1; Danio rerio; RIP Seq", "GSM6932542 r1", "GSM6932542", "1", "For [Dataset 1]  total RNAs were extracted with standard TRIzol protocol. For [Dataset 2]  76 hpf larval zebrafish were UV crosslinked and flash frozen in liquid nitrogen. Pellets were thawed on ice and resuspended in 3 volume of ice cold CLIP lysis buffer 50 mM HEPES pH 7.5  150 mM KCl  2 mM EDTA  0.5% v/v NP 40  0.5 mM DTT  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor. Pellets were lysed by rotating at 4 \u00b0C for 15 minutes post passing through a 26 G needle BD Biosciences. Embryo suspensions were sonicated on a bioruptor Diagenode with 30 s on/30 s off for 5 cycles. Lysates were cleared by centrifugation at 21 000 g for 15 minutes at 4 \u00b0C on a benchtop centrifuge. Supernatants were applied to Flag antibody Abcam conjugated protein A beads Invitrogen and left overnight at 4 \u00b0C on an end to end rotor. Beads were washed extensively with 1 ml wash buffer 50 mM HEPES pH 7.5  300 mM KCl  0.05% v/v NP 40  1 \u00d7 Halt\u2122 Protease and Phosphatase Inhibitor Cocktail  1 \u00d7 RNaseOUT Recombinant Ribonuclease Inhibitor at 4 \u00b0C for 5 times. Protein RNA complex conjugated to the beads were treated by 8 U/\u03bcL RNase T1 Thermo Scientific at 22 \u00b0C for 10 minutes with shaking. Input samples are digested in parallel. Then input and IP samples were separated on an SDS PAGE gel and gel slices at corresponding size ranges were treated by proteinase K Invitrogen elution. RNA was recovered with TRIZol reagent Invitrogen. Then T4 PNK Thermo Scientific end repair was performed with purified RNA before library constructions. For [Dataset 1]  RNA libraries for input samples were constructed by SMARTer Stranded Total RNA Seq Kit v2 TaKaRa  634417 with ribo minus RNA as input.  For [Dataset 2]  RNA libraries were constructed with NEB small RNA kit NEB. Libraries were pooled and sequenced on a NovaSeq 6000 sequencer with paired end mode 50 bp setting.", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP417272", null, "loader:fastq load.py", "ctrl_clip_rep1.r1.fastq.gz ctrl_clip_rep1.r2.fastq.gz", "fastq fastq", 3392768880.0, 28273074.0, "GSM6932542 r1", "0:60 1:60", "A:795387316;C:918606802;G:949982957;T:728782720;N:9085", 60, 60, null, null, 795387316, 918606802, 949982957, 728782720, 9085, "SRX19025108", "SRS16444157", "SRA1573941", "University of Chicago", "University of Chicago", 2, 0.92844, 0.92193, 0.20693, 0.22683, 0.90826, 0.91297, 0.68754, 0.67062, 60, 60, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "small_rna", "smarter", "bulk", "unknown", "unknown", null, "United States", "2023-01-12", "Multi-stage", "Multi-stage", "Whole Organism", "All anatomical structures"], [74097, "SRR23433707", "SRX19347585", "SRS16745103", "SRP422577", "PRJNA934472", "Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]", "GSE225136", "Other", "The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates", "parent bioproject:PRJNA934075", "pubmed:38605226", null, "mt input rep2", "GSM7039976", null, "source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing", "mt input rep2", "Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions \u00d7 exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample", "trunk region of zebrafish embryos", null, "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1", "GSM7039976", "GSM7039976: mt input rep2; Danio rerio; RIP Seq", "GSM7039976 r1", "GSM7039976", "1", "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "loader:fastq load.py", "mt2_input_R1.fastq.gz mt2_input_R2.fastq.gz", "fastq fastq", 11987520719.0, 46102921.0, "GSM7039976 r1", "0:129.98 1:130.04", "A:2818961833;C:3185310727;G:3125514774;T:2857679978;N:53407", 129, 130, null, null, 2818961833, 3185310727, 3125514774, 2857679978, 53407, "SRX19347585", "SRS16745103", "SRA1590470", "Huazhong University of Science and Technology", "Huazhong University of Science and Technology", 2, 0.92498, 0.92723, 0.26901, 0.26318, 0.72691, 0.72646, 0.55297, 0.56674, 103, 103, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [74098, "SRR23433708", "SRX19347584", "SRS16745102", "SRP422577", "PRJNA934472", "Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]", "GSE225136", "Other", "The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates", "parent bioproject:PRJNA934075", "pubmed:38605226", null, "mt IP  rep2", "GSM7039975", null, "source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing", "mt IP  rep2", "Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions \u00d7 exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample", "trunk region of zebrafish embryos", null, "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A", "GSM7039975", "GSM7039975: mt IP  rep2; Danio rerio; RIP Seq", "GSM7039975 r1", "GSM7039975", "1", "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "loader:fastq load.py", "mt2_IP_R1.fastq.gz mt2_IP_R2.fastq.gz", "fastq fastq", 10153956215.0, 38248544.0, "GSM7039975 r1", "0:132.74 1:132.73", "A:2745473943;C:2337991849;G:2337827470;T:2732618213;N:44740", 132, 132, null, null, 2745473943, 2337991849, 2337827470, 2732618213, 44740, "SRX19347584", "SRS16745102", "SRA1590470", "Huazhong University of Science and Technology", "Huazhong University of Science and Technology", 2, 0.91716, 0.92124, 0.17169, 0.17213, 0.69057, 0.69092, 0.45478, 0.4582, 133, 133, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [74099, "SRR23433709", "SRX19347583", "SRS16745101", "SRP422577", "PRJNA934472", "Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]", "GSE225136", "Other", "The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates", "parent bioproject:PRJNA934075", "pubmed:38605226", null, "mt input rep1", "GSM7039974", null, "source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing", "mt input rep1", "Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions \u00d7 exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample", "trunk region of zebrafish embryos", null, "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1", "GSM7039974", "GSM7039974: mt input rep1; Danio rerio; RIP Seq", "GSM7039974 r1", "GSM7039974", "1", "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "loader:fastq load.py", "mt1_input_R1.fastq.gz mt1_input_R2.fastq.gz", "fastq fastq", 11979139891.0, 42665152.0, "GSM7039974 r1", "0:140.37 1:140.40", "A:3143624979;C:2854874515;G:2775482425;T:3204809556;N:348416", 140, 140, null, null, 3143624979, 2854874515, 2775482425, 3204809556, 348416, "SRX19347583", "SRS16745101", "SRA1590470", "Huazhong University of Science and Technology", "Huazhong University of Science and Technology", 2, 0.89189, 0.90001, 0.35263, 0.34917, 0.71058, 0.70907, 0.54777, 0.55293, 125, 125, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [74100, "SRR23433710", "SRX19347582", "SRS16745100", "SRP422577", "PRJNA934472", "Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]", "GSE225136", "Other", "The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates", "parent bioproject:PRJNA934075", "pubmed:38605226", null, "mt IP  rep1", "GSM7039973", null, "source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing", "mt IP  rep1", "Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions \u00d7 exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample", "trunk region of zebrafish embryos", null, "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A", "GSM7039973", "GSM7039973: mt IP  rep1; Danio rerio; RIP Seq", "GSM7039973 r1", "GSM7039973", "1", "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "loader:fastq load.py", "mt1_IP_R1.fastq.gz mt1_IP_R2.fastq.gz", "fastq fastq", 12145897814.0, 43352862.0, "GSM7039973 r1", "0:140.09 1:140.07", "A:3459248498;C:2615706052;G:2628261332;T:3442334843;N:347089", 140, 140, null, null, 3459248498, 2615706052, 2628261332, 3442334843, 347089, "SRX19347582", "SRS16745100", "SRA1590470", "Huazhong University of Science and Technology", "Huazhong University of Science and Technology", 2, 0.86681, 0.87664, 0.304, 0.305, 0.68012, 0.67831, 0.44055, 0.4418, 142, 142, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [74101, "SRR23433711", "SRX19347581", "SRS16745099", "SRP422577", "PRJNA934472", "Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]", "GSE225136", "Other", "The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates", "parent bioproject:PRJNA934075", "pubmed:38605226", null, "sibling input rep2", "GSM7039972", null, "source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing", "sibling input rep2", "Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions \u00d7 exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample", "trunk region of zebrafish embryos", null, "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1", "GSM7039972", "GSM7039972: sibling input rep2; Danio rerio; RIP Seq", "GSM7039972 r1", "GSM7039972", "1", "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "loader:fastq load.py", "sibling2_input_R1.fastq.gz sibling2_input_R2.fastq.gz", "fastq fastq", 12272791017.0, 47579480.0, "GSM7039972 r1", "0:128.94 1:129.00", "A:2905993856;C:3237323144;G:3186607999;T:2942811604;N:54414", 128, 129, null, null, 2905993856, 3237323144, 3186607999, 2942811604, 54414, "SRX19347581", "SRS16745099", "SRA1590470", "Huazhong University of Science and Technology", "Huazhong University of Science and Technology", 2, 0.92733, 0.92947, 0.27234, 0.26711, 0.72391, 0.72409, 0.52625, 0.55052, 126, 126, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [74102, "SRR23433712", "SRX19347580", "SRS16745098", "SRP422577", "PRJNA934472", "Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]", "GSE225136", "Other", "The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates", "parent bioproject:PRJNA934075", "pubmed:38605226", null, "sibling IP  rep2", "GSM7039971", null, "source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing", "sibling IP  rep2", "Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions \u00d7 exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample", "trunk region of zebrafish embryos", null, "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A", "GSM7039971", "GSM7039971: sibling IP  rep2; Danio rerio; RIP Seq", "GSM7039971 r1", "GSM7039971", "1", "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "loader:fastq load.py", "sibling2_IP_R1.fastq.gz sibling2_IP_R2.fastq.gz", "fastq fastq", 10402768351.0, 39113148.0, "GSM7039971 r1", "0:132.99 1:132.98", "A:2806053427;C:2400476074;G:2403977422;T:2792214821;N:46607", 132, 132, null, null, 2806053427, 2400476074, 2403977422, 2792214821, 46607, "SRX19347580", "SRS16745098", "SRA1590470", "Huazhong University of Science and Technology", "Huazhong University of Science and Technology", 2, 0.90198, 0.9063, 0.18008, 0.18091, 0.69428, 0.69396, 0.44811, 0.42925, 147, 147, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [74103, "SRR23433713", "SRX19347579", "SRS16745097", "SRP422577", "PRJNA934472", "Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]", "GSE225136", "Other", "The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates", "parent bioproject:PRJNA934075", "pubmed:38605226", null, "sibling input rep1", "GSM7039970", null, "source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing", "sibling input rep1", "Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions \u00d7 exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample", "trunk region of zebrafish embryos", null, "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1", "GSM7039970", "GSM7039970: sibling input rep1; Danio rerio; RIP Seq", "GSM7039970 r1", "GSM7039970", "1", "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "loader:fastq load.py", "sibling1_input_R1.fastq.gz sibling1_input_R2.fastq.gz", "fastq fastq", 13094981449.0, 46647417.0, "GSM7039970 r1", "0:140.35 1:140.37", "A:3434495131;C:3120669719;G:3036482303;T:3502963330;N:370966", 140, 140, null, null, 3434495131, 3120669719, 3036482303, 3502963330, 370966, "SRX19347579", "SRS16745097", "SRA1590470", "Huazhong University of Science and Technology", "Huazhong University of Science and Technology", 2, 0.89276, 0.90193, 0.352, 0.3489, 0.70905, 0.70719, 0.52165, 0.52427, 142, 142, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [74104, "SRR23433714", "SRX19347578", "SRS16745096", "SRP422577", "PRJNA934472", "Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq]", "GSE225136", "Other", "The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates", "parent bioproject:PRJNA934075", "pubmed:38605226", null, "sibling IP  rep1", "GSM7039969", null, "source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing", "sibling IP  rep1", "Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions \u00d7 exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample", "trunk region of zebrafish embryos", null, "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A", "GSM7039969", "GSM7039969: sibling IP  rep1; Danio rerio; RIP Seq", "GSM7039969 r1", "GSM7039969", "1", "Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 \u03bcg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript\u2122 II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP422577", null, "loader:fastq load.py", "sibling1_IP_R1.fastq.gz sibling1_IP_R2.fastq.gz", "fastq fastq", 12317957591.0, 43954374.0, "GSM7039969 r1", "0:140.17 1:140.08", "A:3509912915;C:2650796924;G:2663699373;T:3493137659;N:410720", 140, 140, null, null, 3509912915, 2650796924, 2663699373, 3493137659, 410720, "SRX19347578", "SRS16745096", "SRA1590470", "Huazhong University of Science and Technology", "Huazhong University of Science and Technology", 2, 0.87054, 0.88058, 0.30375, 0.30421, 0.67783, 0.67584, 0.44329, 0.44327, 142, 142, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-02-12", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [75633, "SRR24746216", "SRX20523363", "SRS17832951", "SRP439774", "PRJNA976671", "RNA seq of RNAs immunoprecipitated with eIF4E1c and eiF4E1c in early zebrafish embryos", "GSE233570", "Other", "To investigate the mRNAs that are bound by eIF4E1b and eIF4E1c  we performed RNA immunoprecipitation RIP experiments using anti GFP beads and transgenic embryos expressing GFP eIF4E1b or GFP eIF4E1c at the 8 cell stage. Overall design: We performed differential expression gene analyses of eIF4E1b n = 3 biological replicates versus eIF4E1c n = 2 biological replciates RIP and input samples.", null, "pubmed:38177902", null, "eIF4E1c input biol rep 3", "GSM7430668", null, "source name:Whole embryo lysate|tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c|geo loc name:missing|collection date:missing", "eIF4E1c input biol rep 3", "RNA seq reads were trimmed using trim galore v0.5.0  and reads mapping to abundant sequences Dr mitochondrial chromosome  SILVA Dr ribosomal RNA  phiX174 genome were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter  s 0 for unstranded analysis subread v1.6.2. Differential gene expression analysis on raw counts and variance stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1. Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files with per gene read counts", "Whole embryo lysate", null, "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1c", "GSM7430668", "GSM7430668: eIF4E1c input biol rep 3; Danio rerio; RIP Seq", "GSM7430668 r1", "GSM7430668", "1", "RNA Clean & Concentrator kit Zymo Research of RIP and input samples SMARTerStrandedRNA library Ribo Zero for input samples; SMARTer ultra low RNA kit for RIP samples RNA Seq RIP and ssRNA seq Ribo Ziro", null, "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP439774", null, "loader:fastq load.py", "e1c-RIP_input_3_1.fastq.gz e1c-RIP_input_3_2.fastq.gz", "fastq fastq", 3690634738.0, 18270469.0, 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