{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", experiment.library_strategy = \"RIP-Seq\" and tissue_curation = \"Whole Organism\"", "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"], [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"], [40576, "SRR3228716", "SRX1634616", "SRS1345843", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A CLIP 8", "GSM2088181", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A CLIP 8", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:8|genotype:WT|treatment:n1", "GSM2088181", "GSM2088181: m6A CLIP 8; Danio rerio; RIP Seq", "GSM2088181", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088181", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_8h-IP.fastq.gz", "fastq", 921977050.0, 18439541.0, "GSM2088181 r1", "0:50", "A:233396466;C:263744643;G:252737160;T:172064890;N:33891", 50, null, null, null, 233396466, 263744643, 252737160, 172064890, 33891, "SRX1634616", "SRS1345843", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.61408, null, 0.1783, null, 0.88032, null, 0.72361, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40577, "SRR3228715", "SRX1634615", "SRS1345844", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A CLIP 6", "GSM2088180", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A CLIP 6", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:6|genotype:WT|treatment:n1", "GSM2088180", "GSM2088180: m6A CLIP 6; Danio rerio; RIP Seq", "GSM2088180", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088180", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_6h-IP.fastq.gz", "fastq", 811777600.0, 16235552.0, "GSM2088180 r1", "0:50", "A:214241727;C:241830821;G:208608337;T:147066789;N:29926", 50, null, null, null, 214241727, 241830821, 208608337, 147066789, 29926, "SRX1634615", "SRS1345844", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.68946, null, 0.17622, null, 0.9194, null, 0.62968, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40578, "SRR3228714", "SRX1634614", "SRS1345845", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A CLIP 4", "GSM2088179", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A CLIP 4", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:4|genotype:WT|treatment:n1", "GSM2088179", "GSM2088179: m6A CLIP 4; Danio rerio; RIP Seq", "GSM2088179", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088179", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_4h-IP.fastq.gz", "fastq", 746223800.0, 14924476.0, "GSM2088179 r1", "0:50", "A:185147085;C:236139555;G:187875436;T:137034934;N:26790", 50, null, null, null, 185147085, 236139555, 187875436, 137034934, 26790, "SRX1634614", "SRS1345845", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.80174, null, 0.17015, null, 0.86164, null, 0.77262, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40579, "SRR3228713", "SRX1634613", "SRS1345846", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A CLIP 2", "GSM2088178", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A CLIP 2", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:2|genotype:WT|treatment:n1", "GSM2088178", "GSM2088178: m6A CLIP 2; Danio rerio; RIP Seq", "GSM2088178", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088178", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_2h-IP.fastq.gz", "fastq", 937426800.0, 18748536.0, "GSM2088178 r1", "0:50", "A:263526034;C:262864870;G:241415141;T:169586820;N:33935", 50, null, null, null, 263526034, 262864870, 241415141, 169586820, 33935, "SRX1634613", "SRS1345846", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.75612, null, 0.2242, null, 0.87823, null, 0.61308, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40580, "SRR3228712", "SRX1634612", "SRS1345847", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A CLIP 0", "GSM2088177", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A CLIP 0", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:0|genotype:WT|treatment:n1", "GSM2088177", "GSM2088177: m6A CLIP 0; Danio rerio; RIP Seq", "GSM2088177", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088177", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_0h-IP.fastq.gz", "fastq", 1320186200.0, 26403724.0, "GSM2088177 r1", "0:50", "A:362282258;C:387362464;G:326692598;T:243799324;N:49556", 50, null, null, null, 362282258, 387362464, 326692598, 243799324, 49556, "SRX1634612", "SRS1345847", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.50689, null, 0.10395, null, 0.89755, null, 0.72663, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40581, "SRR3228711", "SRX1634611", "SRS1345848", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input CLIP 8", "GSM2088176", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input CLIP 8", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:8|genotype:WT|treatment:n1", "GSM2088176", "GSM2088176: input CLIP 8; Danio rerio; RIP Seq", "GSM2088176", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088176", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_8h-input.fastq.gz", "fastq", 1971263900.0, 39425278.0, "GSM2088176 r1", "0:50", "A:530986171;C:559974651;G:547087685;T:333110850;N:104543", 50, null, null, null, 530986171, 559974651, 547087685, 333110850, 104543, "SRX1634611", "SRS1345848", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.64576, null, 0.23563, null, 0.91618, null, 0.71461, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40582, "SRR3228710", "SRX1634610", "SRS1345849", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input CLIP 6", "GSM2088175", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input CLIP 6", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:6|genotype:WT|treatment:n1", "GSM2088175", "GSM2088175: input CLIP 6; Danio rerio; RIP Seq", "GSM2088175", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088175", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_6h-input.fastq.gz", "fastq", 2424925650.0, 48498513.0, "GSM2088175 r1", "0:50", "A:622469966;C:699224547;G:701719139;T:401382845;N:129153", 50, null, null, null, 622469966, 699224547, 701719139, 401382845, 129153, "SRX1634610", "SRS1345849", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.68121, null, 0.23857, null, 0.93123, null, 0.73919, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40583, "SRR3228709", "SRX1634609", "SRS1345850", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input CLIP 4", "GSM2088174", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input CLIP 4", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:4|genotype:WT|treatment:n1", "GSM2088174", "GSM2088174: input CLIP 4; Danio rerio; RIP Seq", "GSM2088174", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088174", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_4h-input.fastq.gz", "fastq", 1996829250.0, 39936585.0, "GSM2088174 r1", "0:50", "A:527211013;C:600800804;G:528828160;T:339883128;N:106145", 50, null, null, null, 527211013, 600800804, 528828160, 339883128, 106145, "SRX1634609", "SRS1345850", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.60745, null, 0.19305, null, 0.92537, null, 0.74508, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40584, "SRR3228708", "SRX1634608", "SRS1345851", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input CLIP 2", "GSM2088173", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input CLIP 2", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:2|genotype:WT|treatment:n1", "GSM2088173", "GSM2088173: input CLIP 2; Danio rerio; RIP Seq", "GSM2088173", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088173", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_2h-input.fastq.gz", "fastq", 2119606350.0, 42392127.0, "GSM2088173 r1", "0:50", "A:555894042;C:598667411;G:609233481;T:355698501;N:112915", 50, null, null, null, 555894042, 598667411, 609233481, 355698501, 112915, "SRX1634608", "SRS1345851", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.65392, null, 0.2263, null, 0.9049, null, 0.72736, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40585, "SRR3228707", "SRX1634607", "SRS1345852", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input CLIP 0", "GSM2088172", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input CLIP 0", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:0|genotype:WT|treatment:n1", "GSM2088172", "GSM2088172: input CLIP 0; Danio rerio; RIP Seq", "GSM2088172", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088172", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "CLIP_0h-input.fastq.gz", "fastq", 2150269400.0, 43005388.0, "GSM2088172 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX1634607", "SRS1345852", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.57233, null, 0.18947, null, 0.91323, null, 0.75741, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40586, "SRR3228706", "SRX1634606", "SRS1345853", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A IP 8", "GSM2088171", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A IP 8", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:8|genotype:WT|treatment:n1", "GSM2088171", "GSM2088171: m6A IP 8; Danio rerio; RIP Seq", "GSM2088171", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088171", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_8h.IP.fastq.gz", "fastq", 527347000.0, 10546940.0, "GSM2088171 r1", "0:50", "A:90387238;C:157767772;G:129133581;T:150048442;N:9967", 50, null, null, null, 90387238, 157767772, 129133581, 150048442, 9967, "SRX1634606", "SRS1345853", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.90207, null, 0.11796, null, 0.80208, null, 0.51587, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40587, "SRR3228705", "SRX1634605", "SRS1345854", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A IP 6", "GSM2088170", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A IP 6", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:6|genotype:WT|treatment:n1", "GSM2088170", "GSM2088170: m6A IP 6; Danio rerio; RIP Seq", "GSM2088170", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088170", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_6h.IP.fastq.gz", "fastq", 606551300.0, 12131026.0, "GSM2088170 r1", "0:50", "A:100429722;C:200919401;G:156361859;T:148828837;N:11481", 50, null, null, null, 100429722, 200919401, 156361859, 148828837, 11481, "SRX1634605", "SRS1345854", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.94517, null, 0.23269, null, 0.84571, null, 0.73203, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40588, "SRR3228704", "SRX1634604", "SRS1345855", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A IP 4", "GSM2088169", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A IP 4", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:4|genotype:WT|treatment:n1", "GSM2088169", "GSM2088169: m6A IP 4; Danio rerio; RIP Seq", "GSM2088169", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088169", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_4h.IP.fastq.gz", "fastq", 616373350.0, 12327467.0, "GSM2088169 r1", "0:50", "A:103511937;C:199101152;G:159952372;T:153796186;N:11703", 50, null, null, null, 103511937, 199101152, 159952372, 153796186, 11703, "SRX1634604", "SRS1345855", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.9484, null, 0.20806, null, 0.81349, null, 0.68893, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40589, "SRR3228703", "SRX1634603", "SRS1345856", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A IP 2", "GSM2088168", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A IP 2", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:2|genotype:WT|treatment:n1", "GSM2088168", "GSM2088168: m6A IP 2; Danio rerio; RIP Seq", "GSM2088168", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088168", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_2h.IP.fastq.gz", "fastq", 560037350.0, 11200747.0, "GSM2088168 r1", "0:50", "A:90079119;C:192220024;G:154098019;T:123629702;N:10486", 50, null, null, null, 90079119, 192220024, 154098019, 123629702, 10486, "SRX1634603", "SRS1345856", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.95056, null, 0.25053, null, 0.87322, null, 0.82008, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40590, "SRR3228702", "SRX1634602", "SRS1345857", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "m6A IP 0", "GSM2088167", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "m6A IP 0", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:0|genotype:WT|treatment:n1", "GSM2088167", "GSM2088167: m6A IP 0; Danio rerio; RIP Seq", "GSM2088167", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088167", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_0h.IP.fastq.gz", "fastq", 458827450.0, 9176549.0, "GSM2088167 r1", "0:50", "A:74889651;C:150121353;G:121032505;T:112775237;N:8704", 50, null, null, null, 74889651, 150121353, 121032505, 112775237, 8704, "SRX1634602", "SRS1345857", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.96567, null, 0.22221, null, 0.84471, null, 0.70341, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40591, "SRR3228701", "SRX1634601", "SRS1345858", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input 8", "GSM2088166", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input 8", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:8|genotype:WT|treatment:n1", "GSM2088166", "GSM2088166: input 8; Danio rerio; RIP Seq", "GSM2088166", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088166", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_8h.input.fastq.gz", "fastq", 575536100.0, 11510722.0, "GSM2088166 r1", "0:50", "A:111158012;C:168916114;G:151564939;T:143886262;N:10773", 50, null, null, null, 111158012, 168916114, 151564939, 143886262, 10773, "SRX1634601", "SRS1345858", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.95515, null, 0.19883, null, 0.79245, null, 0.6247, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40592, "SRR3228700", "SRX1634600", "SRS1345859", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input 6", "GSM2088165", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input 6", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:6|genotype:WT|treatment:n1", "GSM2088165", "GSM2088165: input 6; Danio rerio; RIP Seq", "GSM2088165", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088165", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_6h.input.fastq.gz", "fastq", 613333150.0, 12266663.0, "GSM2088165 r1", "0:50", "A:113451661;C:194144306;G:164598114;T:141127589;N:11480", 50, null, null, null, 113451661, 194144306, 164598114, 141127589, 11480, "SRX1634600", "SRS1345859", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.97989, null, 0.33526, null, 0.84798, null, 0.72512, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40593, "SRR3228699", "SRX1634599", "SRS1345860", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input 4", "GSM2088164", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input 4", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:4|genotype:WT|treatment:n1", "GSM2088164", "GSM2088164: input 4; Danio rerio; RIP Seq", "GSM2088164", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088164", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_4h.input.fastq.gz", "fastq", 576058200.0, 11521164.0, "GSM2088164 r1", "0:50", "A:108062480;C:178888385;G:153976688;T:135119699;N:10948", 50, null, null, null, 108062480, 178888385, 153976688, 135119699, 10948, "SRX1634599", "SRS1345860", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.97495, null, 0.29544, null, 0.81162, null, 0.71268, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40594, "SRR3228698", "SRX1634598", "SRS1345861", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input 2", "GSM2088163", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input 2", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:2|genotype:WT|treatment:n1", "GSM2088163", "GSM2088163: input 2; Danio rerio; RIP Seq", "GSM2088163", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088163", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_2h.input.fastq.gz", "fastq", 703375200.0, 14067504.0, "GSM2088163 r1", "0:50", "A:125686246;C:228251341;G:193846290;T:155577830;N:13493", 50, null, null, null, 125686246, 228251341, 193846290, 155577830, 13493, "SRX1634598", "SRS1345861", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.98596, null, 0.35619, null, 0.88521, null, 0.80927, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [40595, "SRR3228697", "SRX1634597", "SRS1345862", "SRP071818", "PRJNA315314", "The functions of m6A and Ythdf2 during zebrafish early development", "GSE79213", "Other", "We report the m6A methylation maps of zebrafish embryos during early development and transcriptome wide changes occured in ythdf2 LOF mutant embryos. Our study reveals the m6A dependent RNA decay as a previously unidentified maternal mode mechanism to regulate maternal mRNA clearance during zebrafish\u00a0\u00a0 MZT highlighting the critical role of the m6A mRNA methylation in animal development. Overall design: m6A seq of mRNA from zebrafish embryos at 0 2 4 6 8 h.p.f.; mRNA seq of wild type and maternal ythdf2 null mutant embryos at 0 2 4 6 8 h.p.f.; mRNA seq of embryos injected with control or ythdf2 MO at xxx h.p.f.; mRNA seq of wild type and maternal zygotic ythdf2 null mutant embryos at 6 8 12 24 h.p.f; and mRNA seq of wild type and maternal ythdf2 null mutant embryos injected with control or ythdf2 MO at xxx 36 48 h.p.f. Replicate of each seq is also included.", null, "pubmed:28192787", null, "input 0", "GSM2088162", null, "tissue:whole zebrafish embryo|genotype:WT|treatment:n1", "input 0", "Data analysis for each experiment: 1 for m6A seq reads were aligned to the reference genome danRer10 using Tophat v2.0.14 ref with parameter g 1 library type=fr firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp average fragments size and converted from genome based coordinates to isoform based coordinates in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform windows with reads counts less than 1/20 of the top window in both m6A IP and input sample were excluded. For each gene the reads count in each window was normalized by the median count of all windows of that gene. A fisher exact test was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2Enrichment Score >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak or window: reads count of the IP sample in the current peak/window a median reads count of the IP sample in all 100 bp windows on the current mRNA b reads count of the input sample in the current peak/window c and median reads count of the input sample in all 100 bp windows on the current mRNA d. The enrichment score of each window was calculated as a\u00d7d/b\u00d7c. 2 for m6A CLIP seq post removing the adapter sequence the reads were mapped to the reference genome danRer10 using bowtie2. Peak calling method was similar to previous study chen kai's Angew 2015. Briefly mutations were considered as signal and all mapped reads were treated as background. A Gaussian Kernel density estimation were used to identify the binding regions. The motif analysis was performed using HOMER homer ref here to search motifs in each set of m6A peaks. The longest isoform of all genes was used as background. 3 for mRNA Seq Reads were mapped with Tophat and Cufflink v2.2.1 was used to calculate the FPKM of each gene to represent their mRNA expression level.", "whole zebrafish embryo", null, "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "embryos were collected and cultured in medium at 28.5 \u00b0C and then harvested at each time point into TRIzol.", "development time h.p.f.:0|genotype:WT|treatment:n1", "GSM2088162", "GSM2088162: input 0; Danio rerio; RIP Seq", "GSM2088162", null, "1", "total RNA was extracted using Direct zol Zymo from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples mRNA was sonicated and subjected to IP using m6A antibody Synaptic Systems 202003. Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit Illumina.", "GEO Accession:GSM2088162", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP071818", null, null, "m6A_0h.input.fastq.gz", "fastq", 650787500.0, 13015750.0, "GSM2088162 r1", "0:50", "A:117902403;C:207274717;G:177773347;T:147824646;N:12387", 50, null, null, null, 117902403, 207274717, 177773347, 147824646, 12387, "SRX1634597", "SRS1345862", "SRA385720", "GEO", "Chuan He Lab, Chemistry, University of Chicago", 1, 0.98268, null, 0.32108, null, 0.85669, null, 0.76239, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-03-14", "Undetermined", "Embryo", "Whole Organism", "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"], [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"], [53427, "SRR9854014", "SRX6608456", "SRS5172704", "SRP216689", "PRJNA557179", "Role of the Exon Junction Complex in Danio rerio", "GSE135019", "Transcriptome Analysis", "The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants", null, null, null, "RBM8A RIPSEQ Rep3", "GSM3983830", null, "tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma cat# Y1253|genotype/variation:RBM8A", "RBM8A RIPSEQ Rep3", "Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples", "Whole embryo", "None NA", "RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.", "All embryos were raised at 28.5C upto the required developmental timepoint.", "developmental stage:24 hpf|rip antibody:Human Y14 Sigma cat# Y1253|genotype/variation:RBM8A", "GSM3983830", "GSM3983830: RBM8A RIPSEQ Rep3; Danio rerio; RIP Seq", "GSM3983830", null, "1", "RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.", "GEO Accession:GSM3983830", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP216689", null, "loader:fastq load.py", "ripseqB3.fastq.gz", "fastq", 1174462616.0, 32753220.0, "GSM3983830 r1", "0:35.86", "A:277856243;C:303697175;G:340240303;T:252574884;N:94011", 35, null, null, null, 277856243, 303697175, 340240303, 252574884, 94011, "SRX6608456", "SRS5172704", "SRA928193", "GEO", "Guramrit Singh, Molecular Genetics, The Ohio State University", 1, 0.90426, null, 0.1746, null, 0.77341, null, 0.57553, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-29", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [53428, "SRR9854013", "SRX6608455", "SRS5172702", "SRP216689", "PRJNA557179", "Role of the Exon Junction Complex in Danio rerio", "GSE135019", "Transcriptome Analysis", "The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants", null, null, null, "RBM8A RIPSEQ Rep2", "GSM3983829", null, "tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma cat# Y1253|genotype/variation:RBM8A", "RBM8A RIPSEQ Rep2", "Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples", "Whole embryo", "None NA", "RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.", "All embryos were raised at 28.5C upto the required developmental timepoint.", "developmental stage:24 hpf|rip antibody:Human Y14 Sigma cat# Y1253|genotype/variation:RBM8A", "GSM3983829", "GSM3983829: RBM8A RIPSEQ Rep2; Danio rerio; RIP Seq", "GSM3983829", null, "1", "RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.", "GEO Accession:GSM3983829", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP216689", null, "loader:fastq load.py", "ripseqB2.fastq.gz", "fastq", 65641776.0, 2466295.0, "GSM3983829 r1", "0:26.62", "A:18933213;C:16060113;G:13492679;T:17151951;N:3820", 26, null, null, null, 18933213, 16060113, 13492679, 17151951, 3820, "SRX6608455", "SRS5172702", "SRA928193", "GEO", "Guramrit Singh, Molecular Genetics, The Ohio State University", 1, 0.17621, null, 0.02351, null, 0.88069, null, 0.60622, null, 15, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-29", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [53429, "SRR9854012", "SRX6608454", "SRS5172701", "SRP216689", "PRJNA557179", "Role of the Exon Junction Complex in Danio rerio", "GSE135019", "Transcriptome Analysis", "The exon junction complex EJC is composed of three core proteins Rbm8a Magoh and Eif4a3 and is thought to play a role in several post transcriptional processes. In this study we focus on understanding the role of EJC in zebrafish development. We identified transcriptome wide binding sites of EJC in zebrafish via RNA:protein immunoprecipitation followed by deep sequencing RIP Seq. We find that as in human cells zebrafish EJC is deposited about 24 nts upstream of exon exon junctions. We also identify transcripts regulated by Rbm8a and Magoh in zebrafish embryos using whole embryo RNA seq from rbm8a mutant magoh mutant and wild type sibling embryos. This study shows that nonsense mediated mRNA decay is dysregulated in zebrafish EJC mutants. Overall design: Analysis of exon junction complex EJC footprints in Danio rerio and analysis of gene expression in Danio rerio EJC mutants", null, null, null, "RBM8A RIPSEQ Rep1", "GSM3983828", null, "tissue:Whole embryo|developmental stage:24 hpf|rip antibody:Human Y14 Sigma cat# Y1253|genotype/variation:RBM8A", "RBM8A RIPSEQ Rep1", "Base calling was performed automatically in Illumina BaseSpace post sequencing Sequenced reads were trimmed for adaptor sequence and random barcodes using cutadapt v1.16 with parameters m 20 discard untrimmed then mapped to hg38 whole genome using tophat v2.0.14 with default parameters p 12 Multi mapped reads were removed based on tophat alignment score < 50 and PCR duplicates were removed only for the RIP seq data based on random barcodes RIP Seq coverage data was generated using bedtools intersect v 2.25.0 with parameters s c F 0.51 sorted Genome build: GRCz10 Supplementary files format and content: RNA Seq: FPKM as caculated by DESeq2 for each gene in the samples Supplementary files format and content: RIP seq: RPKM each transcript in the samples", "Whole embryo", "None NA", "RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.", "All embryos were raised at 28.5C upto the required developmental timepoint.", "developmental stage:24 hpf|rip antibody:Human Y14 Sigma cat# Y1253|genotype/variation:RBM8A", "GSM3983828", "GSM3983828: RBM8A RIPSEQ Rep1; Danio rerio; RIP Seq", "GSM3983828", null, "1", "RIP Seq samples were extracted from the IP eluate by Phenol Chloroform Isoamyl alcohol extraction. RNA seq samples were obatined by harvesting whole embryos in TRIZOL. Libraries were prepared using a custom protocol described in detail in Gangras et al. Methods Mol Biol. 2018;1680:1 28. Briefly a DNA adapter ligated to RNA fragments was used to obtain a reverse transcription RT product which was circularized and used for PCR amplification with primers for Illumina HiSeq sequencing.", "GEO Accession:GSM3983828", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP216689", null, "loader:fastq load.py", "ripseqB1.fastq.gz", "fastq", 403183413.0, 11908151.0, "GSM3983828 r1", "0:33.86", "A:80085450;C:111343041;G:140916198;T:70619085;N:219639", 33, null, null, null, 80085450, 111343041, 140916198, 70619085, 219639, "SRX6608454", "SRS5172701", "SRA928193", "GEO", "Guramrit Singh, Molecular Genetics, The Ohio State University", 1, 0.862, null, 0.1026, null, 0.95359, null, 0.79372, null, 33, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2019-07-29", "Pharyngula", "Embryo", "Whole Organism", "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 & 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 & 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 & 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 & Blood Diseases Hospital|State Key Laboratory of Experimental Hematology", "Institute of Hematology & Blood Diseases Hospital", 2, 0.34381, 0.34082, 0.09181, 0.09135, 0.95144, 0.95148, 0.81928, 0.81462, 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"], [72384, "SRR22805230", "SRX18764963", "SRS16199859", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "28", "28.ythdf2 MO m6A meRIP replicate 2", null, "strain:AB|isolate:28|dev stage:34hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "28.ythdf2 MO m6A meRIP replicate 2", "28", "28", "28", null, null, "RIP-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", 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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 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"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"], [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, "GSM7430668 r1", "0:101 1:101", "A:844997958;C:941209221;G:1016802233;T:887576626;N:48700", 101, 101, null, null, 844997958, 941209221, 1016802233, 887576626, 48700, "SRX20523363", "SRS17832951", "SRA1645065", "IMP", "IMP", 2, 0.88478, 0.85242, 0.07667, 0.0787, 0.77354, 0.77636, 0.54943, 0.5474, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [75634, "SRR24746217", "SRX20523362", "SRS17832949", "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 2", "GSM7430667", 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 2", "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", "GSM7430667", "GSM7430667: eIF4E1c input biol rep 2; Danio rerio; RIP Seq", "GSM7430667 r1", "GSM7430667", "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_2_1.fastq.gz e1c-RIP_input_2_2.fastq.gz", "fastq fastq", 3698444058.0, 18309129.0, "GSM7430667 r1", "0:101 1:101", "A:882466312;C:908503385;G:987657378;T:919768451;N:48532", 101, 101, null, null, 882466312, 908503385, 987657378, 919768451, 48532, "SRX20523362", "SRS17832949", "SRA1645065", "IMP", "IMP", 2, 0.89236, 0.88681, 0.06986, 0.07322, 0.76897, 0.77037, 0.53302, 0.53232, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [75635, "SRR24746218", "SRX20523361", "SRS17832950", "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 1", "GSM7430666", 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 1", "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", "GSM7430666", "GSM7430666: eIF4E1c input biol rep 1; Danio rerio; RIP Seq", "GSM7430666 r1", "GSM7430666", "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_1_1.fastq.gz e1c-RIP_input_1_2.fastq.gz", "fastq fastq", 3259312622.0, 16135211.0, "GSM7430666 r1", "0:101 1:101", "A:725034304;C:851812248;G:940759649;T:741654528;N:51893", 101, 101, null, null, 725034304, 851812248, 940759649, 741654528, 51893, "SRX20523361", "SRS17832950", "SRA1645065", "IMP", "IMP", 2, 0.82557, 0.81479, 0.09862, 0.09133, 0.78309, 0.78368, 0.5647, 0.47779, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [75636, "SRR24746219", "SRX20523360", "SRS17832944", "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, "eIF4E1b input biol rep 3", "GSM7430665", null, "source name:Whole embryo lysate|tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1b|geo loc name:missing|collection date:missing", "eIF4E1b 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 eIF4E1b", "GSM7430665", "GSM7430665: eIF4E1b input biol rep 3; Danio rerio; RIP Seq", "GSM7430665 r1", "GSM7430665", "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", "e1b-RIP_input_3_1.fastq.gz e1b-RIP_input_3_2.fastq.gz", "fastq fastq", 3660782976.0, 18122688.0, "GSM7430665 r1", "0:101 1:101", "A:876719214;C:899453202;G:975602464;T:908960466;N:47630", 101, 101, null, null, 876719214, 899453202, 975602464, 908960466, 47630, "SRX20523360", "SRS17832944", "SRA1645065", "IMP", "IMP", 2, 0.89893, 0.89289, 0.06445, 0.06826, 0.77114, 0.77106, 0.5217, 0.5193, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [75637, "SRR24746220", "SRX20523359", "SRS17832948", "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, "eIF4E1b input biol rep 2", "GSM7430664", null, "source name:Whole embryo lysate|tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1b|geo loc name:missing|collection date:missing", "eIF4E1b input biol rep 2", "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 eIF4E1b", "GSM7430664", "GSM7430664: eIF4E1b input biol rep 2; Danio rerio; RIP Seq", "GSM7430664 r1", "GSM7430664", "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", "e1b-RIP_input_2_1.fastq.gz e1b-RIP_input_2_2.fastq.gz", "fastq fastq", 3693089644.0, 18282622.0, "GSM7430664 r1", "0:101 1:101", "A:870145891;C:921396875;G:999553442;T:901944778;N:48658", 101, 101, null, null, 870145891, 921396875, 999553442, 901944778, 48658, "SRX20523359", "SRS17832948", "SRA1645065", "IMP", "IMP", 2, 0.90101, 0.89457, 0.06635, 0.06977, 0.76873, 0.77007, 0.54396, 0.53678, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Austria", "2023-05-26", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [75638, "SRR24746221", "SRX20523358", "SRS17832946", "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, "eIF4E1b input biol rep 1", "GSM7430663", null, "source name:Whole embryo lysate|tissue:Whole embryo lysate|cell type:8 cell stage|genotype:tgactb2:3xflag sfGFP eIF4E1b|geo loc name:missing|collection date:missing", "eIF4E1b input biol rep 1", "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. 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