rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
41511,SRR5004963,SRX2336797,SRS1790193,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,zebrafish embryos ythdf2 RIP rep2,GSM2386192,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,zebrafish embryos ythdf2 RIP rep2,Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software,zebrafish embryos,,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,GSM2386192,GSM2386192: zebrafish embryos ythdf2 RIP rep2; Danio rerio; RIP Seq,GSM2386192,,1,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386192,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP092907,,,ythdf2_RIP_rep2_1.fastq.gz ythdf2_RIP_rep2_2.fastq.gz,fastq fastq,4007024510.0,19836755.0,GSM2386192 r1,0:101 1:101,A:769487104;C:1245093129;G:1251328145;T:740377823;N:738309,101,101,,,769487104,1245093129,1251328145,740377823,738309,SRX2336797,SRS1790193,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.97768,0.97802,0.22786,0.21743,0.89885,0.89968,0.77584,0.83808,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
41512,SRR5004962,SRX2336796,SRS1790194,SRP092907,PRJNA352850,Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos,GSE89655,Other,RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells,,pubmed:28869969,,zebrafish embryos ythdf2 RIP rep1,GSM2386191,,source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,zebrafish embryos ythdf2 RIP rep1,Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software,zebrafish embryos,,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,,genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk,GSM2386191,GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq,GSM2386191,,1,For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.,GEO Accession:GSM2386191,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP092907,,,ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz,fastq fastq,6144583662.0,30418731.0,GSM2386191 r1,0:101 1:101,A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305,101,101,,,1227614258,1869131844,1825793436,1220118819,1925305,SRX2336796,SRS1790194,SRA491654,GEO,Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS),2,0.96857,0.96917,0.23397,0.22377,0.89832,0.90147,0.78619,0.8258,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,trueseq,bulk,bulk,bulk,,China,2016-11-08,Pharyngula,Embryo,Trunk,Surface Structure
60021,SRR12103084,SRX8627422,SRS6915731,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,SCI IP,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI IP|BioSampleModel:Model organism or animal,,,,,,,,,IP library sequencing data of treated sample,SCIIP BKDL192540807 1a,SCIIP BKDL192540807 1a,IP library sequencing data of treated sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,SCIIP_BKDL192540807-1a_1.fq.gz SCIIP_BKDL192540807-1a_2.fq.gz,fastq fastq,7110503700.0,23701679.0,SCIIP BKDL192540807 1a 1.fq.gz,0:150 1:150,A:1520693228;C:1953670419;G:2215620460;T:1420407690;N:111903,150,150,,,1520693228,1953670419,2215620460,1420407690,111903,SRX8627422,SRS6915731,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.9115,0.9147,0.19936,0.2033,0.81864,0.81919,0.66838,0.6677,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60022,SRR12103085,SRX8627421,SRS6915730,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,SCI Input,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:SCI Input|BioSampleModel:Model organism or animal,,,,,,,,,Input library sequencing data of treated sample,SCIIN BKDL192540809 1a,SCIIN BKDL192540809 1a,Input library sequencing data of treated sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,SCIIN_BKDL192540809-1a_2.fq.gz SCIIN_BKDL192540809-1a_1.fq.gz,fastq fastq,7774587300.0,25915291.0,SCIIN BKDL192540809 1a 1.fq.gz,0:150 1:150,A:1595151855;C:2243828590;G:2397611978;T:1537918306;N:76571,150,150,,,1595151855,2243828590,2397611978,1537918306,76571,SRX8627421,SRS6915730,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.96018,0.96291,0.23754,0.23744,0.84904,0.85245,0.74661,0.74738,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60023,SRR12103086,SRX8627420,SRS6915729,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,Control IP,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control IP|BioSampleModel:Model organism or animal,,,,,,,,,IP library sequencing data of control sample,controlIP BKDL192540808 1a,controlIP BKDL192540808 1a,IP library sequencing data of control sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,controlIP_BKDL192540808-1a_2.fq.gz controlIP_BKDL192540808-1a_1.fq.gz,fastq fastq,7359972600.0,24533242.0,controlIP BKDL192540808 1a 1.fq.gz,0:150 1:150,A:1569051886;C:2002692591;G:2333418000;T:1454676484;N:133639,150,150,,,1569051886,2002692591,2333418000,1454676484,133639,SRX8627420,SRS6915729,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.92004,0.92293,0.20272,0.20739,0.83254,0.83291,0.68471,0.65224,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
60024,SRR12103087,SRX8627419,SRS6915728,SRP269070,PRJNA642405,Changes of m6A RNA methylation following spinal cord injury,PRJNA642405,Other,Results of methylation profiling by MeRIP Seq in both control and larvae with spinal cord injury,,,,,Control Input,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:trunk|sample type:Control Input|BioSampleModel:Model organism or animal,,,,,,,,,Input library sequencing data of control sample,controlIN BKDL192540810 1a,controlIN BKDL192540810 1a,Input library sequencing data of control sample,,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,HiSeq X Ten,,SRP269070,,,controlIN_BKDL192540810-1a_1.fq.gz controlIN_BKDL192540810-1a_2.fq.gz,fastq fastq,7830123600.0,26100412.0,controlIN BKDL192540810 1a 1.fq.gz,0:150 1:150,A:1589371287;C:2296547915;G:2409439612;T:1534684151;N:80635,150,150,,,1589371287,2296547915,2409439612,1534684151,80635,SRX8627419,SRS6915728,SRA1091926,Nantong University|Key Laboratory of Neuroregeneration of Jiangsu and,Nantong University,2,0.97501,0.97626,0.23177,0.23578,0.89497,0.8971,0.78501,0.77674,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2020-06-28,Undetermined,Larval,Trunk,Surface Structure
74097,SRR23433707,SRX19347585,SRS16745103,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,mt input rep2,GSM7039976,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing,mt input rep2,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1,GSM7039976,GSM7039976: mt input rep2; Danio rerio; RIP Seq,GSM7039976 r1,GSM7039976,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,mt2_input_R1.fastq.gz mt2_input_R2.fastq.gz,fastq fastq,11987520719.0,46102921.0,GSM7039976 r1,0:129.98 1:130.04,A:2818961833;C:3185310727;G:3125514774;T:2857679978;N:53407,129,130,,,2818961833,3185310727,3125514774,2857679978,53407,SRX19347585,SRS16745103,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.92498,0.92723,0.26901,0.26318,0.72691,0.72646,0.55297,0.56674,103,103,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74098,SRR23433708,SRX19347584,SRS16745102,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,mt IP  rep2,GSM7039975,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing,mt IP  rep2,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A,GSM7039975,GSM7039975: mt IP  rep2; Danio rerio; RIP Seq,GSM7039975 r1,GSM7039975,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,mt2_IP_R1.fastq.gz mt2_IP_R2.fastq.gz,fastq fastq,10153956215.0,38248544.0,GSM7039975 r1,0:132.74 1:132.73,A:2745473943;C:2337991849;G:2337827470;T:2732618213;N:44740,132,132,,,2745473943,2337991849,2337827470,2732618213,44740,SRX19347584,SRS16745102,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.91716,0.92124,0.17169,0.17213,0.69057,0.69092,0.45478,0.4582,133,133,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74099,SRR23433709,SRX19347583,SRS16745101,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,mt input rep1,GSM7039974,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1|geo loc name:missing|collection date:missing,mt input rep1,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:n1,GSM7039974,GSM7039974: mt input rep1; Danio rerio; RIP Seq,GSM7039974 r1,GSM7039974,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,mt1_input_R1.fastq.gz mt1_input_R2.fastq.gz,fastq fastq,11979139891.0,42665152.0,GSM7039974 r1,0:140.37 1:140.40,A:3143624979;C:2854874515;G:2775482425;T:3204809556;N:348416,140,140,,,3143624979,2854874515,2775482425,3204809556,348416,SRX19347583,SRS16745101,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.89189,0.90001,0.35263,0.34917,0.71058,0.70907,0.54777,0.55293,125,125,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74100,SRR23433710,SRX19347582,SRS16745100,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,mt IP  rep1,GSM7039973,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A|geo loc name:missing|collection date:missing,mt IP  rep1,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16 / |treatment:gene knockout|rip antibody:anti m6A,GSM7039973,GSM7039973: mt IP  rep1; Danio rerio; RIP Seq,GSM7039973 r1,GSM7039973,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,mt1_IP_R1.fastq.gz mt1_IP_R2.fastq.gz,fastq fastq,12145897814.0,43352862.0,GSM7039973 r1,0:140.09 1:140.07,A:3459248498;C:2615706052;G:2628261332;T:3442334843;N:347089,140,140,,,3459248498,2615706052,2628261332,3442334843,347089,SRX19347582,SRS16745100,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.86681,0.87664,0.304,0.305,0.68012,0.67831,0.44055,0.4418,142,142,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74101,SRR23433711,SRX19347581,SRS16745099,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,sibling input rep2,GSM7039972,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing,sibling input rep2,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1,GSM7039972,GSM7039972: sibling input rep2; Danio rerio; RIP Seq,GSM7039972 r1,GSM7039972,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,sibling2_input_R1.fastq.gz sibling2_input_R2.fastq.gz,fastq fastq,12272791017.0,47579480.0,GSM7039972 r1,0:128.94 1:129.00,A:2905993856;C:3237323144;G:3186607999;T:2942811604;N:54414,128,129,,,2905993856,3237323144,3186607999,2942811604,54414,SRX19347581,SRS16745099,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.92733,0.92947,0.27234,0.26711,0.72391,0.72409,0.52625,0.55052,126,126,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74102,SRR23433712,SRX19347580,SRS16745098,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,sibling IP  rep2,GSM7039971,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing,sibling IP  rep2,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A,GSM7039971,GSM7039971: sibling IP  rep2; Danio rerio; RIP Seq,GSM7039971 r1,GSM7039971,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,sibling2_IP_R1.fastq.gz sibling2_IP_R2.fastq.gz,fastq fastq,10402768351.0,39113148.0,GSM7039971 r1,0:132.99 1:132.98,A:2806053427;C:2400476074;G:2403977422;T:2792214821;N:46607,132,132,,,2806053427,2400476074,2403977422,2792214821,46607,SRX19347580,SRS16745098,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.90198,0.9063,0.18008,0.18091,0.69428,0.69396,0.44811,0.42925,147,147,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74103,SRR23433713,SRX19347579,SRS16745097,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,sibling input rep1,GSM7039970,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1|geo loc name:missing|collection date:missing,sibling input rep1,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:n1,GSM7039970,GSM7039970: sibling input rep1; Danio rerio; RIP Seq,GSM7039970 r1,GSM7039970,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,sibling1_input_R1.fastq.gz sibling1_input_R2.fastq.gz,fastq fastq,13094981449.0,46647417.0,GSM7039970 r1,0:140.35 1:140.37,A:3434495131;C:3120669719;G:3036482303;T:3502963330;N:370966,140,140,,,3434495131,3120669719,3036482303,3502963330,370966,SRX19347579,SRS16745097,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.89276,0.90193,0.352,0.3489,0.70905,0.70719,0.52165,0.52427,142,142,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure
74104,SRR23433714,SRX19347578,SRS16745096,SRP422577,PRJNA934472,Mettl16 promotes hematopoietic stem and progenitor cell expansion in embryonic hematopoiesis [m6A Seq],GSE225136,Other,The RNA N6 methyladenosine m6A modification has emerged as an essential regulator of vertebrate embryogenesis and malignancies. However  its functions and underlying molecular mechanisms in the expansion of hematopoietic stem and progenitor cells HSPCs during early embryonic development remain elusive. Here we show that Mettl16  an RNA methyltransferase identified recently  is specifically required for HSPC expansion during zebrafish early embryonic development in an m6A dependent manner. In mettl16 deficient embryos  HSPCs exhibit defective proliferation capacity due to G0/G1 arrest. Mechanistically  HSPC proliferation is blocked by impaired methyltransferase function of Mettl16 in vivo. We identify cell cycle gene mybl2b as a novel direct m6A target of Mettl16  and Mettl16 deficiency destabilizes mybl2b mRNA  which is mediated by m6A reader Igf2bp1. Moreover  we revealed that the METTL16 m6A MYBL2 IGF2BP1 signaling axis in G1/S progression is conserved in humans. Collectively  our findings demonstrate the critical function of m6A modification deposited by Mettl16 in HSPC expansion during early embryonic development. Overall design: m6A seq profiles of sibling and  mettl16 /  zebrafish embryos at 3 dpf for triplicates,parent bioproject:PRJNA934075,pubmed:38605226,,sibling IP  rep1,GSM7039969,,source name:trunk region of zebrafish embryos|tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A|geo loc name:missing|collection date:missing,sibling IP  rep1,Illumina Casava 1.8 software used for basecalling. fastp software were used to remove the reads that contained adaptor contamination  low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp. HISAT2 was used to map reads to zebrafish reference genome Ensembl GRCz11. Mapped reads of IP and input libraries were provided for R package exomePeak  which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software. StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM total exon fragments /mapped reads millions × exon length kB. The differentially expressed mRNAs were selected by R package edgeR. Assembly: GRCz11 Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample,trunk region of zebrafish embryos,,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,tissue:trunk region of zebrafish embryos|genotype:mettl16+/+|treatment:no treatment|rip antibody:anti m6A,GSM7039969,GSM7039969: sibling IP  rep1; Danio rerio; RIP Seq,GSM7039969 r1,GSM7039969,1,Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent Invitrogen. The RNA quality and quantity of each sample was assessed using NanoDrop ND 1000 and Bioanalyzer 2100 Agilent. Total RNAs 20 μg was depleted of ribosomal RNA by rRNA Depletion Kits Thermo Fisher Scientific and Magnesium RNA Fragmentation Module NEB  cat.e6150 was used to randomly fragment RNA. Anti m6A antibody 202003  Synaptic Systems was applied for m6A immunoprecipitation. Then  the RNA was reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase Invitrogen  cat.1896649. RNA libraries were prepared for sequencing using standard Illumina protocols m6A Seq,,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP422577,,loader:fastq load.py,sibling1_IP_R1.fastq.gz sibling1_IP_R2.fastq.gz,fastq fastq,12317957591.0,43954374.0,GSM7039969 r1,0:140.17 1:140.08,A:3509912915;C:2650796924;G:2663699373;T:3493137659;N:410720,140,140,,,3509912915,2650796924,2663699373,3493137659,410720,SRX19347578,SRS16745096,SRA1590470,Huazhong University of Science and Technology,Huazhong University of Science and Technology,2,0.87054,0.88058,0.30375,0.30421,0.67783,0.67584,0.44329,0.44327,142,142,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-02-12,Undetermined,Embryo,Trunk,Surface Structure