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 63340,SRR13729837,SRX10117846,SRS8272547,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 4E Danio,GSM5088021,,tissue:Oocyte 4E|segment:E last vegetal|cell type:Oocyte|oocyte id:4,Oocyte 4E Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 4E,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:E last vegetal|cell type:Oocyte|oocyte id:4,GSM5088021,GSM5088021: Oocyte 4E Danio; Danio rerio; RNA Seq,GSM5088021,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088021,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,4B5_1_sequence.fastq.gz 4B5_2_sequence.fastq.gz,fastq fastq,4152498238.0,26122638.0,GSM5088021 r1,0:79.49 1:79.47,A:1027163417;C:1014220497;G:1089779374;T:1018004142;N:3330808,79,79,,,1027163417,1014220497,1089779374,1018004142,3330808,SRX10117846,SRS8272547,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.91753,0.91112,0.02745,0.02398,0.80996,0.81292,0.50181,0.50039,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63341,SRR13729836,SRX10117845,SRS8272546,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 4C Danio,GSM5088020,,tissue:Oocyte 4C|segment:C|cell type:Oocyte|oocyte id:4,Oocyte 4C Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 4C,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:C|cell type:Oocyte|oocyte id:4,GSM5088020,GSM5088020: Oocyte 4C Danio; Danio rerio; RNA Seq,GSM5088020,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088020,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,4B3_1_sequence.fastq.gz 4B3_2_sequence.fastq.gz,fastq fastq,4303501885.0,27073674.0,GSM5088020 r1,0:79.48 1:79.47,A:1081539300;C:1029641993;G:1108664145;T:1080227921;N:3428526,79,79,,,1081539300,1029641993,1108664145,1080227921,3428526,SRX10117845,SRS8272546,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.93052,0.92329,0.0289,0.02632,0.80728,0.8086,0.48613,0.49318,79,79,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63342,SRR13729835,SRX10117844,SRS8272545,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 4B Danio,GSM5088019,,tissue:Oocyte 4B|segment:B|cell type:Oocyte|oocyte id:4,Oocyte 4B Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 4B,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:B|cell type:Oocyte|oocyte id:4,GSM5088019,GSM5088019: Oocyte 4B Danio; Danio rerio; RNA Seq,GSM5088019,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088019,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,4B2_1_sequence.fastq.gz 4B2_2_sequence.fastq.gz,fastq fastq,4568445606.0,28740891.0,GSM5088019 r1,0:79.48 1:79.47,A:1129548614;C:1110728719;G:1196533300;T:1127950040;N:3684933,79,79,,,1129548614,1110728719,1196533300,1127950040,3684933,SRX10117844,SRS8272545,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.93047,0.91851,0.03423,0.02988,0.809,0.81117,0.49528,0.49857,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63343,SRR13729834,SRX10117843,SRS8272544,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 4A Danio,GSM5088018,,tissue:Oocyte 4A|segment:A first animal|cell type:Oocyte|oocyte id:4,Oocyte 4A Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 4A,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:A first animal|cell type:Oocyte|oocyte id:4,GSM5088018,GSM5088018: Oocyte 4A Danio; Danio rerio; RNA Seq,GSM5088018,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088018,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,4B1_1_sequence.fastq.gz 4B1_2_sequence.fastq.gz,fastq fastq,3817977815.0,24018320.0,GSM5088018 r1,0:79.49 1:79.47,A:963219571;C:910978829;G:981236983;T:959479009;N:3063423,79,79,,,963219571,910978829,981236983,959479009,3063423,SRX10117843,SRS8272544,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.91985,0.91378,0.02505,0.02244,0.82487,0.82662,0.49099,0.48748,79,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63344,SRR13729833,SRX10117842,SRS8272543,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 3E Danio,GSM5088017,,tissue:Oocyte 3E|segment:E last vegetal|cell type:Oocyte|oocyte id:3,Oocyte 3E Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 3E,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:E last vegetal|cell type:Oocyte|oocyte id:3,GSM5088017,GSM5088017: Oocyte 3E Danio; Danio rerio; RNA Seq,GSM5088017,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088017,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,3B5_1_sequence.fastq.gz 3B5_2_sequence.fastq.gz,fastq fastq,4473509143.0,28141276.0,GSM5088017 r1,0:79.48 1:79.48,A:1097552285;C:1100434019;G:1180150633;T:1091792820;N:3579386,79,79,,,1097552285,1100434019,1180150633,1091792820,3579386,SRX10117842,SRS8272543,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.91717,0.91194,0.03477,0.02973,0.81714,0.81789,0.50164,0.50948,80,79,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63345,SRR13729832,SRX10117841,SRS8272542,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 3D Danio,GSM5088016,,tissue:Oocyte 3D|segment:D|cell type:Oocyte|oocyte id:3,Oocyte 3D Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 3D,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:D|cell type:Oocyte|oocyte id:3,GSM5088016,GSM5088016: Oocyte 3D Danio; Danio rerio; RNA Seq,GSM5088016,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088016,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,3B4_1_sequence.fastq.gz 3B4_2_sequence.fastq.gz,fastq fastq,3795326466.0,23875658.0,GSM5088016 r1,0:79.48 1:79.48,A:920554794;C:947025114;G:1013528010;T:911203644;N:3014904,79,79,,,920554794,947025114,1013528010,911203644,3014904,SRX10117841,SRS8272542,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.91408,0.91455,0.037,0.03125,0.82166,0.82426,0.53064,0.53695,78,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63346,SRR13729831,SRX10117840,SRS8272541,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 3C Danio,GSM5088015,,tissue:Oocyte 3C|segment:C|cell type:Oocyte|oocyte id:3,Oocyte 3C Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 3C,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:C|cell type:Oocyte|oocyte id:3,GSM5088015,GSM5088015: Oocyte 3C Danio; Danio rerio; RNA Seq,GSM5088015,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088015,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,3B3_1_sequence.fastq.gz 3B3_2_sequence.fastq.gz,fastq fastq,4384361494.0,27581768.0,GSM5088015 r1,0:79.49 1:79.47,A:1098383452;C:1051673687;G:1134807000;T:1095992230;N:3505125,79,79,,,1098383452,1051673687,1134807000,1095992230,3505125,SRX10117840,SRS8272541,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.92005,0.91267,0.02325,0.02051,0.84593,0.84652,0.47588,0.47964,80,79,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63347,SRR13729830,SRX10117839,SRS8272540,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 3A Danio,GSM5088014,,tissue:Oocyte 3A|segment:A first animal|cell type:Oocyte|oocyte id:3,Oocyte 3A Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 3A,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:A first animal|cell type:Oocyte|oocyte id:3,GSM5088014,GSM5088014: Oocyte 3A Danio; Danio rerio; RNA Seq,GSM5088014,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088014,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,3B1_1_sequence.fastq.gz 3B1_2_sequence.fastq.gz,fastq fastq,3411652124.0,21461889.0,GSM5088014 r1,0:79.49 1:79.47,A:845211429;C:831298444;G:892682122;T:839715401;N:2744728,79,79,,,845211429,831298444,892682122,839715401,2744728,SRX10117839,SRS8272540,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.91312,0.90785,0.03043,0.03046,0.81227,0.81412,0.47591,0.48217,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63348,SRR13729829,SRX10117838,SRS8272539,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 2D Danio,GSM5088013,,tissue:Oocyte 2D|segment:D|cell type:Oocyte|oocyte id:2,Oocyte 2D Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 2D,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:D|cell type:Oocyte|oocyte id:2,GSM5088013,GSM5088013: Oocyte 2D Danio; Danio rerio; RNA Seq,GSM5088013,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088013,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,2B4_1_sequence.fastq.gz 2B4_2_sequence.fastq.gz,fastq fastq,4315673164.0,27151788.0,GSM5088013 r1,0:79.48 1:79.47,A:1054372456;C:1069138368;G:1139564933;T:1049164939;N:3432468,79,79,,,1054372456,1069138368,1139564933,1049164939,3432468,SRX10117838,SRS8272539,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.92682,0.91833,0.0285,0.02736,0.83128,0.83386,0.49243,0.48841,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63349,SRR13729828,SRX10117837,SRS8272538,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 2C Danio,GSM5088012,,tissue:Oocyte 2C|segment:C|cell type:Oocyte|oocyte id:2,Oocyte 2C Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 2C,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:C|cell type:Oocyte|oocyte id:2,GSM5088012,GSM5088012: Oocyte 2C Danio; Danio rerio; RNA Seq,GSM5088012,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088012,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,2B3_1_sequence.fastq.gz 2B3_2_sequence.fastq.gz,fastq fastq,2940179416.0,18498584.0,GSM5088012 r1,0:79.48 1:79.46,A:706640732;C:738153613;G:787676271;T:705356358;N:2352442,79,79,,,706640732,738153613,787676271,705356358,2352442,SRX10117837,SRS8272538,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.91412,0.90752,0.03266,0.03078,0.81294,0.81544,0.48861,0.50372,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63350,SRR13729827,SRX10117836,SRS8272537,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 2B Danio,GSM5088011,,tissue:Oocyte 2B|segment:B|cell type:Oocyte|oocyte id:2,Oocyte 2B Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 2B,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:B|cell type:Oocyte|oocyte id:2,GSM5088011,GSM5088011: Oocyte 2B Danio; Danio rerio; RNA Seq,GSM5088011,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088011,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,2B2_1_sequence.fastq.gz 2B2_2_sequence.fastq.gz,fastq fastq,4697262619.0,29554887.0,GSM5088011 r1,0:79.47 1:79.46,A:1144577689;C:1159225165;G:1242203382;T:1147513885;N:3742498,79,79,,,1144577689,1159225165,1242203382,1147513885,3742498,SRX10117836,SRS8272537,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.92868,0.92039,0.03005,0.02833,0.83043,0.83201,0.48282,0.4842,80,79,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63351,SRR13729826,SRX10117835,SRS8272536,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 2A Danio,GSM5088010,,tissue:Oocyte 2A|segment:A first animal|cell type:Oocyte|oocyte id:2,Oocyte 2A Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 2A,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:A first animal|cell type:Oocyte|oocyte id:2,GSM5088010,GSM5088010: Oocyte 2A Danio; Danio rerio; RNA Seq,GSM5088010,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088010,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,2B1_1_sequence.fastq.gz 2B1_2_sequence.fastq.gz,fastq fastq,4258170980.0,26788207.0,GSM5088010 r1,0:79.49 1:79.47,A:1030159627;C:1059437908;G:1140549602;T:1024611576;N:3412267,79,79,,,1030159627,1059437908,1140549602,1024611576,3412267,SRX10117835,SRS8272536,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.90756,0.90301,0.03357,0.03114,0.82246,0.82353,0.48748,0.48875,78,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63352,SRR13729825,SRX10117834,SRS8272535,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 1E Danio,GSM5088009,,tissue:Oocyte 1E|segment:E last vegetal|cell type:Oocyte|oocyte id:1,Oocyte 1E Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 1E,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:E last vegetal|cell type:Oocyte|oocyte id:1,GSM5088009,GSM5088009: Oocyte 1E Danio; Danio rerio; RNA Seq,GSM5088009,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088009,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,1B5_1_sequence.fastq.gz 1B5_2_sequence.fastq.gz,fastq fastq,1540315534.0,9689873.0,GSM5088009 r1,0:79.49 1:79.47,A:379857715;C:379231426;G:406324313;T:373666639;N:1235441,79,79,,,379857715,379231426,406324313,373666639,1235441,SRX10117834,SRS8272535,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.90259,0.90038,0.02393,0.02279,0.82538,0.828,0.50474,0.50554,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63353,SRR13729824,SRX10117833,SRS8272534,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 1D Danio,GSM5088008,,tissue:Oocyte 1D|segment:D|cell type:Oocyte|oocyte id:1,Oocyte 1D Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 1D,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:D|cell type:Oocyte|oocyte id:1,GSM5088008,GSM5088008: Oocyte 1D Danio; Danio rerio; RNA Seq,GSM5088008,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088008,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,1B4_1_sequence.fastq.gz 1B4_2_sequence.fastq.gz,fastq fastq,962876607.0,6058091.0,GSM5088008 r1,0:79.47 1:79.47,A:229221564;C:244601669;G:261639054;T:226646308;N:768012,79,79,,,229221564,244601669,261639054,226646308,768012,SRX10117833,SRS8272534,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.90756,0.90342,0.03356,0.03192,0.81418,0.81588,0.53647,0.53381,80,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63354,SRR13729823,SRX10117832,SRS8272532,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 1C Danio,GSM5088007,,tissue:Oocyte 1C|segment:C|cell type:Oocyte|oocyte id:1,Oocyte 1C Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 1C,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:C|cell type:Oocyte|oocyte id:1,GSM5088007,GSM5088007: Oocyte 1C Danio; Danio rerio; RNA Seq,GSM5088007,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088007,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,1B3_1_sequence.fastq.gz 1B3_2_sequence.fastq.gz,fastq fastq,1582022971.0,9951749.0,GSM5088007 r1,0:79.49 1:79.48,A:396538041;C:379495578;G:410865933;T:393855027;N:1268392,79,79,,,396538041,379495578,410865933,393855027,1268392,SRX10117832,SRS8272532,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.93154,0.91852,0.03066,0.02748,0.81874,0.82037,0.50484,0.50755,80,78,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63355,SRR13729822,SRX10117831,SRS8272533,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 1B Danio,GSM5088006,,tissue:Oocyte 1B|segment:B|cell type:Oocyte|oocyte id:1,Oocyte 1B Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 1B,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:B|cell type:Oocyte|oocyte id:1,GSM5088006,GSM5088006: Oocyte 1B Danio; Danio rerio; RNA Seq,GSM5088006,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088006,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,1B2_1_sequence.fastq.gz 1B2_2_sequence.fastq.gz,fastq fastq,1673988669.0,10530092.0,GSM5088006 r1,0:79.49 1:79.48,A:422626348;C:401664830;G:430984922;T:417384157;N:1328412,79,79,,,422626348,401664830,430984922,417384157,1328412,SRX10117831,SRS8272533,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.92018,0.91786,0.03334,0.02831,0.82217,0.82359,0.49692,0.49869,79,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 63356,SRR13729821,SRX10117830,SRS8272531,SRP306811,PRJNA702290,RNA Seq analysis of localization along animal vegetal axis of Danio rerio,GSE166917,Transcriptome Analysis,Asymmetrical localization of biomolecules inside the egg results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal vegetal axis of mature eggs of four diverse models Xenopus laevis Danio rerio Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO Seq. Surprisingly we revealed RNAs that code for many known important genes such as germ layer determinants germ plasm factors and members of key signalling pathways are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model. Overall design: We performed cryosectioning of oocytes along the animal vegetal axis first developmental axis section A first animal to section E last vegetal followed by RNA Seq to determine the localization profiles of RNAs. The method allowed for a complete view on RNA localization. Total RNA was extracted using Qiagen Microkit column based isolation. The concentration of RNA was measured using a spectrophotometer Nanodrop 2000 Thermo Scientific and the quality of RNA was assessed using a Fragment Analyzer AATI High Sensitivity RNA analysis kit. RNA profiles were generated using RNA Sequencing in 4 replicates each divided into five segments.,,pubmed:35752299,,Oocyte 1A Danio,GSM5088005,,tissue:Oocyte 1A|segment:A first animal|cell type:Oocyte|oocyte id:1,Oocyte 1A Danio,Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna version 2 and the SILVA rRNA database version 119. Reads were aligned against reference genome using STAR v 2.5.3a. Annotated reads were counted using htseq count with the reference model Danio rerio.GRCz11.95 Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT qPCR method called NormQ Naraine et al 2020. Genome build: GRCz11.dna.primary assembly Supplementary files format and content: Tab delimited text files include non normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.,Oocyte 1A,,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,,segment:A first animal|cell type:Oocyte|oocyte id:1,GSM5088005,GSM5088005: Oocyte 1A Danio; Danio rerio; RNA Seq,GSM5088005,,1,Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion Lexogen RiboCop rRNA Depletion Kit. Lexogen SENSE TOtal RNA Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.,GEO Accession:GSM5088005,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306811,,,1B1_1_sequence.fastq.gz 1B1_2_sequence.fastq.gz,fastq fastq,2267520035.0,14263997.0,GSM5088005 r1,0:79.47 1:79.49,A:545496147;C:565118612;G:611364916;T:543726981;N:1813379,79,79,,,545496147,565118612,611364916,543726981,1813379,SRX10117830,SRS8272531,SRA1197056,GEO,"Laboratory of Gene Expression, Institute of Biotechnology, Czech Academy of Science, v.v.i.",2,0.93336,0.92007,0.06438,0.05136,0.82349,0.82483,0.54418,0.55879,78,80,B,B,biological fallback assumption,illumina,nextseq,unknown,rrna_depletion,lexogen,bulk,bulk,bulk,,Czech Republic,2021-02-17,Zygote,Embryo,Oocyte,Reproductive System 66194,SRR16096233,SRX12382357,SRS10353019,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 1cell Rep5,GSM5599725,,tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 1cell Rep5,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 1cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599725,GSM5599725: ZF zygote IP 1cell Rep5; Danio rerio; RIP Seq,GSM5599725,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599725,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_1cell_Rep5_R1.fastq.gz ZF_zygote_IP_1cell_Rep5_R2.fastq.gz,fastq fastq,3660517860.0,35887430.0,GSM5599725 r1,0:51 1:51,A:858138600;C:924733544;G:1002150083;T:875349961;N:145672,51,51,,,858138600,924733544,1002150083,875349961,145672,SRX12382357,SRS10353019,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.83384,0.82667,0.09687,0.11892,0.79076,0.79326,0.63739,0.60941,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66195,SRR16096232,SRX12382356,SRS10353018,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 1cell Rep4,GSM5599724,,tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 1cell Rep4,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 1cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599724,GSM5599724: ZF zygote IP 1cell Rep4; Danio rerio; RIP Seq,GSM5599724,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599724,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_1cell_Rep4_R1.fastq.gz ZF_zygote_IP_1cell_Rep4_R2.fastq.gz,fastq fastq,3660205842.0,35884371.0,GSM5599724 r1,0:51 1:51,A:895738659;C:880838836;G:971118499;T:912364119;N:145729,51,51,,,895738659,880838836,971118499,912364119,145729,SRX12382356,SRS10353018,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.87258,0.86932,0.06573,0.07958,0.78044,0.78374,0.55531,0.5462,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66196,SRR16096231,SRX12382355,SRS10353016,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 1cell Rep3,GSM5599723,,tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 1cell Rep3,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 1cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599723,GSM5599723: ZF zygote IP 1cell Rep3; Danio rerio; RIP Seq,GSM5599723,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599723,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_1cell_Rep3_R1.fastq.gz ZF_zygote_IP_1cell_Rep3_R2.fastq.gz,fastq fastq,2732409048.0,26788324.0,GSM5599723 r1,0:51 1:51,A:669345195;C:656715671;G:724415204;T:681825149;N:107829,51,51,,,669345195,656715671,724415204,681825149,107829,SRX12382355,SRS10353016,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.85204,0.83607,0.06526,0.08046,0.78535,0.78748,0.60467,0.50165,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66197,SRR16096230,SRX12382354,SRS10353017,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 1cell Rep2,GSM5599722,,tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 1cell Rep2,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 1cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599722,GSM5599722: ZF zygote IP 1cell Rep2; Danio rerio; RIP Seq,GSM5599722,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599722,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_1cell_Rep2_R1.fastq.gz ZF_zygote_IP_1cell_Rep2_R2.fastq.gz,fastq fastq,2235668028.0,21918314.0,GSM5599722 r1,0:51 1:51,A:552522700;C:535947981;G:588168855;T:558939713;N:88779,51,51,,,552522700,535947981,588168855,558939713,88779,SRX12382354,SRS10353017,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.85597,0.85298,0.06663,0.07927,0.79058,0.79237,0.57626,0.56525,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66198,SRR16096229,SRX12382353,SRS10353015,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 1cell Rep1,GSM5599721,,tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 1cell Rep1,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 1cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599721,GSM5599721: ZF zygote IP 1cell Rep1; Danio rerio; RIP Seq,GSM5599721,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599721,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_1cell_Rep1_R1.fastq.gz ZF_zygote_IP_1cell_Rep1_R2.fastq.gz,fastq fastq,1785761736.0,17507468.0,GSM5599721 r1,0:51 1:51,A:429081683;C:435813601;G:481376346;T:439419714;N:70392,51,51,,,429081683,435813601,481376346,439419714,70392,SRX12382353,SRS10353015,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.75314,0.75693,0.0543,0.06639,0.79482,0.79594,0.57979,0.56522,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66199,SRR16096228,SRX12382352,SRS10353014,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 5cell Rep3,GSM5599720,,tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 5cell Rep3,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 5cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599720,GSM5599720: ZF zygote IP 5cell Rep3; Danio rerio; RIP Seq,GSM5599720,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599720,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_5cell_Rep3_R1.fastq.gz ZF_zygote_IP_5cell_Rep3_R2.fastq.gz,fastq fastq,2179659420.0,21369210.0,GSM5599720 r1,0:51 1:51,A:539092949;C:513857324;G:569620218;T:556940661;N:148268,51,51,,,539092949,513857324,569620218,556940661,148268,SRX12382352,SRS10353014,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.92028,0.90706,0.03967,0.05572,0.78431,0.78886,0.49727,0.48541,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66200,SRR16096227,SRX12382351,SRS10353012,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 5cell Rep2,GSM5599719,,tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 5cell Rep2,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 5cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599719,GSM5599719: ZF zygote IP 5cell Rep2; Danio rerio; RIP Seq,GSM5599719,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599719,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_5cell_Rep2_R1.fastq.gz ZF_zygote_IP_5cell_Rep2_R2.fastq.gz,fastq fastq,2527184538.0,24776319.0,GSM5599719 r1,0:51 1:51,A:628307375;C:594702688;G:657847712;T:646151885;N:174878,51,51,,,628307375,594702688,657847712,646151885,174878,SRX12382351,SRS10353012,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.91811,0.90487,0.03919,0.05376,0.78315,0.78729,0.49414,0.48564,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66201,SRR16096226,SRX12382350,SRS10353011,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 5cell Rep1,GSM5599718,,tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 5cell Rep1,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 5cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599718,GSM5599718: ZF zygote IP 5cell Rep1; Danio rerio; RIP Seq,GSM5599718,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599718,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_5cell_Rep1_R1.fastq.gz ZF_zygote_IP_5cell_Rep1_R2.fastq.gz,fastq fastq,3481342518.0,34130809.0,GSM5599718 r1,0:51 1:51,A:865680250;C:823420389;G:907146965;T:884854199;N:240715,51,51,,,865680250,823420389,907146965,884854199,240715,SRX12382350,SRS10353011,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.91893,0.90939,0.04544,0.06005,0.78025,0.78348,0.50569,0.49155,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66202,SRR16096225,SRX12382349,SRS10353013,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 10cell Rep3,GSM5599717,,tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 10cell Rep3,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 10cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599717,GSM5599717: ZF zygote IP 10cell Rep3; Danio rerio; RIP Seq,GSM5599717,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599717,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_10cell_Rep3_R1.fastq.gz ZF_zygote_IP_10cell_Rep3_R2.fastq.gz,fastq fastq,2172362850.0,21297675.0,GSM5599717 r1,0:51 1:51,A:536043605;C:513512883;G:568368414;T:554284996;N:152952,51,51,,,536043605,513512883,568368414,554284996,152952,SRX12382349,SRS10353013,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.91859,0.90522,0.03736,0.05214,0.78715,0.79129,0.49736,0.48681,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66203,SRR16096224,SRX12382348,SRS10353010,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 10cell Rep2,GSM5599716,,tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 10cell Rep2,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 10cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599716,GSM5599716: ZF zygote IP 10cell Rep2; Danio rerio; RIP Seq,GSM5599716,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599716,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_10cell_Rep2_R1.fastq.gz ZF_zygote_IP_10cell_Rep2_R2.fastq.gz,fastq fastq,1840839492.0,18047446.0,GSM5599716 r1,0:51 1:51,A:454385290;C:437082102;G:482351138;T:466893642;N:127320,51,51,,,454385290,437082102,482351138,466893642,127320,SRX12382348,SRS10353010,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.92217,0.90956,0.04012,0.05483,0.78819,0.79318,0.49756,0.48256,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66204,SRR16096223,SRX12382347,SRS10353009,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote IP 10cell Rep1,GSM5599715,,tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote IP 10cell Rep1,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote IP 10cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599715,GSM5599715: ZF zygote IP 10cell Rep1; Danio rerio; RIP Seq,GSM5599715,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599715,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_IP_10cell_Rep1_R1.fastq.gz ZF_zygote_IP_10cell_Rep1_R2.fastq.gz,fastq fastq,2400553680.0,23534840.0,GSM5599715 r1,0:51 1:51,A:594878203;C:567573525;G:625488388;T:612448386;N:165178,51,51,,,594878203,567573525,625488388,612448386,165178,SRX12382347,SRS10353009,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.91641,0.908,0.03979,0.05394,0.78455,0.7892,0.48862,0.47478,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66205,SRR16096222,SRX12382346,SRS10353008,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote Input 10cell Rep2,GSM5599714,,tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote Input 10cell Rep2,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote Input 10cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599714,GSM5599714: ZF zygote Input 10cell Rep2; Danio rerio; RIP Seq,GSM5599714,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599714,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_Input_10cell_Rep2_R1.fastq.gz ZF_zygote_Input_10cell_Rep2_R2.fastq.gz,fastq fastq,3842772582.0,37674241.0,GSM5599714 r1,0:51 1:51,A:843564828;C:1054412690;G:1130769812;T:813758353;N:266899,51,51,,,843564828,1054412690,1130769812,813758353,266899,SRX12382346,SRS10353008,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.91511,0.90868,0.32791,0.38048,0.89457,0.89441,0.81532,0.75274,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System 66206,SRR16096221,SRX12382345,SRS10353007,SRP339082,PRJNA766854,RNA m6A methylome from zebrafish zygotes mouse liver polyA selected RNAs mouse embryonic stem cells spike in RNA controls and single mouse oocytes and embryos,GSE184893,Other,N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes including meiosis and early embryo development. Despite advances in methodology for m6A mapping the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA mouse embryonic stem cells and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes 3 biological replicates for 5 zygotes and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng 1 ng and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line from ATCC SCRC 1011 samples: 1000 cells 100 cells and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula S. et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula S. et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages and embryos at zygote 2 cell 8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922 zygote GSM5746930 2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.,,pubmed:37349523,,ZF zygote Input 10cell Rep1,GSM5599713,,tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA,ZF zygote Input 10cell Rep1,Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713 GSM5599714 GSM5599715 GSM5599716 GSM5599717 GSM5599718 GSM5599719 GSM5599720 GSM5599721 GSM5599722 GSM5599723 GSM5599724 GSM5599725 mouse polyA selected RNA samples GSM5599726 GSM5599727 GSM5599728 GSM5599729 GSM5599730 GSM5599731 GSM5599732 GSM5599733 and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter “ 5 8 no mixed no discordant”. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter “ bs 10 normalizeUsing RPKM”. Genome build: mm10 for mouse danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.,ZF zygote Input 10cell,For mouse GV oocyte collection 8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida followed by three washes in M2 medium. For mouse MII oocyte collection 4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium. For mouse early embryo collection 8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28 hours zygote 39 43 hours 2 cell 68 70 hours 8 cell and 92 94 hours blastocyst post hCG administration the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida followed by three washes in M2 medium.,For zebrafish bulk zygote samples total RNA was extracted from 100 zebrafish zygotes using TRIzol™ Reagent and eluated in 100 μl of RNase free water. Then 10 μl and 5 μl samples were taken for 10 zygote and 5 zygote samples respectively and volumes were adjusted to 12 μl with nuclease free water. For zebrafish single zygote samples single zygote was manually picked and distributed into 12 μl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples the cells were sorted into 12 μl 1X Lysis buffer using BD FACSMelody™ Cell Sorter BD Biosciences. For mouse oocyte and embryo samples post three washes in M2 medium oocytes and embryos were manually picked and put into 12 μl 1X Lysis buffer. For picoMeRIP seq experiment NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,,developmental stage:Zygote|molecule subtype:rRNA free RNA,GSM5599713,GSM5599713: ZF zygote Input 10cell Rep1; Danio rerio; RIP Seq,GSM5599713,,1,For mouse liver total RNA was extracted using TRIzol™ Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads™ mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote mouse MII oocyte and mouse blastocyst samples the single cells were manually picked and sorted into 12 μl 1X lysis buffer Takara; NEBNext® rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2 × 30 seconds incubated with the anti m6A antibody from Millipore ABE572 and precipitated using ethanol. SMART Seq® Stranded Kit Takara Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.,GEO Accession:GSM5599713,RIP-Seq,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP339082,,loader:fastq load.py,ZF_zygote_Input_10cell_Rep1_R1.fastq.gz ZF_zygote_Input_10cell_Rep1_R2.fastq.gz,fastq fastq,4029368016.0,39503608.0,GSM5599713 r1,0:51 1:51,A:893562237;C:1096986475;G:1180690796;T:857849967;N:278541,51,51,,,893562237,1096986475,1180690796,857849967,278541,SRX12382345,SRS10353007,SRA1301707,GEO,"Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan",2,0.91491,0.90807,0.32799,0.37836,0.89292,0.89282,0.81006,0.73354,51,51,B,B,biological fallback assumption,illumina,novaseq_era,3prime,poly_a,nebnext,bulk,bulk,bulk,,United States,2021-09-28,Zygote,Embryo,Oocyte,Reproductive System