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18 rows where devstage_curation_coarse = "Embryo" and experiment.library_strategy = "Bisulfite-Seq"

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devstage_curation 7

tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

experiment.library_strategy 1

  • Bisulfite-Seq · 18 ✖

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

  • Embryo · 18 ✖
Link 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
51269 51269 SRR8663334 SRX5460031 SRS4433921 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 48hpf rep2 GSM3638675   source name:embryo|tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish ZF 48hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish GSM3638675 GSM3638675: ZF 48hpf rep2; Danio rerio; Bisulfite Seq GSM3638675   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638675 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         21257043600.0 70856812.0 GSM3638675 r1 0:150 1:150 A:7462169931;C:3151216767;G:3428144480;T:7214024902;N:1487520 150 150     7462169931 3151216767 3428144480 7214024902 1487520 SRX5460031 SRS4433921 SRA855736 GEO Sun Yat-sen University 2 0.00062 0.00055 0.00017 0.00013 0.99949 0.99945 0.67901 0.75362 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Hatching Embryo Embryo Imprecise All anatomical structures
51270 51270 SRR8663333 SRX5460030 SRS4433920 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 48hpf rep1 GSM3638674   source name:embryo|tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish ZF 48hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish GSM3638674 GSM3638674: ZF 48hpf rep1; Danio rerio; Bisulfite Seq GSM3638674   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638674 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         20408177400.0 68027258.0 GSM3638674 r1 0:150 1:150 A:6990585654;C:3225159172;G:3562240517;T:6628764661;N:1427396 150 150     6990585654 3225159172 3562240517 6628764661 1427396 SRX5460030 SRS4433920 SRA855736 GEO Sun Yat-sen University 2 0.0009 0.00071 0.0003 0.00019 0.99928 0.99941 0.6 0.64367 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Hatching Embryo Embryo Imprecise All anatomical structures
51271 51271 SRR8663332 SRX5460029 SRS4433919 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 24hpf rep2 GSM3638673   source name:embryo|tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish ZF 24hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish GSM3638673 GSM3638673: ZF 24hpf rep2; Danio rerio; Bisulfite Seq GSM3638673   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638673 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         21961409700.0 73204699.0 GSM3638673 r1 0:150 1:150 A:7568027843;C:3406881222;G:3795216487;T:7190249641;N:1034507 150 150     7568027843 3406881222 3795216487 7190249641 1034507 SRX5460029 SRS4433919 SRA855736 GEO Sun Yat-sen University 2 0.00082 0.0007 0.00032 0.00023 0.99945 0.99947 0.65517 0.65 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
51272 51272 SRR8663331 SRX5460028 SRS4433918 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 24hpf rep1 GSM3638672   source name:embryo|tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish ZF 24hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:24 hpf|strain:wild type AB fish GSM3638672 GSM3638672: ZF 24hpf rep1; Danio rerio; Bisulfite Seq GSM3638672   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638672 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         22998615300.0 76662051.0 GSM3638672 r1 0:150 1:150 A:7938674920;C:3553518327;G:3950127781;T:7555207157;N:1087115 150 150     7938674920 3553518327 3950127781 7555207157 1087115 SRX5460028 SRS4433918 SRA855736 GEO Sun Yat-sen University 2 0.00076 0.00067 0.00027 0.00021 0.99926 0.99937 0.53658 0.58666 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Pharyngula Embryo Embryo Imprecise All anatomical structures
51273 51273 SRR8663330 SRX5460027 SRS4433917 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 16hpf rep2 GSM3638671   source name:embryo|tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish ZF 16hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish GSM3638671 GSM3638671: ZF 16hpf rep2; Danio rerio; Bisulfite Seq GSM3638671   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638671 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         25701246300.0 85670821.0 GSM3638671 r1 0:150 1:150 A:8976132831;C:3855344207;G:4201042226;T:8667517583;N:1209453 150 150     8976132831 3855344207 4201042226 8667517583 1209453 SRX5460027 SRS4433917 SRA855736 GEO Sun Yat-sen University 2 0.00117 0.00107 0.00036 0.00034 0.99928 0.99941 0.73571 0.75206 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Segmentation Embryo Embryo Imprecise All anatomical structures
51274 51274 SRR8663329 SRX5460026 SRS4433916 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 16hpf rep1 GSM3638670   source name:embryo|tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish ZF 16hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:16 hpf|strain:wild type AB fish GSM3638670 GSM3638670: ZF 16hpf rep1; Danio rerio; Bisulfite Seq GSM3638670   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638670 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         21585057600.0 71950192.0 GSM3638670 r1 0:150 1:150 A:7493903581;C:3312864799;G:3567558230;T:7209728977;N:1002013 150 150     7493903581 3312864799 3567558230 7209728977 1002013 SRX5460026 SRS4433916 SRA855736 GEO Sun Yat-sen University 2 0.00125 0.00119 0.00039 0.00034 0.99945 0.99947 0.7551 0.76865 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Segmentation Embryo Embryo Imprecise All anatomical structures
51275 51275 SRR8663328 SRX5460025 SRS4433915 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 10hpf rep2 GSM3638669   source name:embryo|tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish ZF 10hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish GSM3638669 GSM3638669: ZF 10hpf rep2; Danio rerio; Bisulfite Seq GSM3638669   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638669 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         18449316900.0 61497723.0 GSM3638669 r1 0:150 1:150 A:6508135454;C:2695665097;G:2948776234;T:6296104735;N:635380 150 150     6508135454 2695665097 2948776234 6296104735 635380 SRX5460025 SRS4433915 SRA855736 GEO Sun Yat-sen University 2 0.00092 0.00073 0.00035 0.00017 0.99931 0.99933 0.66019 0.6129 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Gastrula Embryo Embryo Imprecise All anatomical structures
51276 51276 SRR8663327 SRX5460024 SRS4433914 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 10hpf rep1 GSM3638668   source name:embryo|tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish ZF 10hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:10 hpf|strain:wild type AB fish GSM3638668 GSM3638668: ZF 10hpf rep1; Danio rerio; Bisulfite Seq GSM3638668   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638668 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         35064552300.0 116881841.0 GSM3638668 r1 0:150 1:150 A:12442483305;C:5073538954;G:5489080636;T:12058238019;N:1211386 150 150     12442483305 5073538954 5489080636 12058238019 1211386 SRX5460024 SRS4433914 SRA855736 GEO Sun Yat-sen University 2 0.0009 0.00072 0.00028 0.00019 0.99926 0.99945 0.61403 0.67045 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Gastrula Embryo Embryo Imprecise All anatomical structures
51277 51277 SRR8663326 SRX5460023 SRS4433913 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 8hpf rep2 GSM3638667   source name:embryo|tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish ZF 8hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish GSM3638667 GSM3638667: ZF 8hpf rep2; Danio rerio; Bisulfite Seq GSM3638667   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638667 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         14346635400.0 47822118.0 GSM3638667 r1 0:150 1:150 A:5096565523;C:2082957184;G:2242869596;T:4923737869;N:505228 150 150     5096565523 2082957184 2242869596 4923737869 505228 SRX5460023 SRS4433913 SRA855736 GEO Sun Yat-sen University 2 0.00107 0.00102 0.00035 0.00021 0.99884 0.99884 0.61068 0.71428 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Gastrula Embryo Embryo Imprecise All anatomical structures
51278 51278 SRR8663325 SRX5460022 SRS4433912 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 8hpf rep1 GSM3638666   source name:embryo|tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish ZF 8hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:8 hpf|strain:wild type AB fish GSM3638666 GSM3638666: ZF 8hpf rep1; Danio rerio; Bisulfite Seq GSM3638666   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638666 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         22564435500.0 75214785.0 GSM3638666 r1 0:150 1:150 A:8037530388;C:3263669666;G:3467393764;T:7794998569;N:843113 150 150     8037530388 3263669666 3467393764 7794998569 843113 SRX5460022 SRS4433912 SRA855736 GEO Sun Yat-sen University 2 0.00089 0.00082 0.00026 0.0002 0.99939 0.99939 0.71171 0.73267 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Gastrula Embryo Embryo Imprecise All anatomical structures
51279 51279 SRR8663324 SRX5460021 SRS4433911 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 6hpf rep2 GSM3638665   source name:embryo|tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish ZF 6hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish GSM3638665 GSM3638665: ZF 6hpf rep2; Danio rerio; Bisulfite Seq GSM3638665   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638665 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         15663840300.0 52212801.0 GSM3638665 r1 0:150 1:150 A:5036459488;C:2768054214;G:3109386160;T:4747198752;N:2741686 150 150     5036459488 2768054214 3109386160 4747198752 2741686 SRX5460021 SRS4433911 SRA855736 GEO Sun Yat-sen University 2 0.00121 0.0008 0.00062 0.00035 0.99922 0.99924 0.41509 0.40789 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Gastrula Embryo Embryo Imprecise All anatomical structures
51280 51280 SRR8663323 SRX5460020 SRS4433910 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 6hpf rep1 GSM3638664   source name:embryo|tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish ZF 6hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:6 hpf|strain:wild type AB fish GSM3638664 GSM3638664: ZF 6hpf rep1; Danio rerio; Bisulfite Seq GSM3638664   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638664 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         13146289500.0 43820965.0 GSM3638664 r1 0:150 1:150 A:4440608717;C:2140855274;G:2250243580;T:4312362152;N:2219777 150 150     4440608717 2140855274 2250243580 4312362152 2219777 SRX5460020 SRS4433910 SRA855736 GEO Sun Yat-sen University 2 0.00073 0.00047 0.00038 0.00014 0.99945 0.99941 0.32812 0.5 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Gastrula Embryo Embryo Imprecise All anatomical structures
51281 51281 SRR8663322 SRX5460019 SRS4433909 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 4hpf rep2 GSM3638663   source name:embryo|tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish ZF 4hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish GSM3638663 GSM3638663: ZF 4hpf rep2; Danio rerio; Bisulfite Seq GSM3638663   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638663 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         14505809700.0 48352699.0 GSM3638663 r1 0:150 1:150 A:4877194269;C:2388898572;G:2560124505;T:4676340810;N:3251544 150 150     4877194269 2388898572 2560124505 4676340810 3251544 SRX5460019 SRS4433909 SRA855736 GEO Sun Yat-sen University 2 0.00065 0.00045 0.00027 0.00016 0.99928 0.99945 0.46376 0.54166 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Blastula Embryo Embryo Imprecise All anatomical structures
51282 51282 SRR8663321 SRX5460018 SRS4433908 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 4hpf rep1 GSM3638662   source name:embryo|tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish ZF 4hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:4 hpf|strain:wild type AB fish GSM3638662 GSM3638662: ZF 4hpf rep1; Danio rerio; Bisulfite Seq GSM3638662   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638662 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         13666257000.0 45554190.0 GSM3638662 r1 0:150 1:150 A:4616947793;C:2221382014;G:2373430205;T:4451384606;N:3112382 150 150     4616947793 2221382014 2373430205 4451384606 3112382 SRX5460018 SRS4433908 SRA855736 GEO Sun Yat-sen University 2 0.00094 0.00054 0.00044 0.00022 0.99928 0.99939 0.38888 0.50943 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Blastula Embryo Embryo Imprecise All anatomical structures
51283 51283 SRR8663320 SRX5460017 SRS4433907 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 2hpf rep2 GSM3638661   source name:embryo|tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish ZF 2hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish GSM3638661 GSM3638661: ZF 2hpf rep2; Danio rerio; Bisulfite Seq GSM3638661   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638661 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         14619051000.0 48730170.0 GSM3638661 r1 0:150 1:150 A:4888878605;C:2423468919;G:2611005028;T:4692396498;N:3301950 150 150     4888878605 2423468919 2611005028 4692396498 3301950 SRX5460017 SRS4433907 SRA855736 GEO Sun Yat-sen University 2 0.00069 0.00053 0.00032 0.00019 0.99943 0.99953 0.28358 0.375 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Cleavage Embryo Embryo Imprecise All anatomical structures
51284 51284 SRR8663319 SRX5460016 SRS4433906 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 2hpf rep1 GSM3638660   source name:embryo|tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish ZF 2hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:2 hpf|strain:wild type AB fish GSM3638660 GSM3638660: ZF 2hpf rep1; Danio rerio; Bisulfite Seq GSM3638660   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638660 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         13281290400.0 44270968.0 GSM3638660 r1 0:150 1:150 A:4501039678;C:2150810078;G:2278027624;T:4348527287;N:2885733 150 150     4501039678 2150810078 2278027624 4348527287 2885733 SRX5460016 SRS4433906 SRA855736 GEO Sun Yat-sen University 2 0.00064 0.00039 0.00025 0.00013 0.99949 0.99963 0.46478 0.63414 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Cleavage Embryo Embryo Imprecise All anatomical structures
51285 51285 SRR8663318 SRX5460015 SRS4433905 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 0hpf rep2 GSM3638659   source name:embryo|tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish ZF 0hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish GSM3638659 GSM3638659: ZF 0hpf rep2; Danio rerio; Bisulfite Seq GSM3638659   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638659 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         11732143200.0 39107144.0 GSM3638659 r1 0:150 1:150 A:4048603242;C:1827111316;G:1904770606;T:3949005244;N:2652792 150 150     4048603242 1827111316 1904770606 3949005244 2652792 SRX5460015 SRS4433905 SRA855736 GEO Sun Yat-sen University 2 0.00152 0.00115 0.00043 0.00016 0.99928 0.99943 0.24509 0.81645 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Zygote Embryo Embryo Imprecise All anatomical structures
51286 51286 SRR8663317 SRX5460014 SRS4433904 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 0hpf rep1 GSM3638658   source name:embryo|tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish ZF 0hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:0 hpf|strain:wild type AB fish GSM3638658 GSM3638658: ZF 0hpf rep1; Danio rerio; Bisulfite Seq GSM3638658   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638658 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         9931664700.0 33105549.0 GSM3638658 r1 0:150 1:150 A:3401474427;C:1566218806;G:1670547045;T:3291140367;N:2284055 150 150     3401474427 1566218806 1670547045 3291140367 2284055 SRX5460014 SRS4433904 SRA855736 GEO Sun Yat-sen University 2 0.00196 0.00154 0.00071 0.00027 0.99928 0.99935 0.80263 0.85024 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Zygote Embryo Embryo Imprecise All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;