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87 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "RANDOM" and tissue_curation = "Embryo Imprecise"

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experiment.library_strategy 2

devstage_curation_coarse 2

tissue_curation_coarse 1

tissue_curation 1

  • Embryo Imprecise · 87 ✖

technology 1

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 87 ✖

experiment.library_layout 1

  • PAIRED · 87 ✖
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
32371 32371 SRR29180531 SRX24700713 SRS21428246 SRP509851 PRJNA1116337 Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish PRJNA1116337 Other Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.         IOX   isolate:exposure to IOX|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to IOX|BioSampleModel:Model organism or animal                 RNA seq of IOX treated IOX IOX Sequencing the transcriptomes of zebrafish embryos of IOX treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP509851     IOX_CGTACT_L001_R1_001.fastq.gz IOX_CGTACT_L001_R2_001.fastq.gz fastq fastq 9547157100.0 31823857.0 IOX CGTACT L001 R1 001.fastq.gz 0:150 1:150 A:2631030736;C:2146265744;G:2124421595;T:2645201596;N:237429 150 150     2631030736 2146265744 2124421595 2645201596 237429 SRX24700713 SRS21428246 SRA1878028 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-05-25 Hatching Embryo Embryo Imprecise All anatomical structures
32372 32372 SRR29180532 SRX24700712 SRS21428244 SRP509851 PRJNA1116337 Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish PRJNA1116337 Other Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.         CTR   isolate:control|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:control|BioSampleModel:Model organism or animal                 RNA seq of CTR treated CTR CTR Sequencing the transcriptomes of zebrafish embryos of control     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP509851     CTR_AGGCAG_L001_R1_001.fastq.gz CTR_AGGCAG_L001_R2_001.fastq.gz fastq fastq 9602954100.0 32009847.0 CTR AGGCAG L001 R1 001.fastq.gz 0:150 1:150 A:2637866848;C:2169057233;G:2152906664;T:2642882530;N:240825 150 150     2637866848 2169057233 2152906664 2642882530 240825 SRX24700712 SRS21428244 SRA1878028 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-05-25 Hatching Embryo Embryo Imprecise All anatomical structures
39911 39911 SRR2255651 SRX1187765 SRS1056695 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           TRAPPC11 Mutant2   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant2|BioSampleModel:Model organism or animal                 TRAPPC11 Mutant2 TRAPPC11 Mutant2 TRAPPC11 Mutant2 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     fattyliver2_S6_L001_R1_001.fastq.gz fattyliver2_S6_L001_R2_001.fastq.gz fastq fastq 836752562.0 5540752.0 TRAPPC11 Mutant2 0:75.54 1:75.48 A:219401421;C:198252489;G:195663968;T:223211242;N:223442 75 75     219401421 198252489 195663968 223211242 223442 SRX1187765 SRS1056695 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.96204 0.96259 0.05777 0.05527 0.74142 0.74089 0.47566 0.47333 75 52 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
39912 39912 SRR2255629 SRX1187764 SRS1056694 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           TRAPPC11 Mutant1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:TRAPPC11 Mutant1|BioSampleModel:Model organism or animal                 TRAPPC11 Mutant1 TRAPPC11 Mutant1 TRAPPC11 Mutant1 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     fattyliver1_S5_L001_R1_001.fastq.gz fattyliver1_S5_L001_R2_001.fastq.gz fastq fastq 752730180.0 4984563.0 TRAPPC11 Mutant1 0:75.53 1:75.48 A:201453785;C:174638707;G:171041330;T:205386632;N:209726 75 75     201453785 174638707 171041330 205386632 209726 SRX1187764 SRS1056694 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.95653 0.95631 0.07274 0.06976 0.70573 0.70664 0.49403 0.49925 74 76 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2015-09-05 Larval Larval Embryo Imprecise All anatomical structures
39913 39913 SRR2255628 SRX1187763 SRS1056693 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           PFOS2   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS2|BioSampleModel:Model organism or animal                 PFOS2 PFOS2 PFOS2 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     PFOS2_S4_L001_R1_001.fastq.gz PFOS2_S4_L001_R2_001.fastq.gz fastq fastq 660339622.0 4372724.0 PFOS2 0:75.53 1:75.48 A:174477377;C:155458423;G:152138367;T:178072878;N:192577 75 75     174477377 155458423 152138367 178072878 192577 SRX1187763 SRS1056693 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.95841 0.95943 0.06213 0.06061 0.71664 0.71717 0.49605 0.5046 76 52 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
39914 39914 SRR2255627 SRX1187762 SRS1056692 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           PFOS1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PFOS1|BioSampleModel:Model organism or animal                 PFOS1 PFOS1 PFOS1 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     PFOS1_S3_L001_R1_001.fastq.gz PFOS1_S3_L001_R2_001.fastq.gz fastq fastq 791950817.0 5244084.0 PFOS1 0:75.53 1:75.48 A:207476025;C:187690975;G:185784999;T:210781701;N:217117 75 75     207476025 187690975 185784999 210781701 217117 SRX1187762 SRS1056692 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.96195 0.96213 0.051 0.04857 0.7386 0.73927 0.49669 0.49151 76 53 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
39915 39915 SRR2255626 SRX1187761 SRS1056691 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           DMSO2   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO2|BioSampleModel:Model organism or animal                 DMSO2 DMSO2 DMSO2 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     DMSO2_S2_L001_R1_001.fastq.gz DMSO2_S2_L001_R2_001.fastq.gz fastq fastq 847975709.0 5615263.0 DMSO2 0:75.53 1:75.48 A:222828293;C:200598370;G:196827420;T:227477582;N:244044 75 75     222828293 200598370 196827420 227477582 244044 SRX1187761 SRS1056691 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.95825 0.95852 0.06376 0.06156 0.71224 0.71313 0.49629 0.49076 76 76 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
39916 39916 SRR2255625 SRX1187760 SRS1056690 SRP063370 PRJNA294819 Danio rerio PFOS FL transcriptome project PRJNA294819 Other           DMSO1   breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:DMSO1|BioSampleModel:Model organism or animal                 DMSO1 DMSO1 DMSO1 cDNA library from 300 ng of total RNA were constructed from two biological replicates using the TruSeq Stranded RNA LT Sample Prep Kit Illumina. The cDNA library was prepared according to the manufacturer’s instruction as previously described Gu et al. 2015. Briefly Index barcodes were first ligated for identification of individual samples. mRNA was purified from the total RNA using poly T oligo attached magnetic beads Illumina San Diego USA follows by random fragmentation using divalent cations at 94?C for 1 min. First and second strand cDNAs were synthesized using random oligonucleotides and SuperScript II followed by DNA polymerase I and RNase H. Exonuclease/polymerase was used to produce blunted overhangs. Illumina PE adapter oligonucleotides were ligated to the cDNA post 3’ end adenylation. DNA fragments were enriched by 15 cycles of PCR reaction. The libraries were purified using the AMPure XP and were quantified using KAPA Library Quantification Kits.     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina MiSeq <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP063370     DMSO1_S1_L001_R1_001.fastq.gz DMSO1_S1_L001_R2_001.fastq.gz fastq fastq 825003413.0 5463030.0 DMSO1 0:75.53 1:75.48 A:217714985;C:193454273;G:192078021;T:221527657;N:228477 75 75     217714985 193454273 192078021 221527657 228477 SRX1187760 SRS1056690 SRA295687 The Chinese University of Hong Kong The Chinese University of Hong Kong 2 0.96443 0.9657 0.05205 0.04878 0.76581 0.76465 0.49046 0.47298 76 54 B B biological fallback assumption illumina miseq unknown random_priming trueseq bulk unknown unknown   China 2016-09-05 Larval Larval Embryo Imprecise All anatomical structures
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
51318 51318 SRR8735311 SRX5528099 SRS4494644 SRP188580 PRJNA527366 Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio PRJNA527366 Other In this study we characterized the function of dachb the zebrafish homologue of human DACH1 in developing zebrafish embryos. Morpholino MO mediated knock down of dachb resulted in impaired islet cell development with a significant decrease in both the ß cell and islet cell numbers.         sample1   strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:Un injected|id:1|BioSampleModel:Model organism or animal                 Un injected1 1 1 rRNA depletion     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP188580     1_2.fastq.gz 1_1.fastq.gz fastq fastq 6454568216.0 31953308.0 1 1.fastq.gz 0:101 1:101 A:1711842196;C:1499359338;G:1512713745;T:1727020570;N:3632367 101 101     1711842196 1499359338 1512713745 1727020570 3632367 SRX5528099 SRS4494644 SRA861332 The Chinese University of Hong Kong|Department of Medicine and Therapeutics The Chinese University of Hong Kong 2 0.92197 0.92401 0.20455 0.20573 0.72452 0.72943 0.63778 0.63469 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-27 Undetermined Embryo Embryo Imprecise All anatomical structures
51319 51319 SRR8735312 SRX5528098 SRS4494643 SRP188580 PRJNA527366 Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio PRJNA527366 Other In this study we characterized the function of dachb the zebrafish homologue of human DACH1 in developing zebrafish embryos. Morpholino MO mediated knock down of dachb resulted in impaired islet cell development with a significant decrease in both the ß cell and islet cell numbers.         sample2   strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO|id:2|BioSampleModel:Model organism or animal                 p53MO2 2 2 rRNA depletion     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP188580     2_2.fastq.gz 2_1.fastq.gz fastq fastq 7923312236.0 39224318.0 2 1.fastq.gz 0:101 1:101 A:2115145426;C:1843204267;G:1845223955;T:2117945529;N:1793059 101 101     2115145426 1843204267 1845223955 2117945529 1793059 SRX5528098 SRS4494643 SRA861332 The Chinese University of Hong Kong|Department of Medicine and Therapeutics The Chinese University of Hong Kong 2 0.93137 0.93358 0.18665 0.18693 0.7025 0.70421 0.55171 0.55971 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-03-16 Undetermined Embryo Embryo Imprecise All anatomical structures
51320 51320 SRR8735313 SRX5528097 SRS4494642 SRP188580 PRJNA527366 Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio PRJNA527366 Other In this study we characterized the function of dachb the zebrafish homologue of human DACH1 in developing zebrafish embryos. Morpholino MO mediated knock down of dachb resulted in impaired islet cell development with a significant decrease in both the ß cell and islet cell numbers.         sample3   strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO dachbMOss|id:3|BioSampleModel:Model organism or animal                 p53MO dachbMOss3 3 3 rRNA depletion     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP188580     3_2.fastq.gz 3_1.fastq.gz fastq fastq 7167410460.0 35482230.0 3 1.fastq.gz 0:101 1:101 A:1924009959;C:1637729174;G:1671772822;T:1929836302;N:4062203 101 101     1924009959 1637729174 1671772822 1929836302 4062203 SRX5528097 SRS4494642 SRA861332 The Chinese University of Hong Kong|Department of Medicine and Therapeutics The Chinese University of Hong Kong 2 0.91551 0.91609 0.20076 0.20036 0.70956 0.71244 0.62871 0.62479 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-27 Undetermined Embryo Embryo Imprecise All anatomical structures
51321 51321 SRR8735314 SRX5528096 SRS4494641 SRP188580 PRJNA527366 Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio PRJNA527366 Other In this study we characterized the function of dachb the zebrafish homologue of human DACH1 in developing zebrafish embryos. Morpholino MO mediated knock down of dachb resulted in impaired islet cell development with a significant decrease in both the ß cell and islet cell numbers.         sample4   strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:Un injected|id:4|BioSampleModel:Model organism or animal                 Un injected4 4 4 rRNA depletion     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP188580     4_1.fastq.gz 4_2.fastq.gz fastq fastq 7730990460.0 38272230.0 4 1.fastq.gz 0:101 1:101 A:2077362460;C:1785598181;G:1793240660;T:2073032897;N:1756262 101 101     2077362460 1785598181 1793240660 2073032897 1756262 SRX5528096 SRS4494641 SRA861332 The Chinese University of Hong Kong|Department of Medicine and Therapeutics The Chinese University of Hong Kong 2 0.93365 0.93546 0.1884 0.18821 0.70299 0.70364 0.57943 0.5807 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-27 Undetermined Embryo Embryo Imprecise All anatomical structures
51322 51322 SRR8735315 SRX5528095 SRS4494640 SRP188580 PRJNA527366 Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio PRJNA527366 Other In this study we characterized the function of dachb the zebrafish homologue of human DACH1 in developing zebrafish embryos. Morpholino MO mediated knock down of dachb resulted in impaired islet cell development with a significant decrease in both the ß cell and islet cell numbers.         sample5   strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO|id:5|BioSampleModel:Model organism or animal                 p53MO5 5 5 rRNA depletion     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP188580     5_1.fastq.gz 5_2.fastq.gz fastq fastq 6268848608.0 31033904.0 5 1.fastq.gz 0:101 1:101 A:1714288048;C:1406856986;G:1416719545;T:1727415480;N:3568549 101 101     1714288048 1406856986 1416719545 1727415480 3568549 SRX5528095 SRS4494640 SRA861332 The Chinese University of Hong Kong|Department of Medicine and Therapeutics The Chinese University of Hong Kong 2 0.91571 0.91742 0.22322 0.2243 0.71187 0.71417 0.63484 0.63493 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-27 Undetermined Embryo Embryo Imprecise All anatomical structures
51323 51323 SRR8735316 SRX5528094 SRS4494639 SRP188580 PRJNA527366 Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio PRJNA527366 Other In this study we characterized the function of dachb the zebrafish homologue of human DACH1 in developing zebrafish embryos. Morpholino MO mediated knock down of dachb resulted in impaired islet cell development with a significant decrease in both the ß cell and islet cell numbers.         sample6   strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO dachbMOss|id:6|BioSampleModel:Model organism or animal                 p53MO dachbMOss6 6 6 rRNA depletion     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP188580     6_1.fastq.gz 6_2.fastq.gz fastq fastq 7551147638.0 37381919.0 6 1.fastq.gz 0:101 1:101 A:2055603662;C:1718965994;G:1723927649;T:2050926435;N:1723898 101 101     2055603662 1718965994 1723927649 2050926435 1723898 SRX5528094 SRS4494639 SRA861332 The Chinese University of Hong Kong|Department of Medicine and Therapeutics The Chinese University of Hong Kong 2 0.92834 0.93211 0.19289 0.19294 0.697 0.69895 0.60804 0.60183 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-27 Undetermined Embryo Embryo Imprecise All anatomical structures
51324 51324 SRR8735317 SRX5528093 SRS4494638 SRP188580 PRJNA527366 Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio PRJNA527366 Other In this study we characterized the function of dachb the zebrafish homologue of human DACH1 in developing zebrafish embryos. Morpholino MO mediated knock down of dachb resulted in impaired islet cell development with a significant decrease in both the ß cell and islet cell numbers.         sample7   strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:Un injected|id:7|BioSampleModel:Model organism or animal                 Un injected7 7 7 rRNA depletion     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP188580     7_1.fastq.gz 7_2.fastq.gz fastq fastq 8054903318.0 39875759.0 7 1.fastq.gz 0:101 1:101 A:2179527852;C:1844086452;G:1846868174;T:2182591371;N:1829469 101 101     2179527852 1844086452 1846868174 2182591371 1829469 SRX5528093 SRS4494638 SRA861332 The Chinese University of Hong Kong|Department of Medicine and Therapeutics The Chinese University of Hong Kong 2 0.93087 0.93266 0.20658 0.20582 0.70465 0.70656 0.5697 0.57048 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-27 Undetermined Embryo Embryo Imprecise All anatomical structures
51325 51325 SRR8735318 SRX5528092 SRS4494637 SRP188580 PRJNA527366 Characterization of the key role of dachshund b in the development of the pancreatic islet in zebrafish Danio rerio PRJNA527366 Other In this study we characterized the function of dachb the zebrafish homologue of human DACH1 in developing zebrafish embryos. Morpholino MO mediated knock down of dachb resulted in impaired islet cell development with a significant decrease in both the ß cell and islet cell numbers.         sample8   strain:NA|isolate:NA|breed:NA|cultivar:NA|ecotype:NA|age:NA|dev stage:NA|sex:NA|tissue:embryos|genotype:p53MO dachbMOss|id:8|BioSampleModel:Model organism or animal                 p53MO dachbMOss8 8 8 rRNA depletion     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP188580     8_1.fastq.gz 8_2.fastq.gz fastq fastq 7770765472.0 38469136.0 8 1.fastq.gz 0:101 1:101 A:2070852269;C:1791977628;G:1814751519;T:2088768678;N:4415378 101 101     2070852269 1791977628 1814751519 2088768678 4415378 SRX5528092 SRS4494637 SRA861332 The Chinese University of Hong Kong|Department of Medicine and Therapeutics The Chinese University of Hong Kong 2 0.91409 0.9159 0.23811 0.23792 0.71804 0.72088 0.66221 0.66365 101 101 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-01-27 Undetermined Embryo Embryo Imprecise All anatomical structures
53387 53387 SRR9849850 SRX6604478 SRS5169417 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         64h   cultivar:Danio rerio|age:64hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 64h 2 64h 2 64h 2 circRNA sequence using embryo from zebrafish 64 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     64h-1_Clean_1.fq.gz 64h-1_Clean_2.fq.gz fastq fastq 12070643714.0 40313092.0 64h 1 Clean 1.fq.gz 0:149.71 1:149.71 A:3237260307;C:2738447871;G:2833701504;T:3260078610;N:1155422 149 149     3237260307 2738447871 2833701504 3260078610 1155422 SRX6604478 SRS5169417 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.83609 0.83872 0.41826 0.41667 0.77557 0.78397 0.47577 0.47371 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Hatching Embryo Embryo Imprecise All anatomical structures
53388 53388 SRR9849851 SRX6604477 SRS5169416 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         56h   cultivar:Danio rerio|age:56hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 56h 2 56h 2 56h 2 circRNA sequence using embryo from zebrafish 56 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     56h-1_Clean_1.fq.gz 56h-1_Clean_2.fq.gz fastq fastq 12652509916.0 42236972.0 56h 1 Clean 1.fq.gz 0:149.78 1:149.78 A:3143250045;C:3111652116;G:3204244162;T:3192159623;N:1203970 149 149     3143250045 3111652116 3204244162 3192159623 1203970 SRX6604477 SRS5169416 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.75422 0.75589 0.33145 0.32138 0.8242 0.82911 0.44098 0.47205 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Hatching Embryo Embryo Imprecise All anatomical structures
53389 53389 SRR9849852 SRX6604476 SRS5169417 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         64h   cultivar:Danio rerio|age:64hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 64h 1 64h 1 64h 1 circRNA sequence using embryo from zebrafish 64 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-438_L4_7008.R1.clean.fastq.gz BN2-438_L4_7008.R2.clean.fastq.gz fastq fastq 10065278400.0 33550928.0 BN2 438 L4 7008.R1.clean.fastq.gz 0:150 1:150 A:1866703079;C:2946459459;G:3062616963;T:2188863630;N:635269 150 150     1866703079 2946459459 3062616963 2188863630 635269 SRX6604476 SRS5169417 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.9213 0.9133 0.81853 0.81548 0.96639 0.96741 0.46951 0.49212 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Hatching Embryo Embryo Imprecise All anatomical structures
53390 53390 SRR9849853 SRX6604475 SRS5169415 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         40h   cultivar:Danio rerio|age:40hpf stage:pharyngula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 40h 2 40h 2 40h 2 circRNA sequence using embryo from zebrafish 40 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     40h-1_Clean_1.fq.gz 40h-1_Clean_2.fq.gz fastq fastq 13039776756.0 43496055.0 40h 1 Clean 1.fq.gz 0:149.90 1:149.90 A:3288491359;C:3163780126;G:3276849759;T:3309186789;N:1468723 149 149     3288491359 3163780126 3276849759 3309186789 1468723 SRX6604475 SRS5169415 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.7816 0.78295 0.30782 0.30455 0.81148 0.82091 0.45266 0.46863 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Pharyngula Embryo Embryo Imprecise All anatomical structures
53391 53391 SRR9849854 SRX6604474 SRS5169416 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         56h   cultivar:Danio rerio|age:56hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 56h 1 56h 1 56h 1 circRNA sequence using embryo from zebrafish 56 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-437_L4_7007.R1.clean.fastq.gz BN2-437_L4_7007.R2.clean.fastq.gz fastq fastq 7808518800.0 26028396.0 BN2 437 L4 7007.R1.clean.fastq.gz 0:150 1:150 A:1446244174;C:2292471599;G:2377378733;T:1691933018;N:491276 150 150     1446244174 2292471599 2377378733 1691933018 491276 SRX6604474 SRS5169416 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.90958 0.89969 0.83016 0.82404 0.9641 0.96558 0.44242 0.44176 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Hatching Embryo Embryo Imprecise All anatomical structures
53392 53392 SRR9849855 SRX6604473 SRS5169409 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         24h   cultivar:Danio rerio|age:24hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 24h 2 24h 2 24h 2 circRNA sequence using embryo from zebrafish 24 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     24h-2_Clean_1.fq.gz 24h-2_Clean_2.fq.gz fastq fastq 14034181236.0 46814505.0 24h 2 Clean 1.fq.gz 0:149.89 1:149.89 A:3573271889;C:3370553727;G:3504868393;T:3583897705;N:1589522 149 149     3573271889 3370553727 3504868393 3583897705 1589522 SRX6604473 SRS5169409 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.6799 0.67993 0.30195 0.29636 0.82453 0.83489 0.46929 0.47455 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Multi-stage Embryo Embryo Imprecise All anatomical structures
53393 53393 SRR9849856 SRX6604472 SRS5169415 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         40h   cultivar:Danio rerio|age:40hpf stage:pharyngula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 40h 1 40h 1 40h 1 circRNA sequence using embryo from zebrafish 40 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-435_L4_7005.R1.clean.fastq.gz BN2-435_L4_7005.R2.clean.fastq.gz fastq fastq 7253248500.0 24177495.0 BN2 435 L4 7005.R1.clean.fastq.gz 0:150 1:150 A:1410890545;C:2084999879;G:2163487041;T:1593413760;N:457275 150 150     1410890545 2084999879 2163487041 1593413760 457275 SRX6604472 SRS5169415 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.87864 0.86461 0.70089 0.69415 0.94899 0.95221 0.45413 0.48608 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Pharyngula Embryo Embryo Imprecise All anatomical structures
53394 53394 SRR9849857 SRX6604471 SRS5169414 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         12h   cultivar:Danio rerio|age:12hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 12h 2 12h 2 12h 2 circRNA sequence using embryo from zebrafish 12 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     12h-1_Clean_1.fq.gz 12h-1_Clean_2.fq.gz fastq fastq 9760537114.0 32612820.0 12h 1 Clean 1.fq.gz 0:149.64 1:149.64 A:2537269193;C:2297094668;G:2379024620;T:2546216364;N:932269 149 149     2537269193 2297094668 2379024620 2546216364 932269 SRX6604471 SRS5169414 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.75204 0.75144 0.34914 0.3456 0.79444 0.80298 0.47617 0.47647 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Segmentation Embryo Embryo Imprecise All anatomical structures
53395 53395 SRR9849858 SRX6604470 SRS5169410 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         16h   cultivar:Danio rerio|age:16hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 16h 1 16h 1 16h 1 circRNA sequence using embryo from zebrafish 16 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-430_L3_56.R1.clean.fastq.gz BN2-430_L3_56.R2.clean.fastq.gz fastq fastq 11290204500.0 37634015.0 BN2 430 L3 56.R1.clean.fastq.gz 0:150 1:150 A:2002607987;C:3409827596;G:3508023598;T:2368035468;N:1709851 150 150     2002607987 3409827596 3508023598 2368035468 1709851 SRX6604470 SRS5169410 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.91788 0.9101 0.83385 0.81588 0.98462 0.9847 0.87183 0.87504 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Segmentation Embryo Embryo Imprecise All anatomical structures
53396 53396 SRR9849859 SRX6604469 SRS5169412 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         8h   cultivar:Danio rerio|age:8hpf stage:gastrula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 8h 2 8h 2 8h 2 circRNA sequence using embryo from zebrafish 8 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     8h-1_Clean_1.fq.gz 8h-1_Clean_2.fq.gz fastq fastq 10251074214.0 34220438.0 8h 1 Clean 1.fq.gz 0:149.78 1:149.78 A:2756560112;C:2322673379;G:2413816656;T:2757047449;N:976618 149 149     2756560112 2322673379 2413816656 2757047449 976618 SRX6604469 SRS5169412 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.64563 0.64819 0.2964 0.2935 0.8314 0.84045 0.48159 0.45437 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Gastrula Embryo Embryo Imprecise All anatomical structures
53397 53397 SRR9849860 SRX6604468 SRS5169414 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         12h   cultivar:Danio rerio|age:12hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 12h 1 12h 1 12h 1 circRNA sequence using embryo from zebrafish 12 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-429_L3_55.R1.clean.fastq.gz BN2-429_L3_55.R2.clean.fastq.gz fastq fastq 9471315300.0 31571051.0 BN2 429 L3 55.R1.clean.fastq.gz 0:150 1:150 A:1671591116;C:2907243262;G:3000871353;T:1890180659;N:1428910 150 150     1671591116 2907243262 3000871353 1890180659 1428910 SRX6604468 SRS5169414 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.76551 0.7596 0.58436 0.57204 0.9853 0.98567 0.95092 0.95274 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Segmentation Embryo Embryo Imprecise All anatomical structures
53398 53398 SRR9849861 SRX6604467 SRS5169413 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         4h   cultivar:Danio rerio|age:4hpf stage:bastula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 4h 1 4h 1 4h 1 circRNA sequence using embryo from zebrafish 4 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-427_L3_53.R1.clean.fastq.gz BN2-427_L3_53.R2.clean.fastq.gz fastq fastq 10733190600.0 35777302.0 BN2 427 L3 53.R1.clean.fastq.gz 0:150 1:150 A:1899542444;C:3199739789;G:3296303811;T:2336021248;N:1583308 150 150     1899542444 3199739789 3296303811 2336021248 1583308 SRX6604467 SRS5169413 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.84333 0.8387 0.65527 0.64575 0.97634 0.97737 0.70606 0.63009 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Blastula Embryo Embryo Imprecise All anatomical structures
53399 53399 SRR9849862 SRX6604466 SRS5169412 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         8h   cultivar:Danio rerio|age:8hpf stage:gastrula|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 8h 1 8h 1 8h 1 circRNA sequence using embryo from zebrafish 8 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-428_L3_54.R1.clean.fastq.gz BN2-428_L3_54.R2.clean.fastq.gz fastq fastq 9969874200.0 33232914.0 BN2 428 L3 54.R1.clean.fastq.gz 0:150 1:150 A:1837074577;C:2926406946;G:3018549867;T:2186360288;N:1482522 150 150     1837074577 2926406946 3018549867 2186360288 1482522 SRX6604466 SRS5169412 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.87531 0.86035 0.62205 0.60979 0.97538 0.97621 0.56075 0.59936 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Gastrula Embryo Embryo Imprecise All anatomical structures
53400 53400 SRR9849863 SRX6604465 SRS5169411 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         0h   cultivar:Danio rerio|age:0hpf stage:zygote|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 0h 1 0h 1 0h 1 circRNA sequence using embryo from zebrafish 0 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-426_L3_52.R1.clean.fastq.gz BN2-426_L3_52.R2.clean.fastq.gz fastq fastq 15572807100.0 51909357.0 BN2 426 L3 52.R1.clean.fastq.gz 0:150 1:150 A:2605617359;C:4885017797;G:5011849012;T:3067990728;N:2332204 150 150     2605617359 4885017797 5011849012 3067990728 2332204 SRX6604465 SRS5169411 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.78804 0.77444 0.56081 0.54686 0.93348 0.93545 0.77104 0.62239 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Zygote Embryo Embryo Imprecise All anatomical structures
53401 53401 SRR9849864 SRX6604464 SRS5169411 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         0h   cultivar:Danio rerio|age:0hpf stage:zygote|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 0h 2 0h 2 0h 2 circRNA sequence using embryo from zebrafish 0 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     0h_Clean_1.fq.gz 0h_Clean_2.fq.gz fastq fastq 17258783034.0 57614191.0 0h Clean 1.fq.gz 0:149.78 1:149.78 A:3915507312;C:4601222856;G:4762519500;T:3977299451;N:2233915 149 149     3915507312 4601222856 4762519500 3977299451 2233915 SRX6604464 SRS5169411 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.82486 0.82843 0.16023 0.14824 0.79971 0.80348 0.48785 0.48902 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Zygote Embryo Embryo Imprecise All anatomical structures
53402 53402 SRR9849865 SRX6604463 SRS5169410 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         16h   cultivar:Danio rerio|age:16hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 16h 2 16h 2 16h 2 circRNA sequence using embryo from zebrafish 16 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     16h-1_Clean_1.fq.gz 16h-1_Clean_2.fq.gz fastq fastq 13746008148.0 45914536.0 16h 1 Clean 1.fq.gz 0:149.69 1:149.69 A:3633911267;C:3175232398;G:3288410708;T:3647163703;N:1290072 149 149     3633911267 3175232398 3288410708 3647163703 1290072 SRX6604463 SRS5169410 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.76446 0.76939 0.32701 0.32679 0.80537 0.8116 0.47029 0.4846 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Segmentation Embryo Embryo Imprecise All anatomical structures
53403 53403 SRR9849866 SRX6604462 SRS5169409 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         24h   cultivar:Danio rerio|age:24hpf stage:segmentation|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 24h 1 24h 1 24h 1 circRNA sequence using embryo from zebrafish 24 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-432_L3_7002.R1.clean.fastq.gz BN2-432_L3_7002.R2.clean.fastq.gz fastq fastq 4964505000.0 16548350.0 BN2 432 L3 7002.R1.clean.fastq.gz 0:150 1:150 A:869476377;C:1551985326;G:1601622154;T:940673581;N:747562 150 150     869476377 1551985326 1601622154 940673581 747562 SRX6604462 SRS5169409 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.90699 0.90038 0.67002 0.65836 0.98528 0.98557 0.90533 0.8368 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Multi-stage Embryo Embryo Imprecise All anatomical structures
57192 57192 SRR11267487 SRX7874167 SRS6282472 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 4   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 2dpf wild type replicate 4 2D wt 4 2D wt 4 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W4_RRA127644-V_2.fq.gz s-2D-W4_RRA127644-V_1.fq.gz fastq fastq 8446821000.0 28156070.0 s 2D W4 RRA127644 V 1.fq.gz 0:150 1:150 A:2097825166;C:2140144849;G:2138243343;T:2070561208;N:46434 150 150     2097825166 2140144849 2138243343 2070561208 46434 SRX7874167 SRS6282472 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96179 0.9619 0.03544 0.03525 0.73484 0.73476 0.46149 0.46378 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57193 57193 SRR11267488 SRX7874166 SRS6282471 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 3   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 2dpf wild type replicate 3 2D wt 3 2D wt 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W3_RRA127643-V_2.fq.gz s-2D-W3_RRA127643-V_1.fq.gz fastq fastq 7574668800.0 25248896.0 s 2D W3 RRA127643 V 1.fq.gz 0:150 1:150 A:1965967840;C:1838044502;G:1837157311;T:1933458605;N:40542 150 150     1965967840 1838044502 1837157311 1933458605 40542 SRX7874166 SRS6282471 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.94714 0.94809 0.06053 0.06005 0.70601 0.7066 0.44616 0.4478 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57194 57194 SRR11267489 SRX7874165 SRS6282470 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 2   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 2dpf wild type replicate 2 2D wt 2 2D wt 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W2_RRA127642-V_1.fq.gz s-2D-W2_RRA127642-V_2.fq.gz fastq fastq 6972507000.0 23241690.0 s 2D W2 RRA127642 V 1.fq.gz 0:150 1:150 A:1813207623;C:1690998145;G:1687754190;T:1780508001;N:39041 150 150     1813207623 1690998145 1687754190 1780508001 39041 SRX7874165 SRS6282470 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.94999 0.95119 0.05951 0.0596 0.7077 0.70778 0.45098 0.44895 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57195 57195 SRR11267490 SRX7874164 SRS6282468 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 1   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 2dpf wild type replicate 1 2D wt 1 2D wt 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W1_RRA127641-V_1.fq.gz s-2D-W1_RRA127641-V_2.fq.gz fastq fastq 7527697800.0 25092326.0 s 2D W1 RRA127641 V 1.fq.gz 0:150 1:150 A:1939383301;C:1841967572;G:1840198678;T:1906107300;N:40949 150 150     1939383301 1841967572 1840198678 1906107300 40949 SRX7874164 SRS6282468 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.93028 0.93025 0.05585 0.05522 0.71163 0.71281 0.45427 0.45339 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57196 57196 SRR11267491 SRX7874163 SRS6282469 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 6   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 2dpf mutant replicate 6 2D mut 6 2D mut 6 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU6_RRA127640-V_1.fq.gz s-2D-MU6_RRA127640-V_2.fq.gz fastq fastq 7468400400.0 24894668.0 s 2D MU6 RRA127640 V 1.fq.gz 0:150 1:150 A:1831861636;C:1917846110;G:1910771652;T:1807881608;N:39394 150 150     1831861636 1917846110 1910771652 1807881608 39394 SRX7874163 SRS6282469 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96824 0.96912 0.02823 0.02789 0.76116 0.76086 0.46225 0.46104 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57205 57205 SRR11267500 SRX7874154 SRS6282459 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 5   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 2dpf mutant replicate 5 2D mut 5 2D mut 5 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU5_RRA127639-V_1.fq.gz s-2D-MU5_RRA127639-V_2.fq.gz fastq fastq 7610707500.0 25369025.0 s 2D MU5 RRA127639 V 1.fq.gz 0:150 1:150 A:1916314949;C:1902998959;G:1903573416;T:1887778592;N:41584 150 150     1916314949 1902998959 1903573416 1887778592 41584 SRX7874154 SRS6282459 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95723 0.95704 0.04362 0.04378 0.7231 0.72196 0.45408 0.45325 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57216 57216 SRR11267511 SRX7874143 SRS6282448 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 4   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 2dpf mutant replicate 4 2D mut 4 2D mut 4 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU4_RRA127638-V_2.fq.gz s-2D-MU4_RRA127638-V_1.fq.gz fastq fastq 7971688200.0 26572294.0 s 2D MU4 RRA127638 V 1.fq.gz 0:150 1:150 A:1975296205;C:2025572304;G:2026332631;T:1944443854;N:43206 150 150     1975296205 2025572304 2026332631 1944443854 43206 SRX7874143 SRS6282448 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96253 0.96256 0.03284 0.03254 0.75057 0.75079 0.45472 0.45579 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57223 57223 SRR11267518 SRX7874136 SRS6282441 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D wt 6   strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 4dpf wild type replicate 6 4D wt 6 4D wt 6 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DW6_RRA129726-V_1.fq.gz s-4DW6_RRA129726-V_2.fq.gz fastq fastq 6290868600.0 20969562.0 s 4DW6 RRA129726 V 1.fq.gz 0:150 1:150 A:1602921878;C:1557114242;G:1554419087;T:1576298561;N:114832 150 150     1602921878 1557114242 1554419087 1576298561 114832 SRX7874136 SRS6282441 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95859 0.95923 0.04563 0.04591 0.70828 0.70865 0.45792 0.46969 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57224 57224 SRR11267519 SRX7874135 SRS6282439 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D wt 5   strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 4dpf wild type replicate 5 4D wt 5 4D wt 5 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DW5_RRA129725-V_2.fq.gz s-4DW5_RRA129725-V_1.fq.gz fastq fastq 6521328900.0 21737763.0 s 4DW5 RRA129725 V 1.fq.gz 0:150 1:150 A:1655910947;C:1620499741;G:1616133473;T:1628664792;N:119947 150 150     1655910947 1620499741 1616133473 1628664792 119947 SRX7874135 SRS6282439 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96275 0.96347 0.03156 0.03162 0.72068 0.71979 0.47386 0.47433 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57225 57225 SRR11267520 SRX7874134 SRS6282438 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D wt 4   strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 4dpf wild type replicate 4 4D wt 4 4D wt 4 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DW4_RRA129724-V_2.fq.gz s-4DW4_RRA129724-V_1.fq.gz fastq fastq 5854878600.0 19516262.0 s 4DW4 RRA129724 V 1.fq.gz 0:150 1:150 A:1516513397;C:1423158456;G:1421167843;T:1493933378;N:105526 150 150     1516513397 1423158456 1421167843 1493933378 105526 SRX7874134 SRS6282438 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95398 0.95372 0.05409 0.05408 0.69193 0.69043 0.47544 0.47498 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57226 57226 SRR11267521 SRX7874133 SRS6282440 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D wt 3   strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 4dpf wild type replicate 3 4D wt 3 4D wt 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DW3_RRA129723-V_1.fq.gz s-4DW3_RRA129723-V_2.fq.gz fastq fastq 6420460500.0 21401535.0 s 4DW3 RRA129723 V 1.fq.gz 0:150 1:150 A:1657978157;C:1569027011;G:1567167327;T:1626170930;N:117075 150 150     1657978157 1569027011 1567167327 1626170930 117075 SRX7874133 SRS6282440 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.9553 0.95688 0.04567 0.04609 0.70076 0.70201 0.47195 0.47051 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57227 57227 SRR11267522 SRX7874132 SRS6282437 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 3   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 2dpf mutant replicate 3 2D mut 3 2D mut 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU3_RRA127637-V_1.fq.gz s-2D-MU3_RRA127637-V_2.fq.gz fastq fastq 8159715900.0 27199053.0 s 2D MU3 RRA127637 V 1.fq.gz 0:150 1:150 A:2021631175;C:2074621188;G:2072837540;T:1990581511;N:44486 150 150     2021631175 2074621188 2072837540 1990581511 44486 SRX7874132 SRS6282437 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96275 0.9634 0.02909 0.02886 0.75035 0.75035 0.46995 0.46205 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57228 57228 SRR11267523 SRX7874131 SRS6282435 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D wt 2   strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 4dpf wild type replicate 2 4D wt 2 4D wt 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DW2_RRA129722-V_2.fq.gz s-4DW2_RRA129722-V_1.fq.gz fastq fastq 6231414600.0 20771382.0 s 4DW2 RRA129722 V 1.fq.gz 0:150 1:150 A:1565996983;C:1561905686;G:1563088801;T:1540306966;N:116164 150 150     1565996983 1561905686 1563088801 1540306966 116164 SRX7874131 SRS6282435 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96185 0.96048 0.02574 0.02597 0.7525 0.75246 0.48131 0.4798 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57229 57229 SRR11267524 SRX7874130 SRS6282434 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D wt 1   strain:Abtu|ecotype:wild type|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 4dpf wild type replicate 1 4D wt 1 4D wt 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DW1_RRA129721-V_1.fq.gz s-4DW1_RRA129721-V_2.fq.gz fastq fastq 6940311000.0 23134370.0 s 4DW1 RRA129721 V 1.fq.gz 0:150 1:150 A:1728701566;C:1758026863;G:1753262837;T:1700189966;N:129768 150 150     1728701566 1758026863 1753262837 1700189966 129768 SRX7874130 SRS6282434 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96581 0.96605 0.0236 0.02384 0.75668 0.7572 0.46377 0.47497 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57230 57230 SRR11267525 SRX7874129 SRS6282436 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D mut 6   strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 4dpf mutant replicate 6 4D mut 6 4D mut 6 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DM6_RRA129732-V_1.fq.gz s-4DM6_RRA129732-V_2.fq.gz fastq fastq 7018647900.0 23395493.0 s 4DM6 RRA129732 V 1.fq.gz 0:150 1:150 A:1721137250;C:1803664148;G:1797589773;T:1696193598;N:63131 150 150     1721137250 1803664148 1797589773 1696193598 63131 SRX7874129 SRS6282436 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.9632 0.963 0.04647 0.04582 0.75469 0.75323 0.49113 0.50374 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57231 57231 SRR11267526 SRX7874128 SRS6282433 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D mut 5   strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 4dpf mutant replicate 5 4D mut 5 4D mut 5 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DM5_RRA129731-V_1.fq.gz s-4DM5_RRA129731-V_2.fq.gz fastq fastq 7041267300.0 23470891.0 s 4DM5 RRA129731 V 1.fq.gz 0:150 1:150 A:1820556438;C:1718486576;G:1709755419;T:1792340292;N:128575 150 150     1820556438 1718486576 1709755419 1792340292 128575 SRX7874128 SRS6282433 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95631 0.95695 0.0493 0.04977 0.69777 0.69818 0.48032 0.4808 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57232 57232 SRR11267527 SRX7874127 SRS6282432 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D mut 4   strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 4dpf mutant replicate 4 4D mut 4 4D mut 4 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DM4_RRA129730-V_1.fq.gz s-4DM4_RRA129730-V_2.fq.gz fastq fastq 6123819300.0 20412731.0 s 4DM4 RRA129730 V 1.fq.gz 0:150 1:150 A:1588852253;C:1490446542;G:1482372430;T:1562034789;N:113286 150 150     1588852253 1490446542 1482372430 1562034789 113286 SRX7874127 SRS6282432 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95504 0.95601 0.05374 0.05397 0.69607 0.69568 0.46267 0.47356 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57233 57233 SRR11267528 SRX7874126 SRS6282430 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D mut 3   strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 4dpf mutant replicate 3 4D mut 3 4D mut 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DM3_RRA129729-V_1.fq.gz s-4DM3_RRA129729-V_2.fq.gz fastq fastq 5935667700.0 19785559.0 s 4DM3 RRA129729 V 1.fq.gz 0:150 1:150 A:1528502547;C:1454741840;G:1448550625;T:1503764733;N:107955 150 150     1528502547 1454741840 1448550625 1503764733 107955 SRX7874126 SRS6282430 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95331 0.95286 0.04982 0.04955 0.70104 0.70147 0.47135 0.47071 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57234 57234 SRR11267529 SRX7874125 SRS6282431 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D mut 2   strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 4dpf mutant replicate 2 4D mut 2 4D mut 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DM2_RRA129728-V-W_1.fq.gz s-4DM2_RRA129728-V-W_2.fq.gz fastq fastq 6097668000.0 20325560.0 s 4DM2 RRA129728 V W 1.fq.gz 0:150 1:150 A:1530973442;C:1532125738;G:1527770104;T:1506686977;N:111739 150 150     1530973442 1532125738 1527770104 1506686977 111739 SRX7874125 SRS6282431 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.9577 0.95944 0.03753 0.03769 0.73657 0.73574 0.4797 0.48662 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57235 57235 SRR11267530 SRX7874124 SRS6282429 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           4D mut 1   strain:Abtu|ecotype:mutant|dev stage:4dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 4dpf mutant replicate 1 4D mut 1 4D mut 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-4DM1_RRA129727-V_1.fq.gz s-4DM1_RRA129727-V_2.fq.gz fastq fastq 6597863100.0 21992877.0 s 4DM1 RRA129727 V 1.fq.gz 0:150 1:150 A:1743922570;C:1570643015;G:1566383758;T:1716793707;N:120050 150 150     1743922570 1570643015 1566383758 1716793707 120050 SRX7874124 SRS6282429 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.94852 0.94862 0.06862 0.06874 0.67862 0.67947 0.47809 0.47844 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Larval Larval Embryo Imprecise All anatomical structures
57236 57236 SRR11267531 SRX7874123 SRS6282428 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 6   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 2dpf wild type replicate 6 2D wt 6 2D wt 6 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W6_RRA127646-V_1.fq.gz s-2D-W6_RRA127646-V_2.fq.gz fastq fastq 7672945500.0 25576485.0 s 2D W6 RRA127646 V 1.fq.gz 0:150 1:150 A:1904102253;C:1945024582;G:1945915237;T:1877861524;N:41904 150 150     1904102253 1945024582 1945915237 1877861524 41904 SRX7874123 SRS6282428 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96213 0.96229 0.02936 0.0295 0.74418 0.74428 0.46242 0.46223 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57237 57237 SRR11267532 SRX7874122 SRS6282426 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 5   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 2dpf wild type replicate 5 2D wt 5 2D wt 5 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W5_RRA127645-V_1.fq.gz s-2D-W5_RRA127645-V_2.fq.gz fastq fastq 6602868900.0 22009563.0 s 2D W5 RRA127645 V 1.fq.gz 0:150 1:150 A:1688419207;C:1625631997;G:1626136783;T:1662643961;N:36952 150 150     1688419207 1625631997 1626136783 1662643961 36952 SRX7874122 SRS6282426 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.956 0.95646 0.04794 0.04766 0.72226 0.72316 0.45044 0.44816 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57238 57238 SRR11267533 SRX7874121 SRS6282427 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 2   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 2dpf mutant replicate 2 2D mut 2 2D mut 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU2_RRA127636-V_1.fq.gz s-2D-MU2_RRA127636-V_2.fq.gz fastq fastq 7639000500.0 25463335.0 s 2D MU2 RRA127636 V 1.fq.gz 0:150 1:150 A:1914314950;C:1916936042;G:1919603914;T:1888104180;N:41414 150 150     1914314950 1916936042 1919603914 1888104180 41414 SRX7874121 SRS6282427 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95818 0.95815 0.03971 0.03906 0.72247 0.72236 0.44884 0.45872 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57239 57239 SRR11267534 SRX7874120 SRS6282425 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 1   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 2dpf mutant replicate 1 2D mut 1 2D mut 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU1_RRA127635-V_1.fq.gz s-2D-MU1_RRA127635-V_2.fq.gz fastq fastq 7955196900.0 26517323.0 s 2D MU1 RRA127635 V 1.fq.gz 0:150 1:150 A:1980678540;C:2010190992;G:2012301601;T:1951981643;N:44124 150 150     1980678540 2010190992 2012301601 1951981643 44124 SRX7874120 SRS6282425 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96174 0.96124 0.03506 0.03487 0.73866 0.73921 0.4672 0.4643 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
73895 73895 SRR23312683 SRX19255357 SRS16658070 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     high concentration   D1 1000   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:1000|Replicate:1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio D1 D1 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     10_R1_001.fastq.gz fastq 4488415650.0 29922771.0 10 R1 001.fastq.gz 0:150 1:0 A:1238382281;C:1019437721;G:1026346198;T:1203790286;N:459164 150 0     1238382281 1019437721 1026346198 1203790286 459164 SRX19255357 SRS16658070 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.91866   0.12395   0.67894   0.47111   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73896 73896 SRR23312684 SRX19255356 SRS16658069 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     medium concentration   C3 100   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:100|Replicate:3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio C3 C3 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     9_R1_001.fastq.gz fastq 5066914650.0 33779431.0 9 R1 001.fastq.gz 0:150 1:0 A:1380446646;C:1166400624;G:1173637886;T:1345919328;N:510166 150 0     1380446646 1166400624 1173637886 1345919328 510166 SRX19255356 SRS16658069 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.92353   0.10534   0.66718   0.46961   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73897 73897 SRR23312685 SRX19255355 SRS16658068 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     medium concentration   C2 100   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:100|Replicate:2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio C2 C2 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     8_R1_001.fastq.gz fastq 5016292200.0 33441948.0 8 R1 001.fastq.gz 0:150 1:0 A:1369655404;C:1151837285;G:1157153916;T:1337126809;N:518786 150 0     1369655404 1151837285 1157153916 1337126809 518786 SRX19255355 SRS16658068 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.92406   0.10869   0.66904   0.47045   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73898 73898 SRR23312686 SRX19255354 SRS16658067 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     medium concentration   C1 100   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:100|Replicate:1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio C1 C1 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     7_R1_001.fastq.gz fastq 5250633750.0 35004225.0 7 R1 001.fastq.gz 0:150 1:0 A:1449073657;C:1192104553;G:1204557007;T:1404369034;N:529499 150 0     1449073657 1192104553 1204557007 1404369034 529499 SRX19255354 SRS16658067 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.92479   0.11397   0.67239   0.49481   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73899 73899 SRR23312687 SRX19255353 SRS16658066 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     low concentration   B3 10   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:10|Replicate:3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio B3 B3 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     6_R1_001.fastq.gz fastq 4621299750.0 30808665.0 6 R1 001.fastq.gz 0:150 1:0 A:1283724967;C:1039098740;G:1051690110;T:1246298234;N:487699 150 0     1283724967 1039098740 1051690110 1246298234 487699 SRX19255353 SRS16658066 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.91793   0.12114   0.67519   0.49228   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73900 73900 SRR23312688 SRX19255352 SRS16658065 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     low concentration   B2 10   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:10|Replicate:2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio B2 B2 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     5_R1_001.fastq.gz fastq 4498030800.0 29986872.0 5 R1 001.fastq.gz 0:150 1:0 A:1231794961;C:1029292947;G:1044561776;T:1191908157;N:472959 150 0     1231794961 1029292947 1044561776 1191908157 472959 SRX19255352 SRS16658065 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.9247   0.10935   0.67643   0.46921   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73901 73901 SRR23312689 SRX19255351 SRS16658064 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     low concentration   B1 10   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:10|Replicate:1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio B1 B1 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     4_R1_001.fastq.gz fastq 4647039750.0 30980265.0 4 R1 001.fastq.gz 0:150 1:0 A:1316546226;C:1021465864;G:1033563752;T:1274977481;N:486427 150 0     1316546226 1021465864 1033563752 1274977481 486427 SRX19255351 SRS16658064 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.91104   0.14067   0.684   0.51319   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73902 73902 SRR23312690 SRX19255350 SRS16658063 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     control without xxx   A3 0   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:0|Replicate:3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio A3 A3 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     3_R1_001.fastq.gz fastq 4770226650.0 31801511.0 3 R1 001.fastq.gz 0:150 1:0 A:1296635395;C:1101384429;G:1107665905;T:1264050013;N:490908 150 0     1296635395 1101384429 1107665905 1264050013 490908 SRX19255350 SRS16658063 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.92793   0.10006   0.66685   0.46338   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73903 73903 SRR23312691 SRX19255349 SRS16658062 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     high concentration   D3 1000   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:1000|Replicate:3|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio D3 D3 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     12_R1_001.fastq.gz fastq 4819346250.0 32128975.0 12 R1 001.fastq.gz 0:150 1:0 A:1315685334;C:1104858071;G:1112230143;T:1286081188;N:491514 150 0     1315685334 1104858071 1112230143 1286081188 491514 SRX19255349 SRS16658062 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.92264   0.11002   0.65896   0.4777   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73904 73904 SRR23312692 SRX19255348 SRS16658061 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     high concentration   D2 1000   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:1000|Replicate:2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio D2 D2 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     11_R1_001.fastq.gz fastq 5197982250.0 34653215.0 11 R1 001.fastq.gz 0:150 1:0 A:1423534245;C:1189161999;G:1198749942;T:1386005659;N:530405 150 0     1423534245 1189161999 1198749942 1386005659 530405 SRX19255348 SRS16658061 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.9217   0.11194   0.67314   0.46463   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73905 73905 SRR23312693 SRX19255347 SRS16658060 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     control without xxx   A2 0   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:0|Replicate:2|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio A2 A2 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     2_R1_001.fastq.gz fastq 4829580900.0 32197206.0 2 R1 001.fastq.gz 0:150 1:0 A:1311877103;C:1115341699;G:1125197926;T:1276668284;N:495888 150 0     1311877103 1115341699 1125197926 1276668284 495888 SRX19255347 SRS16658060 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.92688   0.09556   0.67207   0.46217   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval Embryo Imprecise All anatomical structures
73906 73906 SRR23312694 SRX19255346 SRS16658059 SRP420571 PRJNA929522 Transcriptomic signaling in zebrafish Danio rerio embryos exposed to environmental concentrations of glyphosate PRJNA929522 Other https://doi.org/10.1080/03601234.2022.2115780     control without xxx   A1 0   strain:Wilde type|age:96 hpf|sex:not applicable|tissue:complete embryos|sample type:Pool|treatment:0|Replicate:1|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio A1 A1 pool of embryos     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 1000   SRP420571     1_R1_001.fastq.gz fastq 5317438800.0 35449592.0 1 R1 001.fastq.gz 0:150 1:0 A:1468354160;C:1205889157;G:1218734077;T:1423919579;N:541827 150 0     1468354160 1205889157 1218734077 1423919579 541827 SRX19255346 SRS16658059 SRA1583492 Centro de Investigacion en Alimentacion y Desarrollo|Ecotoxicology Centro de Investigacion en Alimentacion y Desarrollo 1 0.92249   0.11531   0.68112   0.48545   150   B   usable mapping rate illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Mexico 2023-02-02 Larval Larval 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");;