run_metadata
113 rows where experiment.library_selection = "RANDOM", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Embryo Imprecise"
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| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 8088 | 8088 | ERR034127 | ERX012653 | ERS032268 | ERP000635 | PRJEB2512 | The Zebrafish transcriptome during early development | KI-BN-JKE-DRERIO-RNASEQ-2011 | Transcriptome Analysis | Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions. | RNA extracted from zebrafish embryo at 50% epiboly stage | zebrafish embryo 50 epiboly | SAMEA791629 | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791629|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 50epiboly|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 50epiboly|sex:mixed|strain:Tuebingen | Transcriptome profiling of early zebrafish development | KI BN JKE DRERIO RNASEQ 2011 50epiboly | JKE Drerio rna seq | Transcriptome profiling of 50% epiboly stages of zebrafish embryos. | Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000635 | AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development | ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-50epiboly_QV.qual.gz | SOLiD_native SOLiD_native | 3929903550.0 | 78598071.0 | KI BN JKE DRERIO RNASEQ 2011 50epiboly | 0:50 | 50 | ERX012653 | ERS032268 | ERA029959 | KI-BN|Department of Biosciences and Nutrition | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | 1 | 0.60757 | 0.09893 | 0.94899 | 0.77821 | 50 | B | usable mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | Sweden | 2011-06-09 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 8089 | 8089 | ERR034126 | ERX012652 | ERS032267 | ERP000635 | PRJEB2512 | The Zebrafish transcriptome during early development | KI-BN-JKE-DRERIO-RNASEQ-2011 | Transcriptome Analysis | Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions. | RNA extracted from zebrafish embryo at 512 cell stage | zebrafish embryo 512 cell | SAMEA791632 | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791632|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 512cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 512cell|sex:mixed|strain:Tuebingen | Transcriptome profiling of early zebrafish development | KI BN JKE DRERIO RNASEQ 2011 512cell | JKE Drerio rna seq | Transcriptome profiling of 512 cell stage of zebrafish embryos. | Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000635 | AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development | ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-2011-512cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-512cell_QV.qual.gz | SOLiD_native SOLiD_native | 3918756250.0 | 78375125.0 | KI BN JKE DRERIO RNASEQ 2011 512cell | 0:50 | 50 | ERX012652 | ERS032267 | ERA029959 | KI-BN|Department of Biosciences and Nutrition | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | 1 | 0.63824 | 0.09111 | 0.91969 | 0.73496 | 50 | B | usable mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | Sweden | 2011-06-09 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 8090 | 8090 | ERR034125 | ERX012651 | ERS032266 | ERP000635 | PRJEB2512 | The Zebrafish transcriptome during early development | KI-BN-JKE-DRERIO-RNASEQ-2011 | Transcriptome Analysis | Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions. | RNA extracted from zebrafish embryo at 16 cell stage | zebrafish embryo 16 cell | SAMEA791631 | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791631|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 16cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 16cell|sex:mixed|strain:Tuebingen | Transcriptome profiling of early zebrafish development | KI BN JKE DRERIO RNASEQ 2011 16cell | JKE Drerio rna seq | Transcriptome profiling of 16 cell stage of zebrafish embryos. | Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000635 | AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development | ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-2011-16cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-16cell_QV.qual.gz | SOLiD_native SOLiD_native | 4256756500.0 | 85135130.0 | KI BN JKE DRERIO RNASEQ 2011 16cell | 0:50 | 50 | ERX012651 | ERS032266 | ERA029959 | KI-BN|Department of Biosciences and Nutrition | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | 1 | 0.57946 | 0.08115 | 0.91896 | 0.72164 | 50 | B | usable mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | Sweden | 2011-06-09 | Cleavage | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 8091 | 8091 | ERR034124 | ERX012650 | ERS032265 | ERP000635 | PRJEB2512 | The Zebrafish transcriptome during early development | KI-BN-JKE-DRERIO-RNASEQ-2011 | Transcriptome Analysis | Background: Zebrafish Danio rerio is an important model for the study of early vertebrate development. The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression and the transcriptional events that underlie these processes have not been fully characterized. In this study we use RNA Seq to characterize and compare the transcriptome of four early developmental stages in zebrafish on a global scale. Results: An average of 79M total reads were detected from the different stages. Out of the total number of reads 65% 73% reads were successfully mapped to the zebrafish genome and 36% 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187 of which 10096 of these were already present at 1 cell stage. The largest number of common transcripts was observed between 1 cell stage and 16 cell stage. An enrichment of gene transcripts with molecular functions of DNA binding protein folding and processing as well as metal ion binding was observed with progression of development. To confirm our RNA Seq results and to further investigate the developmental expression of specific genes the transcript levels of a subset of genes were analyzed using TaqMan® array micro fluidic card TLDA. Conclusion: Clustering analysis of the detected transcripts show a majority of gene transcripts being present at steady levels with a minority of the gene transcripts clustering as increasing or decreasing in expression during development. Developmental stages pre MBT were similar when comparing highly expressed genes whereas 50% epiboly stage differed from the earlier three stages in highly expressed genes number of uniquely expressed genes and enrichment of GO molecular functions. | RNA extracted from zebrafish embryo at 1 cell stage | zebrafish embryo 1 cell | SAMEA791630 | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | ENA first public:2011 06 09|ENA last update:2018 03 08|External Id:SAMEA791630|INSDC center alias:KI BN|INSDC center name:Department of Biosciences and Nutrition Karolinska Institutet Sweden|INSDC first public:2011 06 09T11:04:10Z|INSDC last update:2018 03 08T15:26:39Z|INSDC status:public|Submitter Id:KI BN JKE DRERIO RNASEQ 2011 1cell|common name:zebrafish|sample name:KI BN JKE DRERIO RNASEQ 2011 1cell|sex:mixed|strain:Tuebingen | Transcriptome profiling of early zebrafish development | KI BN JKE DRERIO RNASEQ 2011 1cell | JKE Drerio rna seq | Transcriptome profiling of 1 cell stage of zebrafish embryos. | Total RNA was extracted from approximately 150 embryos per developmental stage using Trireagent Sigma Aldrich. The total RNA was then processed further according to the Small RNA Expression Kit Applied Biosystems. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | ERP000635 | AB SOLiD System 3.0 sequencing; Transcriptome profiling of early zebrafish development | ENA FIRST PUBLIC:2011 06 09|ENA LAST UPDATE:2018 11 16 | KI-BN-JKE-DRERIO-RNASEQ-2011-1cell.csfasta.gz KI-BN-JKE-DRERIO-RNASEQ-2011-1cell_QV.qual.gz | SOLiD_native SOLiD_native | 3676380950.0 | 73527619.0 | KI BN JKE DRERIO RNASEQ 2011 1cell | 0:50 | 50 | ERX012650 | ERS032265 | ERA029959 | KI-BN|Department of Biosciences and Nutrition | Department of Biosciences and Nutrition, Karolinska Institutet, Sweden | 1 | 0.64855 | 0.08432 | 0.9052 | 0.74223 | 50 | B | usable mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | Sweden | 2011-06-09 | Zygote | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 32370 | 32370 | SRR29180530 | SRX24700714 | SRS21428245 | 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. | DES | isolate:exposure to DES|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to DES|BioSampleModel:Model organism or animal | RNA seq of DES treated | DES | DES | Sequencing the transcriptomes of zebrafish embryos of DES treated | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP509851 | DES_TAAGGC_L001_R1_001.fastq.gz DES_TAAGGC_L001_R2_001.fastq.gz | fastq fastq | 9169560000.0 | 30565200.0 | DES TAAGGC L001 R1 001.fastq.gz | 0:150 1:150 | A:2545096687;C:2037322055;G:2024787099;T:2562124529;N:229630 | 150 | 150 | 2545096687 | 2037322055 | 2024787099 | 2562124529 | 229630 | SRX24700714 | SRS21428245 | 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 | ||||||||||||||||||||||||||||||||
| 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 | |||||||||||||||||||||
| 41782 | 41782 | SRR5162099 | SRX2480053 | SRS1910957 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | PLC5shCtrl1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PLC5shCtrl1|BioSampleModel:Model organism or animal | PLC5shCtrl1 | PLC5shCtrl1 | PLC5shCtrl1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1201388650.0 | 24027773.0 | CL100006841 L02 24 1.fq.gz | 0:50 | A:297299471;C:292335863;G:332701724;T:278571616;N:479976 | 50 | 297299471 | 292335863 | 332701724 | 278571616 | 479976 | SRX2480053 | SRS1910957 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00295 | 0.00039 | 0.99754 | 0.63223 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41783 | 41783 | SRR5162098 | SRX2480052 | SRS1910956 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | Hep3BshS6K1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:Hep3BshS6K1|BioSampleModel:Model organism or animal | Hep3BshS6K1 | Hep3BshS6K1 | Hep3BshS6K1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1205347750.0 | 24106955.0 | CL100006841 L02 21 1.fq.gz | 0:50 | A:312935885;C:282462046;G:322914710;T:286516924;N:518185 | 50 | 312935885 | 282462046 | 322914710 | 286516924 | 518185 | SRX2480052 | SRS1910956 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00262 | 0.00033 | 0.99764 | 0.69195 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41784 | 41784 | SRR5162097 | SRX2480051 | SRS1910955 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | PLC5shS6K1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:PLC5shS6K1|BioSampleModel:Model organism or animal | PLC5shS6K1 | PLC5shS6K1 | PLC5shS6K1 | 1 | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1205157400.0 | 24103148.0 | CL100006841 L02 25 1.fq.gz | 0:50 | A:305738728;C:286350102;G:329378158;T:283136091;N:554321 | 50 | 305738728 | 286350102 | 329378158 | 283136091 | 554321 | SRX2480051 | SRS1910955 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00275 | 0.00036 | 0.99801 | 0.66666 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41785 | 41785 | SRR5162096 | SRX2480050 | SRS1910954 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | HepG2shS6K1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:HepG2shS6K1|BioSampleModel:Model organism or animal | HepG2shS6K1 | HepG2shS6K1 | HepG2shS6K1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1203548150.0 | 24070963.0 | CL100006841 L02 23 1.fq.gz | 0:50 | A:307598832;C:285812241;G:331356323;T:278082314;N:698440 | 50 | 307598832 | 285812241 | 331356323 | 278082314 | 698440 | SRX2480050 | SRS1910954 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00192 | 0.00012 | 0.99784 | 0.60818 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41786 | 41786 | SRR5162095 | SRX2480049 | SRS1910953 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | Hep3BshCtrl1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:Hep3BshCtrl1|BioSampleModel:Model organism or animal | Hep3BshCtrl1 | Hep3BshCtrl1 | Hep3BshCtrl1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1201618100.0 | 24032362.0 | CL100006841 L02 20 1.fq.gz | 0:50 | A:301938424;C:291014141;G:326734280;T:281455564;N:475691 | 50 | 301938424 | 291014141 | 326734280 | 281455564 | 475691 | SRX2480049 | SRS1910953 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00522 | 0.00084 | 0.99722 | 0.61317 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 41787 | 41787 | SRR5162094 | SRX2480048 | SRS1910952 | SRP096313 | PRJNA360680 | S6K1 project raw sequence reads | PRJNA360680 | Other | HepG2shCtrl1 | breed:not applicable|strain:not applicable|age:6 dpf provider:not applicable|sex:not collected|tissue:embryro|treatment:HepG2shCtrl1|BioSampleModel:Model organism or animal | HepG2shCtrl1 | HepG2shCtrl1 | HepG2shCtrl1 | Total RNA was isolated from the stable transfected cells shCtrl and shS6K1 from Hep3B and PLC5 cells using the mirVanaTM RNA isolation kit Applied Biosystems. The quality of RNA was assessed using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. The RNA library was sequenced by the Beijing Genomics Institute Wuhan China. Single end reads 50 bp read length were sequenced on the BGISEQ 500RS sequencer. Qualified raw data were provided by the Beijing Genomics Institute in FASTQ format. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | COMPLETE_GENOMICS | Complete Genomics | SRP096313 | 1205042850.0 | 24100857.0 | CL100006841 L02 22 1.fq.gz | 0:50 | A:310292006;C:282567913;G:329631833;T:282050651;N:500447 | 50 | 310292006 | 282567913 | 329631833 | 282050651 | 500447 | SRX2480048 | SRS1910952 | SRA525651 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong|School of Life Sciences | 1 | 0.00164 | 0.00012 | 0.99784 | 0.62847 | 50 | T | under 1.2% mapping rate | legacy | early | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-01-10 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||||
| 42301 | 42301 | SRR5579865 | SRX2837982 | SRS2212147 | SRP107584 | PRJNA387320 | Danio rerio 1207 Raw sequence reads | PRJNA387320 | Other | 1207 2 | breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 2|BioSampleModel:Model organism or animal | 2002 2 | 1207 2 S1 L001 | 1207 2 S1 L001 | The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina MiSeq | SRP107584 | 1531873131.0 | 5203504.0 | 1207 2 S2 L001 2 paired.fq.gz | 0:148.34 1:146.06 | A:384469512;C:380138079;G:381661689;T:385603823;N:28 | 148 | 146 | 384469512 | 380138079 | 381661689 | 385603823 | 28 | SRX2837982 | SRS2212147 | SRA563090 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong | 2 | 0.97313 | 0.97391 | 0.03931 | 0.03966 | 0.73675 | 0.74186 | 0.47243 | 0.47819 | 151 | 150 | B | B | biological fallback assumption | illumina | miseq | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-05-20 | Juvenile | Juvenile | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||
| 42302 | 42302 | SRR5579866 | SRX2837981 | SRS2212146 | SRP107584 | PRJNA387320 | Danio rerio 1207 Raw sequence reads | PRJNA387320 | Other | 1207 1 | breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 1|BioSampleModel:Model organism or animal | 2002 1 | 1207 1 S1 L001 | 1207 1 S1 L001 | The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina MiSeq | SRP107584 | 1250178633.0 | 4243308.0 | 1207 1 S1 L001 2 paired.fq.gz | 0:148.83 1:145.79 | A:314820390;C:308887372;G:310674271;T:315796566;N:34 | 148 | 145 | 314820390 | 308887372 | 310674271 | 315796566 | 34 | SRX2837981 | SRS2212146 | SRA563090 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong | 2 | 0.97174 | 0.9719 | 0.04506 | 0.04505 | 0.73154 | 0.73683 | 0.4817 | 0.48252 | 150 | 148 | B | B | biological fallback assumption | illumina | miseq | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-05-20 | Juvenile | Juvenile | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||
| 42303 | 42303 | SRR5579867 | SRX2837980 | SRS2212145 | SRP107584 | PRJNA387320 | Danio rerio 1207 Raw sequence reads | PRJNA387320 | Other | AB 1 | breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB1|BioSampleModel:Model organism or animal | WT1 | AB1 S1 L001 | AB1 S1 L001 | The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina MiSeq | SRP107584 | 1819768909.0 | 6190653.0 | AB1 S1 L001 2 paired.fq.gz | 0:148.08 1:145.88 | A:465877977;C:442905762;G:444673127;T:466312043;N:0 | 148 | 145 | 465877977 | 442905762 | 444673127 | 466312043 | 0 | SRX2837980 | SRS2212145 | SRA563090 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong | 2 | 0.97169 | 0.97078 | 0.03527 | 0.03575 | 0.72823 | 0.73338 | 0.48283 | 0.48226 | 151 | 151 | B | B | biological fallback assumption | illumina | miseq | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-05-20 | Juvenile | Juvenile | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||
| 42304 | 42304 | SRR5579868 | SRX2837979 | SRS2212143 | SRP107584 | PRJNA387320 | Danio rerio 1207 Raw sequence reads | PRJNA387320 | Other | 1207 3 | breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:1207 3|BioSampleModel:Model organism or animal | 2002 3 | 1207 3 S1 L001 | 1207 3 S1 L001 | The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina MiSeq | SRP107584 | 1045991851.0 | 3554741.0 | 1207 3 S3 L001 2 paired.fq.gz | 0:148.38 1:145.87 | A:263998819;C:257909132;G:259440555;T:264643331;N:14 | 148 | 145 | 263998819 | 257909132 | 259440555 | 264643331 | 14 | SRX2837979 | SRS2212143 | SRA563090 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong | 2 | 0.97252 | 0.97273 | 0.0409 | 0.04037 | 0.74213 | 0.74574 | 0.48248 | 0.48634 | 151 | 151 | B | B | biological fallback assumption | illumina | miseq | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-05-20 | Juvenile | Juvenile | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||
| 42305 | 42305 | SRR5579869 | SRX2837978 | SRS2212142 | SRP107584 | PRJNA387320 | Danio rerio 1207 Raw sequence reads | PRJNA387320 | Other | AB 3 | breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB3|BioSampleModel:Model organism or animal | WT3 | AB3 S1 L001 | AB3 S1 L001 | The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina MiSeq | SRP107584 | 1126218531.0 | 3826972.0 | AB3 S3 L001 1 paired.fq.gz | 0:148.46 1:145.83 | A:285650942;C:276774884;G:276765238;T:287027467;N:0 | 148 | 145 | 285650942 | 276774884 | 276765238 | 287027467 | 0 | SRX2837978 | SRS2212142 | SRA563090 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong | 2 | 0.97355 | 0.97389 | 0.03977 | 0.04012 | 0.71999 | 0.72506 | 0.47576 | 0.4728 | 149 | 151 | B | B | biological fallback assumption | illumina | miseq | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-05-20 | Juvenile | Juvenile | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||
| 42306 | 42306 | SRR5579870 | SRX2837977 | SRS2212144 | SRP107584 | PRJNA387320 | Danio rerio 1207 Raw sequence reads | PRJNA387320 | Other | AB 2 | breed:not applicable|strain:not applicable|age:1 month|biomaterial provider:not applicable|sex:not collected|tissue:Embyro|treatment:AB2|BioSampleModel:Model organism or animal | WT2 | AB2 S1 L001 | AB2 S1 L001 | The embryos were subjected to RNA isolation. Ten embryos per group n = 10 from wild type control embryos n = 10 from mibnn2002 mutants and n = 10 from mibta52b mutants were used to prepare a pooled RNA sample. Three biological replicates per group were prepared. Total RNA from pooled samples was extracted by using the mirVanaTM RNA isolation kit Applied Biosystems according to the manufacturers protocol as previously described. RNA quality was assessed by using the Agilent 2100 Bioanalyzer system and samples with a RNA Integrity Number RIN greater than 8 were used for RNA library construction. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | Illumina MiSeq | SRP107584 | 1716453669.0 | 5815815.0 | AB2 S2 L001 1 paired.fq.gz | 0:148.63 1:146.50 | A:430519895;C:426826400;G:426635292;T:432472082;N:0 | 148 | 146 | 430519895 | 426826400 | 426635292 | 432472082 | 0 | SRX2837977 | SRS2212144 | SRA563090 | The Chinese University of Hong Kong|School of Life Sciences | The Chinese University of Hong Kong | 2 | 0.97735 | 0.97725 | 0.02854 | 0.02833 | 0.73196 | 0.73484 | 0.48256 | 0.4861 | 151 | 151 | B | B | biological fallback assumption | illumina | miseq | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2017-05-20 | Juvenile | Juvenile | 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 | |||||||||||||||||||||
| 52242 | 52242 | SRR9047069 | SRX5823596 | SRS4751717 | SRP198207 | PRJNA542583 | Migrasomes provide regional cues for organ morphogenesis during zebrafish gastrulation | PRJNA542583 | Other | Our study shows that migrasomes are signaling organelles which provide specific biochemical information to coordinate organ morphogenesis. | stdMO PBS | stdMO PBS | strain:Tu|isolate:primary cell|dev stage:gastrulation|sex:not determined|tissue:embryo|collection date:2016 11 13|genotype:wild type|geo loc name:China: Beijing|sample type:embryos|BioSampleModel:Model organism or animal | tspan RNA seq | uniprot | uniprot | RNA seq | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | BGISEQ | BGISEQ-500 | SRP198207 | 161214_I137_FCHF7TTBBXX_L2_WHFISclfRAAARAAPEI-203_1.fq.gz | fastq | 633650654.0 | 12931646.0 | 161214 I137 FCHF7TTBBXX L2 WHFISclfRAAARAAPEI 203 1.fq.gz | 0:49 1:0 | A:165787428;C:152969494;G:145599180;T:169168973;N:125579 | 49 | 0 | 165787428 | 152969494 | 145599180 | 169168973 | 125579 | SRX5823596 | SRS4751717 | SRA885639 | Tsinghua University|School of Life Sciences | Tsinghua University | 1 | 0.93004 | 0.09559 | 0.753 | 0.47488 | 49 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2019-05-30 | Gastrula | 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 | |||||||||||||||||||||
| 55447 | 55447 | SRR10436022 | SRX7131796 | SRS5640788 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | 2bp 120hpf | strain:rnf213a mutant|dev stage:120hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 8 | rnf213a 8 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_8 | fastq | 4982904300.0 | 33219362.0 | rnf213a 8.gz | 0:0 1:150 | A:1324339848;C:1163795168;G:1165190242;T:1329576411;N:2631 | 0 | 150 | 1324339848 | 1163795168 | 1165190242 | 1329576411 | 2631 | SRX7131796 | SRS5640788 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.92735 | 0.08973 | 0.66523 | 0.48455 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 55448 | 55448 | SRR10436027 | SRX7131795 | SRS5640788 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | 2bp 120hpf | strain:rnf213a mutant|dev stage:120hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 7 | rnf213a 7 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_7 | fastq | 4982904300.0 | 33219362.0 | rnf213a 7.gz | 0:150 1:0 | A:1334481379;C:1157336743;G:1153222575;T:1337750420;N:113183 | 150 | 0 | 1334481379 | 1157336743 | 1153222575 | 1337750420 | 113183 | SRX7131795 | SRS5640788 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.92697 | 0.08859 | 0.6522 | 0.47736 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 55449 | 55449 | SRR10436023 | SRX7131794 | SRS5640787 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | normal 120hpf | strain:wild type|dev stage:120hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 6 | rnf213a 6 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_6 | fastq | 4604017500.0 | 30693450.0 | rnf213a 6.gz | 0:0 1:150 | A:1223063228;C:1075059595;G:1073833007;T:1232058851;N:2819 | 0 | 150 | 1223063228 | 1075059595 | 1073833007 | 1232058851 | 2819 | SRX7131794 | SRS5640787 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.9235 | 0.09498 | 0.66827 | 0.47851 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 55450 | 55450 | SRR10436026 | SRX7131793 | SRS5640787 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | normal 120hpf | strain:wild type|dev stage:120hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 5 | rnf213a 5 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_5 | fastq | 4604017500.0 | 30693450.0 | rnf213a 5.gz | 0:150 1:0 | A:1233642245;C:1066547157;G:1063728944;T:1239996010;N:103144 | 150 | 0 | 1233642245 | 1066547157 | 1063728944 | 1239996010 | 103144 | SRX7131793 | SRS5640787 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.9238 | 0.09388 | 0.6549 | 0.4787 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 55451 | 55451 | SRR10436024 | SRX7131792 | SRS5640786 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | 2bp 72hpf | strain:rnf213a mutant|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 4 | rnf213a 4 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_4 | fastq | 3640003350.0 | 24266689.0 | rnf213a 4.gz | 0:0 1:150 | A:957485805;C:856078896;G:866344396;T:959578628;N:515625 | 0 | 150 | 957485805 | 856078896 | 866344396 | 959578628 | 515625 | SRX7131792 | SRS5640786 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.93507 | 0.08252 | 0.67186 | 0.4731 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 55452 | 55452 | SRR10436025 | SRX7131791 | SRS5640786 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | 2bp 72hpf | strain:rnf213a mutant|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 3 | rnf213a 3 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_3 | fastq | 3640003350.0 | 24266689.0 | rnf213a 3.gz | 0:150 1:0 | A:959700410;C:857785674;G:859574997;T:962707972;N:234297 | 150 | 0 | 959700410 | 857785674 | 859574997 | 962707972 | 234297 | SRX7131791 | SRS5640786 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.93504 | 0.08216 | 0.66541 | 0.4721 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 55453 | 55453 | SRR10436028 | SRX7131790 | SRS5640785 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | normal 72hpf | strain:wild type|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 2 | rnf213a 2 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_2 | fastq | 3592044900.0 | 23946966.0 | rnf213a 2.gz | 0:0 1:150 | A:950382154;C:839432686;G:850391648;T:951328573;N:509839 | 0 | 150 | 950382154 | 839432686 | 850391648 | 951328573 | 509839 | SRX7131790 | SRS5640785 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.93222 | 0.09138 | 0.66087 | 0.48076 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 55454 | 55454 | SRR10436029 | SRX7131789 | SRS5640785 | SRP229649 | PRJNA588137 | rnf213a knockout zebrafish Transcriptome or Gene expression | PRJNA588137 | Transcriptome Analysis | To explore the downstream molecules of rnf213a we conducted transcriptome sequencing to detect differentially expressed genes DEGs between +2bp rnf213a / mutant and wild type zebrafish at 72hpf and 120hpf. | normal 72hpf | strain:wild type|dev stage:72hpf|sex:pooled male and female|tissue:whole mount embryos|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: whole mount embryos | rnf213a 1 | rnf213a 1 | The polyA mRNA isolation was performed using NEBNext PolyA mRNA Magnetic Isolation Module NEB or Ribo Zero rRNA removal Kit illumina. The mRNA fragmentation and priming was performed using NEBNext First Strand Synthesis Reaction Buffer and NEBNext Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double stranded cDNAby AxyPrep Mag PCR Clean up Axygenwas then treated with End Prep Enzyme Mix to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using AxyPrep Mag PCR Clean up Axygen and fragments of 360 bp with the approximate insert size of 300 bp were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean up Axygen validated using an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and quantified by Qubit 2.0 Fluorometer Invitrogen Carlsbad CA USA. | RNA-Seq | TRANSCRIPTOMIC | RANDOM | SINGLE | ILLUMINA | HiSeq X Ten | SRP229649 | rnf213a_1 | fastq | 3592044900.0 | 23946966.0 | rnf213a 1.gz | 0:150 1:0 | A:952165099;C:842448366;G:843305876;T:953891694;N:233865 | 150 | 0 | 952165099 | 842448366 | 843305876 | 953891694 | 233865 | SRX7131789 | SRS5640785 | SRA993760 | First affiliated hospital of Sun Yat-sen university|neurology | First affiliated hospital of Sun Yat-sen university | 1 | 0.93128 | 0.09035 | 0.65445 | 0.47792 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | random_priming | nebnext | bulk | unknown | unknown | China | 2019-11-13 | Larval | Larval | 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 |
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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");;