run_metadata
80 rows where experiment.library_selection = "size fractionation", 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 15081 | 15081 | ERR12476478 | ERX11852299 | ERS17743543 | ERP156655 | PRJEB71869 | Effects of paternal starvation in the offspring development of zebrafish | 33b9d14c-4211-4249-aede-f0f021d197e6 | Other | Dietary restriction in the form of fasting is a putative key to a healthier and longer life but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant directed and potentially adaptive response transmitted by the father independently from the offspring's nutritional state which was defined by the mother. | ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15 | 24 hpf embryo collected at 1242 from a cross with a starved father | 1242D Starved | 1242SD | organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden | NextSeq 500 sequencing | ena EXPERIMENT TAB 15 01 2024 21:42:36:201 277053 | 1242SD | 1 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | NextSeq 500 | ERP156655 | NextSeq 500 sequencing | ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22 | 1242SD_S14_L003_R1_001.fastq.gz | fastq | 95457398.0 | 1268859.0 | ena RUN TAB 15 01 2024 21:42:36:202 277054 | 0:75.23 | A:33339157;C:18598733;G:20350072;T:23148005;N:21431 | 75 | 33339157 | 18598733 | 20350072 | 23148005 | 21431 | ERX11852299 | ERS17743543 | ERA27788968 | University of Birmingham|European Nucleotide Archive | University of Birmingham | B | usable mapping rate | illumina | nextseq | unknown | size_fractionation | unknown | bulk | unknown | unknown | United Kingdom | 2024-01-15 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||||
| 25277 | 25277 | SRR30160454 | SRX25627658 | SRS22272474 | SRP457111 | PRJNA1009808 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] | GSE241754 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT bud 10 hpf charged tRNA seqrep 3 | GSM8441306 | tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing | WT bud 10 hpf charged tRNA seqrep 3 | Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions | 10 hpf embryos | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | cell type:10 hpf embryos | GSM8441306 | GSM8441306: WT bud 10 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq | GSM8441306 r1 | GSM8441306 | 1 | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP457111 | 10hpf_aa_rep3.fastq.gz | fastq | 193965330.0 | 3367323.0 | GSM8441306 r1 | 0:57.60 | A:36799299;C:55100074;G:53758955;T:48306966;N:36 | 57 | 36799299 | 55100074 | 53758955 | 48306966 | 36 | SRX25627658 | SRS22272474 | SRA1941998 | Max Planck Institute of Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.34405 | 0.05049 | 0.89471 | 0.46469 | 88 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Germany | 2024-08-05 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 25278 | 25278 | SRR30160455 | SRX25627657 | SRS22272473 | SRP457111 | PRJNA1009808 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] | GSE241754 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT bud 10 hpf charged tRNA seqrep 2 | GSM8441305 | tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing | WT bud 10 hpf charged tRNA seqrep 2 | Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions | 10 hpf embryos | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | cell type:10 hpf embryos | GSM8441305 | GSM8441305: WT bud 10 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq | GSM8441305 r1 | GSM8441305 | 1 | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP457111 | 10hpf_aa_rep2.fastq.gz | fastq | 138524715.0 | 2369009.0 | GSM8441305 r1 | 0:58.47 | A:26396279;C:39139297;G:38459048;T:34530060;N:31 | 58 | 26396279 | 39139297 | 38459048 | 34530060 | 31 | SRX25627657 | SRS22272473 | SRA1941998 | Max Planck Institute of Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.35458 | 0.05179 | 0.89424 | 0.46401 | 74 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Germany | 2024-08-05 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 25279 | 25279 | SRR30160456 | SRX25627656 | SRS22272472 | SRP457111 | PRJNA1009808 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] | GSE241754 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT bud 10 hpf charged tRNA seqrep 1 | GSM8441304 | tissue:10 hpf embryos|cell type:10 hpf embryos|geo loc name:missing|collection date:missing | WT bud 10 hpf charged tRNA seqrep 1 | Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions | 10 hpf embryos | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | cell type:10 hpf embryos | GSM8441304 | GSM8441304: WT bud 10 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq | GSM8441304 r1 | GSM8441304 | 1 | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP457111 | 10hpf_aa_rep1.fastq.gz | fastq | 54473618.0 | 946419.0 | GSM8441304 r1 | 0:57.56 | A:10345022;C:15413782;G:15135500;T:13579304;N:10 | 57 | 10345022 | 15413782 | 15135500 | 13579304 | 10 | SRX25627656 | SRS22272472 | SRA1941998 | Max Planck Institute of Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.36103 | 0.0515 | 0.89227 | 0.4748 | 81 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Germany | 2024-08-05 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 25280 | 25280 | SRR30160457 | SRX25627655 | SRS22272471 | SRP457111 | PRJNA1009808 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] | GSE241754 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT sphere 4 hpf charged tRNA seqrep 3 | GSM8441303 | tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing | WT sphere 4 hpf charged tRNA seqrep 3 | Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions | 4 hpf embryos | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | cell type:4 hpf embryos | GSM8441303 | GSM8441303: WT sphere 4 hpf charged tRNA seqrep 3; Danio rerio; ncRNA Seq | GSM8441303 r1 | GSM8441303 | 1 | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP457111 | 4hpf_aa_rep3.fastq.gz | fastq | 100810543.0 | 1747597.0 | GSM8441303 r1 | 0:57.69 | A:20466558;C:28054923;G:26849246;T:25439798;N:18 | 57 | 20466558 | 28054923 | 26849246 | 25439798 | 18 | SRX25627655 | SRS22272471 | SRA1941998 | Max Planck Institute of Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.36374 | 0.06294 | 0.87316 | 0.54642 | 39 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Germany | 2024-08-05 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 25281 | 25281 | SRR30160458 | SRX25627654 | SRS22272470 | SRP457111 | PRJNA1009808 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] | GSE241754 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT sphere 4 hpf charged tRNA seqrep 2 | GSM8441302 | tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing | WT sphere 4 hpf charged tRNA seqrep 2 | Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions | 4 hpf embryos | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | cell type:4 hpf embryos | GSM8441302 | GSM8441302: WT sphere 4 hpf charged tRNA seqrep 2; Danio rerio; ncRNA Seq | GSM8441302 r1 | GSM8441302 | 1 | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP457111 | 4hpf_aa_rep2.fastq.gz | fastq | 121662759.0 | 2046536.0 | GSM8441302 r1 | 0:59.45 | A:24519095;C:33689156;G:32726095;T:30728382;N:31 | 59 | 24519095 | 33689156 | 32726095 | 30728382 | 31 | SRX25627654 | SRS22272470 | SRA1941998 | Max Planck Institute of Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.3726 | 0.06263 | 0.87136 | 0.55584 | 31 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Germany | 2024-08-05 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 25282 | 25282 | SRR30160459 | SRX25627653 | SRS22272469 | SRP457111 | PRJNA1009808 | Dynamics of the zebrafish tRNAome during the maternal to zygotic transition [tRNA Seq] | GSE241754 | Transcriptome Analysis | Time course analysis of tRNA abundance during zebrafish early embryonic development. Overall design: Wild type TLAB strain zebrafish embryos were grown in standard housing conditions.Unfertilized eggs 0 hpf were collected or embryos were staged and collected at consecutive developmental time points namelyat the 256 cell 2.5 hpf 1000 cell 3 hpf sphere 4 hpf shield 6 hpf and bud 10 hpf stages. Eggs and embryos were either flash frozen in liquid nitrogen or immediately processed. Samples were used for western blotting analysis polysome profiling ribosome profiling or mRNA and tRNA sequencing for investigating the regulation of tRNA gene expression and translational status during early zebrafish embryogenesis. | parent bioproject:PRJNA1009800 | pubmed:39402326 | WT sphere 4 hpf charged tRNA seqrep 1 | GSM8441301 | tissue:4 hpf embryos|cell type:4 hpf embryos|geo loc name:missing|collection date:missing | WT sphere 4 hpf charged tRNA seqrep 1 | Read demultiplexing and adapter trimming performed with cutadapt v3.5 where bases were quality trimmed from five prime and three prime ends using a phred score cutoff of 30. Only trimmed reads were retained and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’ RN nucleotides introduced by circularization from the RT primer. Reads were processed with the mim tRNAseq computational pipeline v1.3.8 using the parameters: species Drer cluster id 0.93 threads 40 min cov 0.001 deconv cov ratio 0.4 max mismatches 0.075 remap remap mismatches 0.075 max multi 10 max multi 6 remap remap mismatches 0.075 crosstalks. Assembly: GRCz11 Supplementary files format and content: csv; mim tRNAseq generated CCA proportions | 4 hpf embryos | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | cell type:4 hpf embryos | GSM8441301 | GSM8441301: WT sphere 4 hpf charged tRNA seqrep 1; Danio rerio; ncRNA Seq | GSM8441301 r1 | GSM8441301 | 1 | Total RNA from D.rerio embryos collected at the sphere 4 hpf or bud 10 hpf stage was extracted with TRIZOL under mild acidic conditions to preserve tRNA charging and subjected to oxidation and beta elimination Behrens and Nedialkova 2022. tRNA seq libraries were prepared using the mim tRNAseq workflow Behrens and Nedialkova 2022 and sequenced on an Illumina NovaSeq 6000 platform. | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP457111 | 4hpf_aa_rep1.fastq.gz | fastq | 124990980.0 | 2116213.0 | GSM8441301 r1 | 0:59.06 | A:25487542;C:34621140;G:33284460;T:31597816;N:22 | 59 | 25487542 | 34621140 | 33284460 | 31597816 | 22 | SRX25627653 | SRS22272469 | SRA1941998 | Max Planck Institute of Biochemistry | Max Planck Institute of Biochemistry | 1 | 0.36013 | 0.05967 | 0.87387 | 0.55002 | 44 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | Germany | 2024-08-05 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 36195 | 36195 | SRR042434 | SRX020028 | SRS066219 | SRP002411 | PRJNA126003 | A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity | GSE21503 | Transcriptome Analysis | Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf | pubmed:20448148 | MZago2 mutant YΔ90 | GSM540646 | tissue:48hpf embryo MZago2 mutant|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZago2 Δ90/Δ90 | MZago2 mutant YΔ90 | Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. | 48hpf embryo MZago2 mutant | Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. | Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. | strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZago2 Δ90/Δ90 | GSM540646 | GSM540646: MZago2 mutant YΔ90 | GSM540646: MZago2 mutant YΔ90 | GSM540646: MZago2 mutant YΔ90 | 1 | GEO Accession:GSM540646 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> | SRP002411 | Ago2_ydelta90.fastq | fastq | 437752008.0 | 12159778.0 | GSM540646 1 | 0:36 | A:96750665;C:83495585;G:119239752;T:138073795;N:192211 | 36 | 96750665 | 83495585 | 119239752 | 138073795 | 192211 | SRX020028 | SRS066219 | SRA012683 | GEO | Giraldez Lab, Genetics, Yale University | 1 | 0.03964 | 0.0 | 0.99985 | 0.00052 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2010-05-04 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 36196 | 36196 | SRR042433 | SRX020027 | SRS066218 | SRP002411 | PRJNA126003 | A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity | GSE21503 | Transcriptome Analysis | Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf | pubmed:20448148 | WT2 | GSM540645 | tissue:48hpf embryo WT|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:wild type | WT2 | Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. | 48hpf embryo WT | Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. | Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. | strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:wild type | GSM540645 | GSM540645: WT2 | GSM540645: WT2 | GSM540645: WT2 | 1 | GEO Accession:GSM540645 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> | SRP002411 | WT2.fastq | fastq | 59530030.0 | 1700858.0 | GSM540645 1 | 0:35 | A:12981942;C:11521313;G:16378279;T:18609524;N:38972 | 35 | 12981942 | 11521313 | 16378279 | 18609524 | 38972 | SRX020027 | SRS066218 | SRA012683 | GEO | Giraldez Lab, Genetics, Yale University | 1 | 0.06435 | 0.0 | 0.99995 | 0.0 | 35 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2010-05-04 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 36197 | 36197 | SRR042432 | SRX020026 | SRS066217 | SRP002411 | PRJNA126003 | A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity | GSE21503 | Transcriptome Analysis | Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf | pubmed:20448148 | MZdicer mutant2 hu896 | GSM540644 | tissue:48hpf embryo Mzdicer mutant|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu896/hu896 | MZdicer mutant2 hu896 | Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. | 48hpf embryo Mzdicer mutant | Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. | Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. | strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu896/hu896 | GSM540644 | GSM540644: MZdicer mutant2 hu896 | GSM540644: MZdicer mutant2 hu896 | GSM540644: MZdicer mutant2 hu896 | 1 | GEO Accession:GSM540644 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> | SRP002411 | MZdicer2_hu896.fastq | fastq | 4268740.0 | 121964.0 | GSM540644 1 | 0:35 | A:813936;C:1034356;G:1131604;T:1280756;N:8088 | 35 | 813936 | 1034356 | 1131604 | 1280756 | 8088 | SRX020026 | SRS066217 | SRA012683 | GEO | Giraldez Lab, Genetics, Yale University | 1 | 0.03836 | 0.0009 | 0.99849 | 0.3021 | 35 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2010-05-04 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 36198 | 36198 | SRR042431 | SRX020025 | SRS066216 | SRP002411 | PRJNA126003 | A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity | GSE21503 | Transcriptome Analysis | Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf | pubmed:20448148 | WT1 | GSM540643 | tissue:48hpf embryo WT|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:wild type | WT1 | Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. | 48hpf embryo WT | Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. | Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. | strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:wild type | GSM540643 | GSM540643: WT1 | GSM540643: WT1 | GSM540643: WT1 | 1 | GEO Accession:GSM540643 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> | SRP002411 | quality book char:@|quality scoring system:log odds | WT1.fastq | fastq | 26959392.0 | 748872.0 | GSM540643 1 | 0:36 | A:6097309;C:6093948;G:6950185;T:7813829;N:4121 | 36 | 6097309 | 6093948 | 6950185 | 7813829 | 4121 | SRX020025 | SRS066216 | SRA012683 | GEO | Giraldez Lab, Genetics, Yale University | 1 | 0.0022 | 0.0 | 0.99993 | 0.0 | 36 | T | under 1.2% mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2010-05-04 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 36199 | 36199 | SRR042430 | SRX020024 | SRS066215 | SRP002411 | PRJNA126003 | A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity | GSE21503 | Transcriptome Analysis | Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs we sequenced small RNAs in wild type maternal zygotic dicer MZdicer and MZago2 mutants using zebrafish as a model system. We find that in contrast to other miRNAs miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs followed by uridylation and trimming generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type MZago2 MZdicer at 48 hpf | pubmed:20448148 | MZdicer mutant1 hu715 | GSM540642 | tissue:48hpf embryo Mzdicer mutant|strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu715/hu715 | MZdicer mutant1 hu715 | Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file. | 48hpf embryo Mzdicer mutant | Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5’ and 3’ adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols. | Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen. | strain:mixed AB TU TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu715/hu715 | GSM540642 | GSM540642: MZdicer mutant1 hu715 | GSM540642: MZdicer mutant1 hu715 | GSM540642: MZdicer mutant1 hu715 | 1 | GEO Accession:GSM540642 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><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> | SRP002411 | quality book char:@|quality scoring system:log odds | MZdicer1_hu715.fastq | fastq | 11972772.0 | 332577.0 | GSM540642 1 | 0:36 | A:2703131;C:3062840;G:3338413;T:2867600;N:788 | 36 | 2703131 | 3062840 | 3338413 | 2867600 | 788 | SRX020024 | SRS066215 | SRA012683 | GEO | Giraldez Lab, Genetics, Yale University | 1 | 0.00678 | 0.00073 | 0.99847 | 0.3421 | 36 | T | under 1.2% mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2010-05-04 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 36333 | 36333 | SRR398324 | SRX115582 | SRS285699 | SRP010291 | PRJNA150927 | miR 221 is required for endothelial tip cell behaviors during vascular development | GSE35078 | Transcriptome Analysis | Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells. | pubmed:22340502 | kdrl:egfp min microRNA | GSM861786 | tissue:FACS isolated egfp negative cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:non endothelial cells | kdrl:egfp min microRNA | The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. | FACS isolated egfp negative cells | Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. | Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers. | genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:non endothelial cells | GSM861786 | GSM861786: kdrl:egfp min microRNA; Danio rerio; RNA Seq | GSM861786 1 | GSM861786: kdrl:egfp min microRNA | 1 | GEO Accession:GSM861786 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> | SRP010291 | miRNA_GFP_MINUS.fastq.gz | fastq | 206441460.0 | 5734485.0 | GSM861786 r1 | 0:36 | A:53061964;C:48186825;G:47161433;T:53484016;N:4547222 | 36 | 53061964 | 48186825 | 47161433 | 53484016 | 4547222 | SRX115582 | SRS285699 | SRA049243 | GEO | Nathan Lawson Lab, PGFE, Umass Medical School | 1 | 0.01499 | 0.01416 | 0.99922 | 0.4 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-01-12 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 36334 | 36334 | SRR398323 | SRX115581 | SRS285698 | SRP010291 | PRJNA150927 | miR 221 is required for endothelial tip cell behaviors during vascular development | GSE35078 | Transcriptome Analysis | Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells. | pubmed:22340502 | kdrl:egfp pos microRNA | GSM861785 | tissue:FACS isolated kdrl:egfp positive cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:endothelial cells | kdrl:egfp pos microRNA | The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. | FACS isolated kdrl:egfp positive cells | Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. | Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers. | genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:endothelial cells | GSM861785 | GSM861785: kdrl:egfp pos microRNA; Danio rerio; RNA Seq | GSM861785 1 | GSM861785: kdrl:egfp pos microRNA | 1 | GEO Accession:GSM861785 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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> | SRP010291 | miRNA_GFP_PLUS.fastq.gz | fastq | 265629096.0 | 7378586.0 | GSM861785 r1 | 0:36 | A:67563811;C:62134550;G:62283750;T:67966396;N:5680589 | 36 | 67563811 | 62134550 | 62283750 | 67966396 | 5680589 | SRX115581 | SRS285698 | SRA049243 | GEO | Nathan Lawson Lab, PGFE, Umass Medical School | 1 | 0.01356 | 0.01279 | 0.99924 | 0.3125 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-01-12 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 36482 | 36482 | SRR530894 | SRX172598 | SRS352620 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 60hpf TCDD 3 | GSM979608 | source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD | 60hpf TCDD 3 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD | GSM979608 | GSM979608: 60hpf TCDD 3; Danio rerio; RNA Seq | GSM979608 1 | GSM979608: 60hpf TCDD 3 | 1 | GEO Accession:GSM979608 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | 1007239870.0 | 28778282.0 | GSM979608 r1 | 0:35 | 0:284531587;1:248579138;2:213782485;3:258771962;.:1574698 | 35 | SRX172598 | SRS352620 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.04824 | 0.03 | 0.981 | 0.49967 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||
| 36483 | 36483 | SRR530893 | SRX172597 | SRS352619 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 60hpf TCDD 2 | GSM979607 | source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD | 60hpf TCDD 2 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD | GSM979607 | GSM979607: 60hpf TCDD 2; Danio rerio; RNA Seq | GSM979607 1 | GSM979607: 60hpf TCDD 2 | 1 | GEO Accession:GSM979607 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0011.csfasta | SOLiD_native | 407347325.0 | 11638495.0 | GSM979607 r1 | 0:35 | 0:99062820;1:113921998;2:81336108;3:112422342;.:604057 | 35 | SRX172597 | SRS352619 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.04258 | 0.02455 | 0.98287 | 0.5048 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36484 | 36484 | SRR530892 | SRX172596 | SRS352618 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 60hpf TCDD 1 | GSM979606 | source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD | 60hpf TCDD 1 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD | GSM979606 | GSM979606: 60hpf TCDD 1; Danio rerio; RNA Seq | GSM979606 1 | GSM979606: 60hpf TCDD 1 | 1 | GEO Accession:GSM979606 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0010.csfasta | SOLiD_native | 680837045.0 | 19452487.0 | GSM979606 r1 | 0:35 | 0:165079839;1:167219862;2:147812329;3:199659766;.:1065249 | 35 | SRX172596 | SRS352618 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.02295 | 0.01479 | 0.98884 | 0.55191 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36485 | 36485 | SRR530891 | SRX172595 | SRS352617 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 60hpf DMSO 3 | GSM979605 | source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO | 60hpf DMSO 3 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO | GSM979605 | GSM979605: 60hpf DMSO 3; Danio rerio; RNA Seq | GSM979605 1 | GSM979605: 60hpf DMSO 3 | 1 | GEO Accession:GSM979605 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0009.csfasta | SOLiD_native | 495019840.0 | 14143424.0 | GSM979605 r1 | 0:35 | 0:134854583;1:126192934;2:102458221;3:130747961;.:766141 | 35 | SRX172595 | SRS352617 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.06707 | 0.04409 | 0.97285 | 0.5058 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36486 | 36486 | SRR530890 | SRX172594 | SRS352616 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 60hpf DMSO 2 | GSM979604 | source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO | 60hpf DMSO 2 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO | GSM979604 | GSM979604: 60hpf DMSO 2; Danio rerio; RNA Seq | GSM979604 1 | GSM979604: 60hpf DMSO 2 | 1 | GEO Accession:GSM979604 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0008.qual | SOLiD_native | 440403425.0 | 12582955.0 | GSM979604 r1 | 0:35 | 0:110302240;1:106481197;2:104551283;3:118415637;.:653068 | 35 | SRX172594 | SRS352616 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.05778 | 0.03522 | 0.97423 | 0.50884 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36487 | 36487 | SRR530889 | SRX172593 | SRS352615 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 60hpf DMSO 1 | GSM979603 | source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO | 60hpf DMSO 1 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO | GSM979603 | GSM979603: 60hpf DMSO 1; Danio rerio; RNA Seq | GSM979603 1 | GSM979603: 60hpf DMSO 1 | 1 | GEO Accession:GSM979603 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0007.csfasta MH_0007.qual | SOLiD_native SOLiD_native | 583800490.0 | 16680014.0 | GSM979603 r1 | 0:35 | 0:166122108;1:149534173;2:111986455;3:155255262;.:902492 | 35 | SRX172593 | SRS352615 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.05644 | 0.03829 | 0.9781 | 0.4997 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36488 | 36488 | SRR530888 | SRX172592 | SRS352614 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 36hpf TCDD 3 | GSM979602 | source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD | 36hpf TCDD 3 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD | GSM979602 | GSM979602: 36hpf TCDD 3; Danio rerio; RNA Seq | GSM979602 1 | GSM979602: 36hpf TCDD 3 | 1 | GEO Accession:GSM979602 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0006.qual MH_0006.csfasta | SOLiD_native SOLiD_native | 214059615.0 | 6115989.0 | GSM979602 r1 | 0:35 | 0:56635752;1:54053300;2:48355842;3:54677354;.:337367 | 35 | SRX172592 | SRS352614 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.13044 | 0.07694 | 0.95704 | 0.53005 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36489 | 36489 | SRR530887 | SRX172591 | SRS352613 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 36hpf TCDD 2 | GSM979601 | source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD | 36hpf TCDD 2 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD | GSM979601 | GSM979601: 36hpf TCDD 2; Danio rerio; RNA Seq | GSM979601 1 | GSM979601: 36hpf TCDD 2 | 1 | GEO Accession:GSM979601 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | 388475115.0 | 11099289.0 | GSM979601 r1 | 0:35 | 0:103611863;1:99408831;2:86592980;3:98238344;.:623097 | 35 | SRX172591 | SRS352613 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.15634 | 0.10763 | 0.96069 | 0.47755 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||
| 36490 | 36490 | SRR530886 | SRX172590 | SRS352612 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 36hpf TCDD 1 | GSM979600 | source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD | 36hpf TCDD 1 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD | GSM979600 | GSM979600: 36hpf TCDD 1; Danio rerio; RNA Seq | GSM979600 1 | GSM979600: 36hpf TCDD 1 | 1 | GEO Accession:GSM979600 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0004.csfasta | SOLiD_native | 366389765.0 | 10468279.0 | GSM979600 r1 | 0:35 | 0:100797199;1:91391785;2:80412155;3:93217840;.:570786 | 35 | SRX172590 | SRS352612 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.14106 | 0.09874 | 0.95724 | 0.49685 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36491 | 36491 | SRR530885 | SRX172589 | SRS352611 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 36hpf DMSO 3 | GSM979599 | source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO | 36hpf DMSO 3 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO | GSM979599 | GSM979599: 36hpf DMSO 3; Danio rerio; RNA Seq | GSM979599 1 | GSM979599: 36hpf DMSO 3 | 1 | GEO Accession:GSM979599 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0003.csfasta | SOLiD_native | 2108864835.0 | 60253281.0 | GSM979599 r1 | 0:35 | 0:591489585;1:461028640;2:379338654;3:673048278;.:3959678 | 35 | SRX172589 | SRS352611 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.09321 | 0.06563 | 0.98244 | 0.50577 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36492 | 36492 | SRR530884 | SRX172588 | SRS352610 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 36hpf DMSO 2 | GSM979598 | source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO | 36hpf DMSO 2 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO | GSM979598 | GSM979598: 36hpf DMSO 2; Danio rerio; RNA Seq | GSM979598 1 | GSM979598: 36hpf DMSO 2 | 1 | GEO Accession:GSM979598 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0002.qual | SOLiD_native | 363765885.0 | 10393311.0 | GSM979598 r1 | 0:35 | 0:99316622;1:92947128;2:80099367;3:90839592;.:563176 | 35 | SRX172588 | SRS352610 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.13435 | 0.09839 | 0.96146 | 0.49914 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 36493 | 36493 | SRR530883 | SRX172587 | SRS352609 | SRP014646 | PRJNA171751 | MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data] | GSE39808 | Transcriptome Analysis | Although many drugs and environmental chemicals are teratogenic the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR verifying the effectiveness of the exposure. microRNA expression profiles were determined using microarrays Agilent and Exiqon next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451 23a 23b 24 and 27e at 60 hpf. Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos. However miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays SOLiD sequencing and qPCR. These results suggest that TCDD exposure causes modest changes in expression of microRNAs including some miR 451 23a 23b 24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing | parent bioproject:PRJNA171747 | pubmed:22921993 | 36hpf DMSO 1 | GSM979597 | source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO | 36hpf DMSO 1 | CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files | Embryos | Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems Foster City CA. Sequencing was done on a SOLiD V3 system Applied Biosystems. | strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO | GSM979597 | GSM979597: 36hpf DMSO 1; Danio rerio; RNA Seq | GSM979597 1 | GSM979597: 36hpf DMSO 1 | 1 | GEO Accession:GSM979597 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</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> | SRP014646 | MH_0001F3.csfasta MH_0001F3_QV.qual | SOLiD_native SOLiD_native | 309659000.0 | 8847400.0 | GSM979597 r1 | 0:35 | 0:83729307;1:78100521;2:70827559;3:76531823;.:469790 | 35 | SRX172587 | SRS352609 | SRA056525 | GEO | Aluru Lab, Biology, Woods Hole Oceanographic Institution | 1 | 0.56398 | 0.33182 | 0.91092 | 0.5842 | 35 | B | usable mapping rate | legacy | early | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-08-01 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||
| 37121 | 37121 | SRR952244 | SRX334986 | SRS469877 | SRP028754 | PRJNA214896 | Danio rerio Transcriptome or Gene expression | PRJNA214896 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | embryonic development | General Sample for zebrafish | 1 cell | breed:wild type zebrafish | 1 cell developmental stage of zebrafish | 1 cell | 1 | Zebrafish embryos were collected at 1 cell 0.2 hpf 16 cell 1.5 hpf 512 cell 2.75 hpf oblong 3.7 hpf 5.3 hpf 50% epibody 6 somite 12 hpf 24 hpf day1 hpf and 48 hpf day2 stages. Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</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> | SRP028754 | s1-cell.fq | fastq | 1002077048.0 | 20450552.0 | 1 cell | 0:49 1:0 | A:210178307;C:226566574;G:255003953;T:310259058;N:69156 | 49 | 0 | 210178307 | 226566574 | 255003953 | 310259058 | 69156 | SRX334986 | SRS469877 | SRA097312 | Huazhong University of Science and Technology|CUCKOO | Huazhong University of Science and Technology | 1 | 0.0001 | 3e-05 | 0.99977 | 0.58333 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2014-08-12 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||
| 37122 | 37122 | SRR953569 | SRX336211 | SRS470740 | SRP028862 | PRJNA215266 | Danio rerio Transcriptome or Gene expression | PRJNA215266 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | small RNA sequencing for zebrafish early development | General Sample for zebrafish | zebrafish early development | breed:wild type zebrafish | 48hpf of zebrafish development | 48hpf stage | 1 | Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> | SRP028862 | day2.fq | fastq | 628342631.0 | 12823319.0 | 48hpf | 0:49 | A:148145336;C:136573491;G:166351863;T:177234943;N:36998 | 49 | 148145336 | 136573491 | 166351863 | 177234943 | 36998 | SRX336211 | SRS470740 | SRA098041 | Huazhong University of Science and Technology|cuckoo | Huazhong University of Science and Technology | 1 | 1e-05 | 0.0 | 0.99997 | 1.0 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2015-07-22 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||
| 37123 | 37123 | SRR953568 | SRX336209 | SRS470740 | SRP028862 | PRJNA215266 | Danio rerio Transcriptome or Gene expression | PRJNA215266 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | small RNA sequencing for zebrafish early development | General Sample for zebrafish | zebrafish early development | breed:wild type zebrafish | 24hpf of zebrafish development | 24hpf stage | 1 | Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> | SRP028862 | day1.fq | fastq | 575258726.0 | 11739974.0 | 24hpf | 0:49 | A:132961290;C:123570971;G:152269421;T:166422672;N:34372 | 49 | 132961290 | 123570971 | 152269421 | 166422672 | 34372 | SRX336209 | SRS470740 | SRA098041 | Huazhong University of Science and Technology|cuckoo | Huazhong University of Science and Technology | 1 | 0.0 | 0.0 | 1.0 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2015-07-22 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||||
| 37124 | 37124 | SRR953567 | SRX336208 | SRS470740 | SRP028862 | PRJNA215266 | Danio rerio Transcriptome or Gene expression | PRJNA215266 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | small RNA sequencing for zebrafish early development | General Sample for zebrafish | zebrafish early development | breed:wild type zebrafish | 6 somite of zebrafish development | 6 somite stage | 1 | Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> | SRP028862 | s6-somite.fq | fastq | 1023786106.0 | 20893594.0 | 6 somite | 0:49 | A:231966134;C:225595480;G:271618141;T:294536757;N:69594 | 49 | 231966134 | 225595480 | 271618141 | 294536757 | 69594 | SRX336208 | SRS470740 | SRA098041 | Huazhong University of Science and Technology|cuckoo | Huazhong University of Science and Technology | 1 | 0.0 | 0.0 | 1.0 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2015-07-22 | Segmentation | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||||
| 37125 | 37125 | SRR953532 | SRX336173 | SRS470740 | SRP028862 | PRJNA215266 | Danio rerio Transcriptome or Gene expression | PRJNA215266 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | small RNA sequencing for zebrafish early development | General Sample for zebrafish | zebrafish early development | breed:wild type zebrafish | 5.3hpf of zebrafish development | 5.3hpf stage | 1 | Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> | SRP028862 | s53-h.fq | fastq | 1007880412.0 | 20568988.0 | 5.3hpf | 0:49 | A:226128850;C:222011747;G:262126135;T:297544238;N:69442 | 49 | 226128850 | 222011747 | 262126135 | 297544238 | 69442 | SRX336173 | SRS470740 | SRA098041 | Huazhong University of Science and Technology|cuckoo | Huazhong University of Science and Technology | 1 | 0.0 | 0.0 | 1.0 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2015-07-22 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||||||||
| 37126 | 37126 | SRR953531 | SRX336172 | SRS470740 | SRP028862 | PRJNA215266 | Danio rerio Transcriptome or Gene expression | PRJNA215266 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | small RNA sequencing for zebrafish early development | General Sample for zebrafish | zebrafish early development | breed:wild type zebrafish | oblong of zebrafish development | oblong stage | 1 | Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> | SRP028862 | oblong.fq | fastq | 1016928850.0 | 20753650.0 | oblong | 0:49 | A:224798674;C:224915257;G:271761873;T:295384794;N:68252 | 49 | 224798674 | 224915257 | 271761873 | 295384794 | 68252 | SRX336172 | SRS470740 | SRA098041 | Huazhong University of Science and Technology|cuckoo | Huazhong University of Science and Technology | 1 | 1e-05 | 0.0 | 0.99997 | 1.0 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2015-07-22 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||
| 37127 | 37127 | SRR953530 | SRX336171 | SRS470740 | SRP028862 | PRJNA215266 | Danio rerio Transcriptome or Gene expression | PRJNA215266 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | small RNA sequencing for zebrafish early development | General Sample for zebrafish | zebrafish early development | breed:wild type zebrafish | 512 cell of zebrafish development | 512 cell stage | 1 | Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> | SRP028862 | s512-cell.fq | fastq | 991550035.0 | 20235715.0 | 512 cell | 0:49 | A:213493042;C:219665976;G:263488396;T:294834622;N:67999 | 49 | 213493042 | 219665976 | 263488396 | 294834622 | 67999 | SRX336171 | SRS470740 | SRA098041 | Huazhong University of Science and Technology|cuckoo | Huazhong University of Science and Technology | 1 | 4e-05 | 1e-05 | 0.99993 | 1.0 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2015-07-22 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||
| 37128 | 37128 | SRR953522 | SRX336167 | SRS470740 | SRP028862 | PRJNA215266 | Danio rerio Transcriptome or Gene expression | PRJNA215266 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | small RNA sequencing for zebrafish early development | General Sample for zebrafish | zebrafish early development | breed:wild type zebrafish | 16 cell of zebrafish development | 16 cell stage | 1 | Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> | SRP028862 | s16-cell.fq | fastq | 857702468.0 | 17504132.0 | 16 cell stage | 0:49 | A:188518867;C:188172489;G:222316155;T:258636924;N:58033 | 49 | 188518867 | 188172489 | 222316155 | 258636924 | 58033 | SRX336167 | SRS470740 | SRA098041 | Huazhong University of Science and Technology|cuckoo | Huazhong University of Science and Technology | 1 | 3e-05 | 1e-05 | 0.99993 | 1.0 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2015-07-22 | Cleavage | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||
| 37129 | 37129 | SRR953087 | SRX335692 | SRS470740 | SRP028862 | PRJNA215266 | Danio rerio Transcriptome or Gene expression | PRJNA215266 | Other | During early vertebrate development various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. | small RNA sequencing for zebrafish early development | General Sample for zebrafish | zebrafish early development | breed:wild type zebrafish | 1 cell of zebrafish development | 1 cell stage | 1 | Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels and small RNAs were isolated and purified. Subsequently small RNAs were ligated with both a 5’ adapter and 3’ adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that the reverse transcribed product cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec followed by 15 cycles consisting of 10 sec at 98 oC 15 sec at 72 oC and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher. | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</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> | SRP028862 | 1002077048.0 | 20450552.0 | 1 cell stage | 0:49 | A:210178307;C:226566574;G:255003953;T:310259058;N:69156 | 49 | 210178307 | 226566574 | 255003953 | 310259058 | 69156 | SRX335692 | SRS470740 | SRA098041 | Huazhong University of Science and Technology|cuckoo | Huazhong University of Science and Technology | 1 | 0.0001 | 3e-05 | 0.99975 | 0.76923 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2015-07-22 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||||||||||
| 37905 | 37905 | SRR1138230 | SRX445323 | SRS540474 | SRP035565 | PRJNA236050 | Systematic Transcriptome Analysis of Zebrafish Model of Diamond Blackfan Anemia from RPS24 Deficiency miRNA Seq | GSE54259 | Transcriptome Analysis | In this study we found RPS24 is required for both the primitive hematopoiesis and definitive hematopoiesis process partly mediated by P53 pathway. With the RNA seq and miRNA seq technique several deregulated genes and miRNAs were found to be related with hematopoiesis vascular development and apoptosis process in RPS24 deficient zebrafish. Meanwhile a comprehensive regulatory network was firstly constructed to indentify the mechanisms of key miRNAs and gene pathways in this Model of Diamond Blackfan Anemia. Interestingly we found that the central nodes genes in the network were almost all targeted by significantly deregulated miRNAs with partial verification from previous studies revealing that our network based approach is promising for the identification of new and important miRNAs in DBA. The present study provided comprehensive potential pathogenic genes and miRNAs data that are associated with RPS24 deficient zebrafish embryos as a model of DBA which should provide a valuable resource for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases. Overall design: Determine the differences of miRNome between RPS24 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases | parent bioproject:PRJNA236073 | pubmed:25189322;pubmed:26961822 | RPS24 MO miRNA Seq | GSM1311219 | tissue:embryo|genotype:RPS24 morpholino knockdown|developmental stage:embryo 48hpf | RPS24 MO miRNA Seq | FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9 | embryo | Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration. | Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions. | Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf | genotype:RPS24 morpholino knockdown|developmental stage:embryo 48hpf | GSM1311219 | GSM1311219: RPS24 MO miRNA Seq; Danio rerio; RNA Seq | GSM1311219 | 1 | Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions. | GEO Accession:GSM1311219 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP035565 | s_7_IDX18_1.fq | fastq | 883114731.0 | 10902651.0 | GSM1311219 r1 | 0:81 | A:189355667;C:238092214;G:225845644;T:229789867;N:31339 | 81 | 189355667 | 238092214 | 225845644 | 229789867 | 31339 | SRX445323 | SRS540474 | SRA128456 | GEO | Beijing Institute of Genomics | 1 | 4e-05 | 0.0 | 0.99991 | 1.0 | 81 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2014-01-21 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 37906 | 37906 | SRR1138229 | SRX445322 | SRS540473 | SRP035565 | PRJNA236050 | Systematic Transcriptome Analysis of Zebrafish Model of Diamond Blackfan Anemia from RPS24 Deficiency miRNA Seq | GSE54259 | Transcriptome Analysis | In this study we found RPS24 is required for both the primitive hematopoiesis and definitive hematopoiesis process partly mediated by P53 pathway. With the RNA seq and miRNA seq technique several deregulated genes and miRNAs were found to be related with hematopoiesis vascular development and apoptosis process in RPS24 deficient zebrafish. Meanwhile a comprehensive regulatory network was firstly constructed to indentify the mechanisms of key miRNAs and gene pathways in this Model of Diamond Blackfan Anemia. Interestingly we found that the central nodes genes in the network were almost all targeted by significantly deregulated miRNAs with partial verification from previous studies revealing that our network based approach is promising for the identification of new and important miRNAs in DBA. The present study provided comprehensive potential pathogenic genes and miRNAs data that are associated with RPS24 deficient zebrafish embryos as a model of DBA which should provide a valuable resource for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases. Overall design: Determine the differences of miRNome between RPS24 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases | parent bioproject:PRJNA236073 | pubmed:25189322;pubmed:26961822 | morpholino control miRNA Seq | GSM1311218 | tissue:embryo|genotype:control morpholino|developmental stage:embryo 48hpf | morpholino control miRNA Seq | FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9 | embryo | Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration. | Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions. | Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf | genotype:control morpholino|developmental stage:embryo 48hpf | GSM1311218 | GSM1311218: morpholino control miRNA Seq; Danio rerio; RNA Seq | GSM1311218 | 1 | Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions. | GEO Accession:GSM1311218 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP035565 | s_8_IDX21_1.fq | fastq | 308681847.0 | 3810887.0 | GSM1311218 r1 | 0:81 | A:63686404;C:75263287;G:80056961;T:89650625;N:24570 | 81 | 63686404 | 75263287 | 80056961 | 89650625 | 24570 | SRX445322 | SRS540473 | SRA128456 | GEO | Beijing Institute of Genomics | 1 | 8e-05 | 2e-05 | 0.99991 | 0.42857 | 81 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2014-01-21 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 38020 | 38020 | SRR1265736 | SRX529131 | SRS598827 | SRP041544 | PRJNA245824 | Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish | GSE57169 | Transcriptome Analysis | The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform. | pubmed:26574018 | Embryo Replicate 3 sRNAseq | GSM1376619 | source name:Embryo|tissue:Embryo|genetic background:Wild type Singapore strain | Embryo Replicate 3 sRNAseq | Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. | Embryo | N/A | Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. | Fishes were purchased from a local supplier and acclimatized before tissue extraction. | tissue:Embryo|genetic background:Wild type Singapore strain | GSM1376619 | GSM1376619: Embryo Replicate 3 sRNAseq; Danio rerio; miRNA Seq | GSM1376619 | 1 | Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. | GEO Accession:GSM1376619 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP041544 | MZE006_CTTGTA_L008_R1.fastq.gz | fastq | 1714180635.0 | 33611385.0 | GSM1376619 r1 | 0:51 | A:338559677;C:431494863;G:537012008;T:406904091;N:209996 | 51 | 338559677 | 431494863 | 537012008 | 406904091 | 209996 | SRX529131 | SRS598827 | SRA160430 | GEO | Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore | 1 | 0.09044 | 0.01776 | 0.97782 | 0.77023 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | size_fractionation | trueseq | bulk | unknown | unknown | Singapore | 2014-04-29 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 38021 | 38021 | SRR1265735 | SRX529130 | SRS598828 | SRP041544 | PRJNA245824 | Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish | GSE57169 | Transcriptome Analysis | The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform. | pubmed:26574018 | Embryo Replicate 2 sRNAseq | GSM1376618 | source name:Embryo|tissue:Embryo|genetic background:Wild type Singapore strain | Embryo Replicate 2 sRNAseq | Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. | Embryo | N/A | Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. | Fishes were purchased from a local supplier and acclimatized before tissue extraction. | tissue:Embryo|genetic background:Wild type Singapore strain | GSM1376618 | GSM1376618: Embryo Replicate 2 sRNAseq; Danio rerio; miRNA Seq | GSM1376618 | 1 | Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. | GEO Accession:GSM1376618 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP041544 | MZE005_GGCTAC_L008_R1.fastq.gz | fastq | 736486002.0 | 14440902.0 | GSM1376618 r1 | 0:51 | A:145757737;C:194417932;G:231157927;T:165060763;N:91643 | 51 | 145757737 | 194417932 | 231157927 | 165060763 | 91643 | SRX529130 | SRS598828 | SRA160430 | GEO | Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore | 1 | 0.01133 | 0.00234 | 0.99515 | 0.73854 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | trueseq | bulk | unknown | unknown | Singapore | 2014-04-29 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 38022 | 38022 | SRR1265734 | SRX529129 | SRS598825 | SRP041544 | PRJNA245824 | Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish | GSE57169 | Transcriptome Analysis | The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform. | pubmed:26574018 | Embryo Replicate 1 sRNAseq | GSM1376617 | source name:Embryo|tissue:Embryo|genetic background:Wild type Singapore strain | Embryo Replicate 1 sRNAseq | Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis. | Embryo | N/A | Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. | Fishes were purchased from a local supplier and acclimatized before tissue extraction. | tissue:Embryo|genetic background:Wild type Singapore strain | GSM1376617 | GSM1376617: Embryo Replicate 1 sRNAseq; Danio rerio; miRNA Seq | GSM1376617 | 1 | Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing. | GEO Accession:GSM1376617 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP041544 | MZE004_TAGCTT_L008_R1.fastq.gz | fastq | 477426912.0 | 9361312.0 | GSM1376617 r1 | 0:51 | A:93534991;C:123428376;G:148877677;T:111524753;N:61115 | 51 | 93534991 | 123428376 | 148877677 | 111524753 | 61115 | SRX529129 | SRS598825 | SRA160430 | GEO | Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore | 1 | 0.02061 | 0.00461 | 0.99379 | 0.8448 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | size_fractionation | trueseq | bulk | unknown | unknown | Singapore | 2014-04-29 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 38042 | 38042 | SRR1371226 | SRX585640 | SRS631986 | SRP043064 | PRJNA252044 | Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond Blackfan Anemia from RPL5 Deficiency [miRNA Seq] | GSE58344 | Transcriptome Analysis | In this study we generated a zebrafish model of DBA with RPL5 morphants and implemented high throughput RNA seq and miRNA seq to identify key genes lncRNAs and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a noc2l tars and nol6 and miRNAs such as dre miR 10a* dre miR 722 dre miR 737 and dre miR 142a 3p were significantly deregulated and these changes may play a crucial role in hematopoiesis ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network we identified central node genes in the network connected to the P53 pathway almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5 deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5 mediated DBA and other ribosomopathies. Overall design: Determine the differences of miRNome between RPL5 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5 mediated human diseases | parent bioproject:PRJNA252043 | pubmed:26961822 | RPL5 MO [miRNA] | GSM1408095 | tissue:embryo|genotype/variation:RPL5 morpholino knockdown|developmental stage:48hpf | RPL5 MO [miRNA] | FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9 | embryo | Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration. | Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions. | Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf | genotype/variation:RPL5 morpholino knockdown|developmental stage:48hpf | GSM1408095 | GSM1408095: RPL5 MO [miRNA]; Danio rerio; miRNA Seq | GSM1408095 | 1 | Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions. | GEO Accession:GSM1408095 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP043064 | s_7_IDX19_1.fq | fastq | 1093234725.0 | 13496725.0 | GSM1408095 r1 | 0:81 | A:263908052;C:257987133;G:278889068;T:292410262;N:40210 | 81 | 263908052 | 257987133 | 278889068 | 292410262 | 40210 | SRX585640 | SRS631986 | SRA169796 | GEO | Beijing Institute of Genomics | 1 | 3e-05 | 0.0 | 0.99991 | 0.5 | 81 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2014-06-10 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 38043 | 38043 | SRR1371225 | SRX585639 | SRS631982 | SRP043064 | PRJNA252044 | Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond Blackfan Anemia from RPL5 Deficiency [miRNA Seq] | GSE58344 | Transcriptome Analysis | In this study we generated a zebrafish model of DBA with RPL5 morphants and implemented high throughput RNA seq and miRNA seq to identify key genes lncRNAs and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a noc2l tars and nol6 and miRNAs such as dre miR 10a* dre miR 722 dre miR 737 and dre miR 142a 3p were significantly deregulated and these changes may play a crucial role in hematopoiesis ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network we identified central node genes in the network connected to the P53 pathway almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5 deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5 mediated DBA and other ribosomopathies. Overall design: Determine the differences of miRNome between RPL5 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5 mediated human diseases | parent bioproject:PRJNA252043 | pubmed:26961822 | morpholino control [miRNA] | GSM1408094 | tissue:embryo|genotype/variation:control morpholino|developmental stage:48hpf | morpholino control [miRNA] | FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9 | embryo | Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration. | Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions. | Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf | genotype/variation:control morpholino|developmental stage:48hpf | GSM1408094 | GSM1408094: morpholino control [miRNA]; Danio rerio; miRNA Seq | GSM1408094 | 1 | Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions. | GEO Accession:GSM1408094 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP043064 | 308681847.0 | 3810887.0 | GSM1408094 r1 | 0:81 | A:63686404;C:75263287;G:80056961;T:89650625;N:24570 | 81 | 63686404 | 75263287 | 80056961 | 89650625 | 24570 | SRX585639 | SRS631982 | SRA169796 | GEO | Beijing Institute of Genomics | 1 | 8e-05 | 2e-05 | 0.99991 | 0.42857 | 81 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2014-06-10 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 38252 | 38252 | SRR1593717 | SRX718003 | SRS713863 | SRP048545 | PRJNA262696 | Adenylation of maternally inherited microRNAs by Wispy | GSE61931 | Other | Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing | pubmed:25454948 | Zeb fish Emb t 24h | GSM1517418 | tissue:embryo|genotype/variation:WT|developmental stage:embryo 24h | Zeb fish Emb t 24h | The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample. | embryo | Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition. | genotype/variation:WT|developmental stage:embryo 24h | GSM1517418 | GSM1517418: Zeb fish Emb t 24h; Danio rerio; miRNA Seq | GSM1517418 | 1 | Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition. | GEO Accession:GSM1517418 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP048545 | Zeb_fish_Emb_t_24h_1.fastq.gz | fastq | 2747798604.0 | 53878404.0 | GSM1517418 r1 | 0:51 | A:675086979;C:579211488;G:812576920;T:680856005;N:67212 | 51 | 675086979 | 579211488 | 812576920 | 680856005 | 67212 | SRX718003 | SRS713863 | SRA188351 | GEO | Narry Kim Lab, School of Biological Sciences, Seoul National University | 1 | 0.0 | 0.0 | 1.0 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | 3prime | size_fractionation | trueseq | bulk | unknown | unknown | South Korea | 2014-09-30 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 38253 | 38253 | SRR1593716 | SRX718002 | SRS713862 | SRP048545 | PRJNA262696 | Adenylation of maternally inherited microRNAs by Wispy | GSE61931 | Other | Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing | pubmed:25454948 | Zeb fish Emb t 30m | GSM1517417 | tissue:embryo|genotype/variation:WT|developmental stage:embryo 30m | Zeb fish Emb t 30m | The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample. | embryo | Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition. | genotype/variation:WT|developmental stage:embryo 30m | GSM1517417 | GSM1517417: Zeb fish Emb t 30m; Danio rerio; miRNA Seq | GSM1517417 | 1 | Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition. | GEO Accession:GSM1517417 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP048545 | Zeb_fish_Emb_t_30m_1.fastq.gz | fastq | 3380715591.0 | 66288541.0 | GSM1517417 r1 | 0:51 | A:854040134;C:726173965;G:952338238;T:848081062;N:82192 | 51 | 854040134 | 726173965 | 952338238 | 848081062 | 82192 | SRX718002 | SRS713862 | SRA188351 | GEO | Narry Kim Lab, School of Biological Sciences, Seoul National University | 1 | 1e-05 | 0.0 | 0.99997 | 1.0 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | 3prime | size_fractionation | trueseq | bulk | unknown | unknown | South Korea | 2014-09-30 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 38254 | 38254 | SRR1593715 | SRX718001 | SRS713861 | SRP048545 | PRJNA262696 | Adenylation of maternally inherited microRNAs by Wispy | GSE61931 | Other | Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing | pubmed:25454948 | Zeb fish Emb t 10m | GSM1517416 | tissue:embryo|genotype/variation:WT|developmental stage:embryo 10m | Zeb fish Emb t 10m | The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample. | embryo | Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition. | genotype/variation:WT|developmental stage:embryo 10m | GSM1517416 | GSM1517416: Zeb fish Emb t 10m; Danio rerio; miRNA Seq | GSM1517416 | 1 | Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition. | GEO Accession:GSM1517416 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP048545 | Zeb_fish_Emb_t_10m_1.fastq.gz | fastq | 3339395697.0 | 65478347.0 | GSM1517416 r1 | 0:51 | A:847877403;C:714050198;G:934084609;T:843302102;N:81385 | 51 | 847877403 | 714050198 | 934084609 | 843302102 | 81385 | SRX718001 | SRS713861 | SRA188351 | GEO | Narry Kim Lab, School of Biological Sciences, Seoul National University | 1 | 0.0 | 0.0 | 1.0 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | 3prime | size_fractionation | trueseq | bulk | unknown | unknown | South Korea | 2014-09-30 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 38255 | 38255 | SRR1593714 | SRX718000 | SRS713860 | SRP048545 | PRJNA262696 | Adenylation of maternally inherited microRNAs by Wispy | GSE61931 | Other | Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing | pubmed:25454948 | Zeb fish Emb t 0m | GSM1517415 | tissue:egg|genotype/variation:WT|developmental stage:embryo 0m | Zeb fish Emb t 0m | The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample. | egg | Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition. | genotype/variation:WT|developmental stage:embryo 0m | GSM1517415 | GSM1517415: Zeb fish Emb t 0m; Danio rerio; miRNA Seq | GSM1517415 | 1 | Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition. | GEO Accession:GSM1517415 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP048545 | Zeb_fish_Emb_t_0m_1.fastq.gz | fastq | 3135589293.0 | 61482143.0 | GSM1517415 r1 | 0:51 | A:800912828;C:671516191;G:883139862;T:779944407;N:76005 | 51 | 800912828 | 671516191 | 883139862 | 779944407 | 76005 | SRX718000 | SRS713860 | SRA188351 | GEO | Narry Kim Lab, School of Biological Sciences, Seoul National University | 1 | 0.0 | 0.0 | 1.0 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | 3prime | size_fractionation | trueseq | bulk | unknown | unknown | South Korea | 2014-09-30 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||||
| 38321 | 38321 | SRR1732707 | SRX822003 | SRS801698 | SRP051503 | PRJNA271079 | Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq] | GSE64465 | Transcriptome Analysis | To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA271069 | pubmed:27471727 | Emb MO Ct 48hpf | GSM1571860 | source name:Embryos MO Ct 48hpf|tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:48hpf | Emb MO Ct 48hpf | Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Ct 48hpf | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:48hpf | GSM1571860 | GSM1571860: Emb MO Ct 48hpf; Danio rerio; miRNA Seq | GSM1571860 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1571860 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP051503 | L.T.fq.gz | fastq | 338322717.0 | 11175516.0 | GSM1571860 r1 | 0:30.27 1:0 | A:72708202;C:91561004;G:102921744;T:71122135;N:9632 | 30 | 0 | 72708202 | 91561004 | 102921744 | 71122135 | 9632 | SRX822003 | SRS801698 | SRA221043 | GEO | IIT, CNR | 1 | 0.86712 | 0.22408 | 0.92725 | 0.50365 | 23 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2014-12-23 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 38322 | 38322 | SRR1732706 | SRX822002 | SRS801697 | SRP051503 | PRJNA271079 | Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq] | GSE64465 | Transcriptome Analysis | To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA271069 | pubmed:27471727 | Emb MO Tbx5a 48hpf | GSM1571859 | source name:Embryos MO Tbx5a 48hpf|tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:48hpf | Emb MO Tbx5a 48hpf | Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Tbx5a 48hpf | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:48hpf | GSM1571859 | GSM1571859: Emb MO Tbx5a 48hpf; Danio rerio; miRNA Seq | GSM1571859 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1571859 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP051503 | I.T.fq.gz | fastq | 262219132.0 | 10137926.0 | GSM1571859 r1 | 0:25.87 1:0 | A:60415193;C:62111082;G:75168882;T:64515539;N:8436 | 25 | 0 | 60415193 | 62111082 | 75168882 | 64515539 | 8436 | SRX822002 | SRS801697 | SRA221043 | GEO | IIT, CNR | 1 | 0.52287 | 0.13984 | 0.8788 | 0.6354 | 30 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2014-12-23 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 38323 | 38323 | SRR1732705 | SRX822001 | SRS801696 | SRP051503 | PRJNA271079 | Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq] | GSE64465 | Transcriptome Analysis | To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA271069 | pubmed:27471727 | Emb MO Ct 24hpf rep2 | GSM1571858 | source name:Embryos MO Ct 24hpf replicate2|tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:24hpf | Emb MO Ct 24hpf rep2 | Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Ct 24hpf replicate2 | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:24hpf | GSM1571858 | GSM1571858: Emb MO Ct 24hpf rep2; Danio rerio; miRNA Seq | GSM1571858 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1571858 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP051503 | H.T.fq.gz | fastq | 281909951.0 | 10806197.0 | GSM1571858 r1 | 0:26.09 1:0 | A:66055828;C:65184020;G:81768559;T:68892445;N:9099 | 26 | 0 | 66055828 | 65184020 | 81768559 | 68892445 | 9099 | SRX822001 | SRS801696 | SRA221043 | GEO | IIT, CNR | 1 | 0.56084 | 0.23499 | 0.86819 | 0.64638 | 22 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2014-12-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 38324 | 38324 | SRR1732704 | SRX822000 | SRS801695 | SRP051503 | PRJNA271079 | Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq] | GSE64465 | Transcriptome Analysis | To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA271069 | pubmed:27471727 | Emb MO Ct 24hpf rep1 | GSM1571857 | source name:Embryos MO Ct 24hpf replicate1|tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:24hpf | Emb MO Ct 24hpf rep1 | Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Ct 24hpf replicate1 | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:24hpf | GSM1571857 | GSM1571857: Emb MO Ct 24hpf rep1; Danio rerio; miRNA Seq | GSM1571857 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1571857 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP051503 | G.T.fq.gz | fastq | 541546124.0 | 19319535.0 | GSM1571857 r1 | 0:28.03 1:0 | A:126881333;C:133281439;G:163930613;T:117435553;N:17186 | 28 | 0 | 126881333 | 133281439 | 163930613 | 117435553 | 17186 | SRX822000 | SRS801695 | SRA221043 | GEO | IIT, CNR | 1 | 0.53436 | 0.20796 | 0.9009 | 0.55394 | 34 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2014-12-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 38325 | 38325 | SRR1732703 | SRX821999 | SRS801694 | SRP051503 | PRJNA271079 | Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq] | GSE64465 | Transcriptome Analysis | To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA271069 | pubmed:27471727 | Emb MO Tbx5a 24hpf rep2 | GSM1571856 | source name:Embryos MO Tbx5a 24hpf replicate2|tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf | Emb MO Tbx5a 24hpf rep2 | Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Tbx5a 24hpf replicate2 | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf | GSM1571856 | GSM1571856: Emb MO Tbx5a 24hpf rep2; Danio rerio; miRNA Seq | GSM1571856 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1571856 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP051503 | F.T.fq.gz | fastq | 362513460.0 | 13684345.0 | GSM1571856 r1 | 0:26.49 1:0 | A:82709386;C:83987865;G:107681867;T:88122760;N:11582 | 26 | 0 | 82709386 | 83987865 | 107681867 | 88122760 | 11582 | SRX821999 | SRS801694 | SRA221043 | GEO | IIT, CNR | 1 | 0.58925 | 0.2498 | 0.86821 | 0.65549 | 30 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2014-12-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 38326 | 38326 | SRR1732702 | SRX821998 | SRS801693 | SRP051503 | PRJNA271079 | Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq] | GSE64465 | Transcriptome Analysis | To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA271069 | pubmed:27471727 | Emb MO Tbx5a 24hpf rep1 | GSM1571855 | source name:Embryos MO Tbx5a 24hpf replicate1|tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf | Emb MO Tbx5a 24hpf rep1 | Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Tbx5a 24hpf replicate1 | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf | GSM1571855 | GSM1571855: Emb MO Tbx5a 24hpf rep1; Danio rerio; miRNA Seq | GSM1571855 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1571855 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP051503 | E.T.fq.gz | fastq | 399134579.0 | 13766109.0 | GSM1571855 r1 | 0:28.99 1:0 | A:88725326;C:102855219;G:121123717;T:86418155;N:12162 | 28 | 0 | 88725326 | 102855219 | 121123717 | 86418155 | 12162 | SRX821998 | SRS801693 | SRA221043 | GEO | IIT, CNR | 1 | 0.66472 | 0.25948 | 0.89623 | 0.54913 | 34 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2014-12-23 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||
| 39703 | 39703 | SRR2057604 | SRX1054376 | SRS957216 | SRP059278 | PRJNA286201 | MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome [miRNA seq] | GSE69690 | Transcriptome Analysis | The regulative role of miRNAs in Holt Oram Syndrome is investigated in a zebrafish model. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT sample. 1.5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxxhpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA286199 | pubmed:26657204 | Emb MO Ct 48hpf [miRNA seq] | GSM1707594 | source name:Embryos MO Ct 48hpf|strain background:AB|infected with:MO C|tissue:embryo|developmental stage:48hpf | Emb MO Ct 48hpf [miRNA seq] | Basecalls performed using GA Pipeline v1.5 Sequenced reads were filtered for low quality and trimmed for three prime adaptor sequence. Reads were algned to mirBase v16.0 using CLC workbench Expression values were normalized to reads per million rpm Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Ct 48hpf | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | strain background:AB|infected with:MO C|tissue:embryo|developmental stage:48hpf | GSM1707594 | GSM1707594: Emb MO Ct 48hpf [miRNA seq]; Danio rerio; miRNA Seq | GSM1707594 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1707594 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP059278 | Dre_FC_4.fq.gz | fastq | 1033068440.0 | 25826711.0 | GSM1707594 r1 | 0:40 | A:417902194;C:195580811;G:153264728;T:266159736;N:160971 | 40 | 417902194 | 195580811 | 153264728 | 266159736 | 160971 | SRX1054376 | SRS957216 | SRA272222 | GEO | IIT, CNR | 1 | 0.05412 | 0.01319 | 0.97693 | 0.22489 | 40 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2015-06-09 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 39704 | 39704 | SRR2057603 | SRX1054375 | SRS957217 | SRP059278 | PRJNA286201 | MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome [miRNA seq] | GSE69690 | Transcriptome Analysis | The regulative role of miRNAs in Holt Oram Syndrome is investigated in a zebrafish model. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT sample. 1.5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxxhpf.The Zebrafish wild type AB strain line was used. | parent bioproject:PRJNA286199 | pubmed:26657204 | Emb MO Tbx5a 48hpf [miRNA seq] | GSM1707593 | source name:Embryos MO Tbx5a 48hpf|strain background:AB|infected with:MO Tbx5a|tissue:embryo|developmental stage:48hpf | Emb MO Tbx5a 48hpf [miRNA seq] | Basecalls performed using GA Pipeline v1.5 Sequenced reads were filtered for low quality and trimmed for three prime adaptor sequence. Reads were algned to mirBase v16.0 using CLC workbench Expression values were normalized to reads per million rpm Supplementary files format and content: tab delimited text file includes normalized read count per sample | Embryos MO Tbx5a 48hpf | 1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy. | strain background:AB|infected with:MO Tbx5a|tissue:embryo|developmental stage:48hpf | GSM1707593 | GSM1707593: Emb MO Tbx5a 48hpf [miRNA seq]; Danio rerio; miRNA Seq | GSM1707593 | 1 | For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt. | GEO Accession:GSM1707593 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP059278 | Dre_FC_3.fq.gz | fastq | 1038855840.0 | 25971396.0 | GSM1707593 r1 | 0:40 | A:430923990;C:193052690;G:149627446;T:265119627;N:132087 | 40 | 430923990 | 193052690 | 149627446 | 265119627 | 132087 | SRX1054375 | SRS957217 | SRA272222 | GEO | IIT, CNR | 1 | 0.01858 | 0.00322 | 0.98699 | 0.23156 | 40 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | Italy | 2015-06-09 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 39760 | 39760 | SRR2127901 | SRX1118699 | SRS1011434 | SRP061587 | PRJNA290964 | Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos | GSE71346 | Transcriptome Analysis | To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar. | pubmed:30090366 | 6 48 0.5µM OTA [miRNA seq] | GSM1832841 | tissue:embryo control|strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:0.5 µM ochratoxin A from 6 hpf to 48 hpf | 6 48 0.5µM OTA [miRNA seq] | Initially the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3′ adapter sequence and discarding reads shorter than 18 nucleotides before aligning reads to the Zebrafish genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome | embryo control | 6 hpf embryos were treated with ochratoxin A 0.5 mM till 48 hpf. | Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software | zebrafish embryos were selected at 6 hph with normal development. | strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:0.5 µM ochratoxin A from 6 hpf to 48 hpf | GSM1832841 | GSM1832841: 6 48 0.5µM OTA [miRNA seq]; Danio rerio; miRNA Seq | GSM1832841 | 1 | Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software | GEO Accession:GSM1832841 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP061587 | 6_48_0.5um_OTA.fastq.gz | fastq | 310077729.0 | 6130868.0 | GSM1832841 r1 | 0:50.58 1:0 | A:74462826;C:72958352;G:87201353;T:75455198;N:0 | 50 | 0 | 74462826 | 72958352 | 87201353 | 75455198 | 0 | SRX1118699 | SRS1011434 | SRA280185 | GEO | ntu | 1 | 0.00671 | 0.00134 | 0.99594 | 0.39026 | 51 | T | under 1.2% mapping rate | illumina | early_illumina | unknown | size_fractionation | trueseq | bulk | unknown | unknown | Unknown | 2015-07-25 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 39761 | 39761 | SRR2127900 | SRX1118698 | SRS1011435 | SRP061587 | PRJNA290964 | Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos | GSE71346 | Transcriptome Analysis | To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar. | pubmed:30090366 | 6 48 control [miRNA seq] | GSM1832840 | tissue:embryo control|strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:n1 control | 6 48 control [miRNA seq] | Initially the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3′ adapter sequence and discarding reads shorter than 18 nucleotides before aligning reads to the Zebrafish genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome | embryo control | 6 hpf embryos were treated with ochratoxin A 0.5 mM till 48 hpf. | Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software | zebrafish embryos were selected at 6 hph with normal development. | strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:n1 control | GSM1832840 | GSM1832840: 6 48 control [miRNA seq]; Danio rerio; miRNA Seq | GSM1832840 | 1 | Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software | GEO Accession:GSM1832840 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP061587 | 6_48_control.fastq.gz | fastq | 308947811.0 | 6107500.0 | GSM1832840 r1 | 0:50.58 1:0 | A:75126425;C:71798677;G:85490341;T:76532368;N:0 | 50 | 0 | 75126425 | 71798677 | 85490341 | 76532368 | 0 | SRX1118698 | SRS1011435 | SRA280185 | GEO | ntu | 1 | 0.00833 | 0.00166 | 0.99476 | 0.42762 | 51 | T | under 1.2% mapping rate | illumina | early_illumina | unknown | size_fractionation | trueseq | bulk | unknown | unknown | Unknown | 2015-07-25 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||
| 49101 | 49101 | SRR7726444 | SRX4582847 | SRS3697100 | SRP158508 | PRJNA487021 | MicroRNA expression signatures for gata4/5/6 knocking down in zebrafish | GSE118850 | Transcriptome Analysis | Previous works showed that gata4/5/6 lie at the hierarchical apex of the regulatory network of the hemangioblast formation and primitive myelopoiesis in zebrafish. To explore the roles of miRNAs in zebrafish primitive myelopoiesis we employed deep sequencing to analyze the difference of miRNA expression profiles between gata4/5/6 knockdown embryos gata5/6 morphants and control embryos. Overall design: The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for collected for miRNA deep sequencing.The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo. | G56 miRNA | GSM3349122 | tissue:G56 embryos|genotype:gata4/5/6 knockdown|developmental stage:embryos|age:14hpf | G56 miRNA | The cDNA library was sequenced using Illumina Solexa following version 8 multiplexed single read sequencing recipe. Fastx fastx toolkit 0.0.13.2 was used to preprocess the original reads of the sequence. The CLC genomics workbench5.5 was applied to match the preprocessed sequence to the Sanger miRBase database version 19.0. Genome build: Sanger miRBase database version 19.0 Supplementary files format and content: .csv file includes small RNA sequences and counts Supplementary files format and content: .xls file includes effective reads and fold changes | G56 embryos | Morpholinos MOs were purchased from Gene Tools http://www.gene tools.com. MOs were dissolved in nanopure water and microinjected into the embryos at xxx cell stages. The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo. The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for analyzing the miRNA expression changes affected by knocking down gata4/5/6. | Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The 3’ and 5’ adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp. | Zebrafish were housed in the zebrafish room of Model Animal Research Center Nanjing University in accordance with IACUC approved protocol. All methods were performed in accordance with the relevant guidelines and regulations. | genotype:gata4/5/6 knockdown|developmental stage:embryos|age:14hpf | GSM3349122 | GSM3349122: G56 miRNA; Danio rerio; miRNA Seq | GSM3349122 | 1 | Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The three prime and five prime adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp. | GEO Accession:GSM3349122 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina MiSeq | SRP158508 | 655037050.0 | 13100741.0 | GSM3349122 r1 | 0:50 1:0 | A:161448247;C:135821164;G:200213833;T:156824030;N:729776 | 50 | 0 | 161448247 | 135821164 | 200213833 | 156824030 | 729776 | SRX4582847 | SRS3697100 | SRA761361 | GEO | Nanjing University | 1 | 0.00066 | 6e-05 | 0.99896 | 0.64583 | 50 | T | under 1.2% mapping rate | illumina | miseq | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-08-21 | Segmentation | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 49102 | 49102 | SRR7726443 | SRX4582846 | SRS3697099 | SRP158508 | PRJNA487021 | MicroRNA expression signatures for gata4/5/6 knocking down in zebrafish | GSE118850 | Transcriptome Analysis | Previous works showed that gata4/5/6 lie at the hierarchical apex of the regulatory network of the hemangioblast formation and primitive myelopoiesis in zebrafish. To explore the roles of miRNAs in zebrafish primitive myelopoiesis we employed deep sequencing to analyze the difference of miRNA expression profiles between gata4/5/6 knockdown embryos gata5/6 morphants and control embryos. Overall design: The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for collected for miRNA deep sequencing.The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo. | WT miRNA | GSM3349121 | tissue:WT embryos|genotype:wild type|developmental stage:embryos|age:14hpf | WT miRNA | The cDNA library was sequenced using Illumina Solexa following version 8 multiplexed single read sequencing recipe. Fastx fastx toolkit 0.0.13.2 was used to preprocess the original reads of the sequence. The CLC genomics workbench5.5 was applied to match the preprocessed sequence to the Sanger miRBase database version 19.0. Genome build: Sanger miRBase database version 19.0 Supplementary files format and content: .csv file includes small RNA sequences and counts Supplementary files format and content: .xls file includes effective reads and fold changes | WT embryos | Morpholinos MOs were purchased from Gene Tools http://www.gene tools.com. MOs were dissolved in nanopure water and microinjected into the embryos at xxx cell stages. The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo. The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for analyzing the miRNA expression changes affected by knocking down gata4/5/6. | Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The 3’ and 5’ adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp. | Zebrafish were housed in the zebrafish room of Model Animal Research Center Nanjing University in accordance with IACUC approved protocol. All methods were performed in accordance with the relevant guidelines and regulations. | genotype:wild type|developmental stage:embryos|age:14hpf | GSM3349121 | GSM3349121: WT miRNA; Danio rerio; miRNA Seq | GSM3349121 | 1 | Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The three prime and five prime adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp. | GEO Accession:GSM3349121 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina MiSeq | SRP158508 | 627151350.0 | 12543027.0 | GSM3349121 r1 | 0:50 1:0 | A:153340174;C:128104541;G:192611227;T:152395340;N:700068 | 50 | 0 | 153340174 | 128104541 | 192611227 | 152395340 | 700068 | SRX4582846 | SRS3697099 | SRA761361 | GEO | Nanjing University | 1 | 0.0006 | 0.00012 | 0.99904 | 0.60759 | 50 | T | under 1.2% mapping rate | illumina | miseq | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-08-21 | Segmentation | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||||
| 49332 | 49332 | SRR7888761 | SRX4726390 | SRS3810123 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 72h | GSM3397729 | source name:Embryo|tissue:Embryo|age:72 hpf|developmental stage:incubation|strain:Tubingenz|genotype:WT | 72h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:72 hpf|developmental stage:incubation|strain:Tubingenz|genotype:WT | GSM3397729 | GSM3397729: 72h; Danio rerio; ncRNA Seq | GSM3397729 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397729 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 72h_1.fq.gz 72h_2.fq.gz | fastq fastq | 12097159200.0 | 40323864.0 | GSM3397729 r1 | 0:150 1:150 | A:2809307023;C:3169515166;G:3184429517;T:2931448896;N:2458598 | 150 | 150 | 2809307023 | 3169515166 | 3184429517 | 2931448896 | 2458598 | SRX4726390 | SRS3810123 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.90426 | 0.90717 | 0.27165 | 0.26439 | 0.70739 | 0.72397 | 0.60155 | 0.60561 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Larval | Larval | Embryo Imprecise | All anatomical structures | ||||||||||||
| 49333 | 49333 | SRR7888760 | SRX4726389 | SRS3810122 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 48h | GSM3397728 | source name:Embryo|tissue:Embryo|age:48 hpf|developmental stage:throat|strain:Tubingenz|genotype:WT | 48h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:48 hpf|developmental stage:throat|strain:Tubingenz|genotype:WT | GSM3397728 | GSM3397728: 48h; Danio rerio; ncRNA Seq | GSM3397728 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397728 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 48h_2.fq.gz 48h_1.fq.gz | fastq fastq | 13525174500.0 | 45083915.0 | GSM3397728 r1 | 0:150 1:150 | A:2352542664;C:4312268007;G:4256218842;T:2601416951;N:2728036 | 150 | 150 | 2352542664 | 4312268007 | 4256218842 | 2601416951 | 2728036 | SRX4726389 | SRS3810122 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.91614 | 0.91412 | 0.12891 | 0.12218 | 0.76751 | 0.77948 | 0.71008 | 0.73648 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Hatching | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 49334 | 49334 | SRR7888759 | SRX4726388 | SRS3810120 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 24h | GSM3397727 | source name:Embryo|tissue:Embryo|age:24 hpf|developmental stage:segmentation|strain:Tubingenz|genotype:WT | 24h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:24 hpf|developmental stage:segmentation|strain:Tubingenz|genotype:WT | GSM3397727 | GSM3397727: 24h; Danio rerio; ncRNA Seq | GSM3397727 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397727 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 24h_1.fq.gz 24h_2.fq.gz | fastq fastq | 14333175000.0 | 47777250.0 | GSM3397727 r1 | 0:150 1:150 | A:2728754113;C:4276840070;G:4344116037;T:2980570245;N:2894535 | 150 | 150 | 2728754113 | 4276840070 | 4344116037 | 2980570245 | 2894535 | SRX4726388 | SRS3810120 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.89719 | 0.89478 | 0.18044 | 0.18119 | 0.76942 | 0.7876 | 0.75758 | 0.75366 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 49335 | 49335 | SRR7888758 | SRX4726387 | SRS3810121 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 8h | GSM3397726 | source name:Embryo|tissue:Embryo|age:8 hpf|developmental stage:gastrula|strain:Tubingenz|genotype:WT | 8h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:8 hpf|developmental stage:gastrula|strain:Tubingenz|genotype:WT | GSM3397726 | GSM3397726: 8h; Danio rerio; ncRNA Seq | GSM3397726 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397726 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 8h_2.fq.gz 8h_1.fq.gz | fastq fastq | 15434085600.0 | 51446952.0 | GSM3397726 r1 | 0:150 1:150 | A:2318158791;C:5134519748;G:5292209580;T:2686084369;N:3113112 | 150 | 150 | 2318158791 | 5134519748 | 5292209580 | 2686084369 | 3113112 | SRX4726387 | SRS3810121 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.95788 | 0.95584 | 0.07233 | 0.07686 | 0.81889 | 0.82946 | 0.81383 | 0.80143 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 49336 | 49336 | SRR7888757 | SRX4726386 | SRS3810119 | SRP162319 | PRJNA492406 | Profiles analysis reveals circRNAs involving zebrafish physiological development | GSE120289 | Transcriptome Analysis | Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins modulation of transcription and interference with splicing and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period gastrula period segmentation period throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways cardiovascular system development retinal ganglion cell axon guidance and so on. Moreover circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b miR 124 and so on some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula gastrula segmentation throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500. | 4.5h | GSM3397725 | source name:Embryo|tissue:Embryo|age:4.5 hpf|developmental stage:blastula|strain:Tubingenz|genotype:WT | 4.5h | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters "mem T 19". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC ≥2 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample. | Embryo | Zebrafish were reared at 28±1℃ in a water circulatory system that osmotic pressure stability UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5±0.5℃. Morphological features were used to judge the stage of embryonic development. | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer’s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer’s instructions Illumina | tissue:Embryo|age:4.5 hpf|developmental stage:blastula|strain:Tubingenz|genotype:WT | GSM3397725 | GSM3397725: 4.5h; Danio rerio; ncRNA Seq | GSM3397725 | 1 | Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina | GEO Accession:GSM3397725 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP162319 | 4_5h_2.fq.gz 4_5h_1.fq.gz | fastq fastq | 12988242600.0 | 43294142.0 | GSM3397725 r1 | 0:150 1:150 | A:2232301074;C:3998769528;G:4233380689;T:2521224783;N:2566526 | 150 | 150 | 2232301074 | 3998769528 | 4233380689 | 2521224783 | 2566526 | SRX4726386 | SRS3810119 | SRA781248 | GEO | Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital | 2 | 0.96961 | 0.96817 | 0.05627 | 0.05463 | 0.77068 | 0.78198 | 0.74899 | 0.75759 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2018-09-21 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||
| 53169 | 53169 | SRR9697470 | SRX6455747 | SRS5113424 | SRP215029 | PRJNA555064 | Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells | GSE134399 | Transcriptome Analysis | MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica. | pubmed:31923196 | ZF4 18 30d cold3 | GSM3946004 | tissue:embryonic fibroblast cells|cell line:ZF4|cell type:fibroblast cell line|growth temperature:cultured at 18 C for 30 days|treatment:cold treatment for 30 days | ZF4 18 30d cold3 | Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs | embryonic fibroblast cells | For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days. | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2. | cell line:ZF4|cell type:fibroblast cell line|growth temperature:cultured at 18 C for 30 days|treatment:cold treatment for 30 days | GSM3946004 | GSM3946004: ZF4 18 30d cold3; Danio rerio; miRNA Seq | GSM3946004 | 1 | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | GEO Accession:GSM3946004 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq X Ten | SRP215029 | 6.fq.gz | fastq | 888718150.0 | 17774363.0 | GSM3946004 r1 | 0:50 | A:200112040;C:206776226;G:254640770;T:227172753;N:16361 | 50 | 200112040 | 206776226 | 254640770 | 227172753 | 16361 | SRX6455747 | SRS5113424 | SRA922199 | GEO | Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University | 1 | 0.00546 | 0.00027 | 0.99799 | 0.4985 | 50 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2019-07-17 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 53170 | 53170 | SRR9697469 | SRX6455746 | SRS5113421 | SRP215029 | PRJNA555064 | Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells | GSE134399 | Transcriptome Analysis | MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica. | pubmed:31923196 | ZF4 18 30d cold2 | GSM3946003 | tissue:embryonic fibroblast cells|cell line:ZF4|cell type:fibroblast cell line|growth temperature:cultured at 18 C for 30 days|treatment:cold treatment for 30 days | ZF4 18 30d cold2 | Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs | embryonic fibroblast cells | For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days. | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2. | cell line:ZF4|cell type:fibroblast cell line|growth temperature:cultured at 18 C for 30 days|treatment:cold treatment for 30 days | GSM3946003 | GSM3946003: ZF4 18 30d cold2; Danio rerio; miRNA Seq | GSM3946003 | 1 | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | GEO Accession:GSM3946003 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq X Ten | SRP215029 | 5.fq.gz | fastq | 853031700.0 | 17060634.0 | GSM3946003 r1 | 0:50 | A:192338096;C:205750986;G:242627478;T:212299265;N:15875 | 50 | 192338096 | 205750986 | 242627478 | 212299265 | 15875 | SRX6455746 | SRS5113421 | SRA922199 | GEO | Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University | 1 | 0.00538 | 0.00045 | 0.99738 | 0.47457 | 50 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2019-07-17 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 53171 | 53171 | SRR9697468 | SRX6455745 | SRS5113422 | SRP215029 | PRJNA555064 | Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells | GSE134399 | Transcriptome Analysis | MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica. | pubmed:31923196 | ZF4 18 30d cold1 | GSM3946002 | tissue:embryonic fibroblast cells|cell line:ZF4|cell type:fibroblast cell line|growth temperature:cultured at 18 C for 30 days|treatment:cold treatment for 30 days | ZF4 18 30d cold1 | Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs | embryonic fibroblast cells | For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days. | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2. | cell line:ZF4|cell type:fibroblast cell line|growth temperature:cultured at 18 C for 30 days|treatment:cold treatment for 30 days | GSM3946002 | GSM3946002: ZF4 18 30d cold1; Danio rerio; miRNA Seq | GSM3946002 | 1 | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | GEO Accession:GSM3946002 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq X Ten | SRP215029 | 4.fq.gz | fastq | 878731000.0 | 17574620.0 | GSM3946002 r1 | 0:50 | A:196907854;C:209105082;G:251308531;T:221393524;N:16009 | 50 | 196907854 | 209105082 | 251308531 | 221393524 | 16009 | SRX6455745 | SRS5113422 | SRA922199 | GEO | Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University | 1 | 0.01219 | 0.00089 | 0.99691 | 0.52247 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2019-07-17 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 53172 | 53172 | SRR9697467 | SRX6455744 | SRS5113420 | SRP215029 | PRJNA555064 | Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells | GSE134399 | Transcriptome Analysis | MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica. | pubmed:31923196 | ZF4 28 con3 | GSM3946001 | tissue:embryonic fibroblast cells|cell line:ZF4|cell type:fibroblast cell line|growth temperature:normal cultured 28 C|treatment:control | ZF4 28 con3 | Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs | embryonic fibroblast cells | For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days. | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2. | cell line:ZF4|cell type:fibroblast cell line|growth temperature:normal cultured 28 C|treatment:control | GSM3946001 | GSM3946001: ZF4 28 con3; Danio rerio; miRNA Seq | GSM3946001 | 1 | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | GEO Accession:GSM3946001 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq X Ten | SRP215029 | 3.fq.gz | fastq | 908953950.0 | 18179079.0 | GSM3946001 r1 | 0:50 | A:206519605;C:210829105;G:259204569;T:232383846;N:16825 | 50 | 206519605 | 210829105 | 259204569 | 232383846 | 16825 | SRX6455744 | SRS5113420 | SRA922199 | GEO | Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University | 1 | 0.00508 | 0.00042 | 0.99756 | 0.48 | 50 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2019-07-17 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 53173 | 53173 | SRR9697466 | SRX6455743 | SRS5113423 | SRP215029 | PRJNA555064 | Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells | GSE134399 | Transcriptome Analysis | MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica. | pubmed:31923196 | ZF4 28 con2 | GSM3946000 | tissue:embryonic fibroblast cells|cell line:ZF4|cell type:fibroblast cell line|growth temperature:normal cultured 28 C|treatment:control | ZF4 28 con2 | Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs | embryonic fibroblast cells | For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days. | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2. | cell line:ZF4|cell type:fibroblast cell line|growth temperature:normal cultured 28 C|treatment:control | GSM3946000 | GSM3946000: ZF4 28 con2; Danio rerio; miRNA Seq | GSM3946000 | 1 | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | GEO Accession:GSM3946000 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq X Ten | SRP215029 | 2.fq.gz | fastq | 876929500.0 | 17538590.0 | GSM3946000 r1 | 0:50 | A:198651931;C:204780756;G:249251465;T:224229047;N:16301 | 50 | 198651931 | 204780756 | 249251465 | 224229047 | 16301 | SRX6455743 | SRS5113423 | SRA922199 | GEO | Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University | 1 | 0.01465 | 0.00237 | 0.99559 | 0.5232 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2019-07-17 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 53174 | 53174 | SRR9697465 | SRX6455742 | SRS5113425 | SRP215029 | PRJNA555064 | Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells | GSE134399 | Transcriptome Analysis | MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica. | pubmed:31923196 | ZF4 28 con1 | GSM3945999 | tissue:embryonic fibroblast cells|cell line:ZF4|cell type:fibroblast cell line|growth temperature:normal cultured 28 C|treatment:control | ZF4 28 con1 | Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs | embryonic fibroblast cells | For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days. | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2. | cell line:ZF4|cell type:fibroblast cell line|growth temperature:normal cultured 28 C|treatment:control | GSM3945999 | GSM3945999: ZF4 28 con1; Danio rerio; miRNA Seq | GSM3945999 | 1 | Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads. | GEO Accession:GSM3945999 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq X Ten | SRP215029 | 1.fq.gz | fastq | 957098100.0 | 19141962.0 | GSM3945999 r1 | 0:50 | A:217645979;C:223129215;G:273039214;T:243266316;N:17376 | 50 | 217645979 | 223129215 | 273039214 | 243266316 | 17376 | SRX6455742 | SRS5113425 | SRA922199 | GEO | Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University | 1 | 0.00967 | 0.0007 | 0.99701 | 0.51905 | 50 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2019-07-17 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 57186 | 57186 | SRR11263444 | SRX7870077 | SRS6278494 | SRP251978 | PRJNA611062 | Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq] | GSE146605 | Transcriptome Analysis | Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate. | parent bioproject:PRJNA611061 | miRNA of MZdgcr8 3 | GSM4396432 | source name:Embryo|strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8 | miRNA of MZdgcr8 3 | Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles | Embryo | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8 | GSM4396432 | GSM4396432: miRNA of MZdgcr8 3; Danio rerio; miRNA Seq | GSM4396432 | 1 | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4396432 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP251978 | MZ_3_miRNA.fq.gz | fastq | 602855750.0 | 12057115.0 | GSM4396432 r1 | 0:50 1:0 | A:146678206;C:139956283;G:181049484;T:135139840;N:31937 | 50 | 0 | 146678206 | 139956283 | 181049484 | 135139840 | 31937 | SRX7870077 | SRS6278494 | SRA1052219 | GEO | The Chinese University of Hong Kong | 1 | 0.00091 | 0.0001 | 0.9987 | 0.73076 | 50 | T | under 1.2% mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | China | 2020-03-08 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 57187 | 57187 | SRR11263443 | SRX7870076 | SRS6278493 | SRP251978 | PRJNA611062 | Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq] | GSE146605 | Transcriptome Analysis | Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate. | parent bioproject:PRJNA611061 | miRNA of MZdgcr8 2 | GSM4396431 | source name:Embryo|strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8 | miRNA of MZdgcr8 2 | Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles | Embryo | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8 | GSM4396431 | GSM4396431: miRNA of MZdgcr8 2; Danio rerio; miRNA Seq | GSM4396431 | 1 | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4396431 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP251978 | MZ_2_miRNA.fq.gz | fastq | 532605954.0 | 10443254.0 | GSM4396431 r1 | 0:51 1:0 | A:124901241;C:134604417;G:148078897;T:124932015;N:89384 | 51 | 0 | 124901241 | 134604417 | 148078897 | 124932015 | 89384 | SRX7870076 | SRS6278493 | SRA1052219 | GEO | The Chinese University of Hong Kong | 1 | 0.0002 | 2e-05 | 0.99935 | 0.51428 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | China | 2020-03-08 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 57188 | 57188 | SRR11263442 | SRX7870075 | SRS6278492 | SRP251978 | PRJNA611062 | Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq] | GSE146605 | Transcriptome Analysis | Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate. | parent bioproject:PRJNA611061 | miRNA of MZdgcr8 1 | GSM4396430 | source name:Embryo|strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8 | miRNA of MZdgcr8 1 | Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles | Embryo | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8 | GSM4396430 | GSM4396430: miRNA of MZdgcr8 1; Danio rerio; miRNA Seq | GSM4396430 | 1 | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4396430 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP251978 | MZ_1_miRNA.fq.gz | fastq | 588374148.0 | 11536748.0 | GSM4396430 r1 | 0:51 1:0 | A:137533072;C:149724383;G:163915952;T:137198731;N:2010 | 51 | 0 | 137533072 | 149724383 | 163915952 | 137198731 | 2010 | SRX7870075 | SRS6278492 | SRA1052219 | GEO | The Chinese University of Hong Kong | 1 | 0.0014 | 0.00031 | 0.99795 | 0.62441 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | China | 2020-03-08 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 57189 | 57189 | SRR11263441 | SRX7870074 | SRS6278490 | SRP251978 | PRJNA611062 | Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq] | GSE146605 | Transcriptome Analysis | Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate. | parent bioproject:PRJNA611061 | miRNA of Wild type 3 | GSM4396429 | source name:Embryo|strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type | miRNA of Wild type 3 | Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles | Embryo | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type | GSM4396429 | GSM4396429: miRNA of Wild type 3; Danio rerio; miRNA Seq | GSM4396429 | 1 | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4396429 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP251978 | WT_3_miRNA.fq.gz | fastq | 688929450.0 | 13778589.0 | GSM4396429 r1 | 0:50 1:0 | A:171239999;C:140558088;G:209452609;T:167641448;N:37306 | 50 | 0 | 171239999 | 140558088 | 209452609 | 167641448 | 37306 | SRX7870074 | SRS6278490 | SRA1052219 | GEO | The Chinese University of Hong Kong | 1 | 0.00247 | 0.00016 | 0.99797 | 0.60356 | 50 | T | under 1.2% mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | China | 2020-03-08 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 57190 | 57190 | SRR11263440 | SRX7870073 | SRS6278491 | SRP251978 | PRJNA611062 | Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq] | GSE146605 | Transcriptome Analysis | Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate. | parent bioproject:PRJNA611061 | miRNA of Wild type 2 | GSM4396428 | source name:Embryo|strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type | miRNA of Wild type 2 | Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles | Embryo | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type | GSM4396428 | GSM4396428: miRNA of Wild type 2; Danio rerio; miRNA Seq | GSM4396428 | 1 | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4396428 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP251978 | WT_2_miRNA.fq.gz | fastq | 680017935.0 | 13333685.0 | GSM4396428 r1 | 0:51 1:0 | A:161673690;C:168811670;G:190321246;T:159208682;N:2647 | 51 | 0 | 161673690 | 168811670 | 190321246 | 159208682 | 2647 | SRX7870073 | SRS6278491 | SRA1052219 | GEO | The Chinese University of Hong Kong | 1 | 0.03809 | 0.00119 | 0.99318 | 0.59584 | 51 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | China | 2020-03-08 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 57191 | 57191 | SRR11263439 | SRX7870072 | SRS6278489 | SRP251978 | PRJNA611062 | Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq] | GSE146605 | Transcriptome Analysis | Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate. | parent bioproject:PRJNA611061 | miRNA of Wild type 1 | GSM4396427 | source name:Embryo|strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type | miRNA of Wild type 1 | Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles | Embryo | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type | GSM4396427 | GSM4396427: miRNA of Wild type 1; Danio rerio; miRNA Seq | GSM4396427 | 1 | small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM4396427 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP251978 | WT_1_miRNA.fq.gz | fastq | 606884853.0 | 11899703.0 | GSM4396427 r1 | 0:51 1:0 | A:144656910;C:150045615;G:169161904;T:143018153;N:2271 | 51 | 0 | 144656910 | 150045615 | 169161904 | 143018153 | 2271 | SRX7870072 | SRS6278489 | SRA1052219 | GEO | The Chinese University of Hong Kong | 1 | 0.0559 | 0.00242 | 0.99064 | 0.54228 | 51 | B | usable mapping rate | illumina | hiseq_era | 5prime | size_fractionation | unknown | bulk | unknown | unknown | China | 2020-03-08 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | ||||||||||||||||||
| 58542 | 58542 | SRR13652355 | SRX10049118 | SRS8212347 | SRP253438 | PRJNA613601 | five prime half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA Seq ssDRIP seq] | GSE147253 | Other | five primetRFls are small tRNA fragments derived from five prime half of mature tRNAs. However it is unknown whether five primetRFls could feed back to regulate tRNA biogenesis. Here we show that five primetRFlGly/GCC and five primetRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis dynamics of five primetRFlGly/GCC and five primetRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino mediated knockdown of five primetRFlGly/GCC or five primetRFlGlu/CTC down regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively and causes embryonic lethality that is efficiently rescued by co injection of properly refolded corresponding tRNA. In zebrafish embryos tRNA:DNA and five primetRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically unstable five primetRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes. Overall design: For small RNA sequencing total RNA were extracted respectively from wildtype zebrafish embryos Tübingen Strain of 6 chosen stages and then subjected to small RNA library preparation individually. To investigate the distribution and stability of R loop on genome we performed ssDRIP seq with S9.6 antibody which specifically recognize RNA:DNA hybrid. Two replicates from wildtype embryos of 256c sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre treated genome DNA was used as negative control which was also performed the standard ssDRIP seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation. | parent bioproject:PRJNA753013 | pubmed:34797706 | 24hpf ncRNA seq | GSM5069285 | tissue:embryo|strain:Tubingen|developmental stage:24 hpf stage|treatement:no | 24hpf ncRNA seq | For data processing reads were quality checked by FastQCVersion 0.11.8 and adaptors were cut off by Cutadapt Version 1.16 and only reads that lay between 18 40 nt were kept. The reads of each sample were first aligned to different database by using Bowtie2 Version 2.3.4.1 count table was generated by featureCounts. Genome build: GRCz11 genome and cDNA tRNA database GtRNAdb GRCz11 | embryo | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 3’ cyclic phosphate group from the 3’end of 5’tRFls and add phosphate group to the 5’end of 3’tRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | strain:Tubingen|developmental stage:24 hpf stage|treatement:no | GSM5069285 | GSM5069285: 24hpf ncRNA seq; Danio rerio; ncRNA Seq | GSM5069285 | 1 | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 three prime cyclic phosphate group from the three primeend of five primetRFls and add phosphate group to the five primeend of three primetRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | GEO Accession:GSM5069285 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP253438 | 24hpf-RNA_seq.fq.gz | fastq | 4887202650.0 | 32581351.0 | GSM5069285 r1 | 0:150 1:0 | A:821306307;C:893949781;G:2431277343;T:739975843;N:693376 | 150 | 0 | 821306307 | 893949781 | 2431277343 | 739975843 | 693376 | SRX10049118 | SRS8212347 | SRA1056877 | GEO | Anming Meng Lab, School of Life Science, Tsinghua University | 1 | 0.60067 | 0.12422 | 0.81132 | 0.45351 | 150 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | nebnext | bulk | unknown | unknown | China | 2021-02-08 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 58543 | 58543 | SRR13652354 | SRX10049117 | SRS8212344 | SRP253438 | PRJNA613601 | five prime half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA Seq ssDRIP seq] | GSE147253 | Other | five primetRFls are small tRNA fragments derived from five prime half of mature tRNAs. However it is unknown whether five primetRFls could feed back to regulate tRNA biogenesis. Here we show that five primetRFlGly/GCC and five primetRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis dynamics of five primetRFlGly/GCC and five primetRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino mediated knockdown of five primetRFlGly/GCC or five primetRFlGlu/CTC down regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively and causes embryonic lethality that is efficiently rescued by co injection of properly refolded corresponding tRNA. In zebrafish embryos tRNA:DNA and five primetRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically unstable five primetRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes. Overall design: For small RNA sequencing total RNA were extracted respectively from wildtype zebrafish embryos Tübingen Strain of 6 chosen stages and then subjected to small RNA library preparation individually. To investigate the distribution and stability of R loop on genome we performed ssDRIP seq with S9.6 antibody which specifically recognize RNA:DNA hybrid. Two replicates from wildtype embryos of 256c sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre treated genome DNA was used as negative control which was also performed the standard ssDRIP seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation. | parent bioproject:PRJNA753013 | pubmed:34797706 | Shield ncRNA seq | GSM5069284 | tissue:embryo|strain:Tubingen|developmental stage:Shield stage|treatement:no | Shield ncRNA seq | For data processing reads were quality checked by FastQCVersion 0.11.8 and adaptors were cut off by Cutadapt Version 1.16 and only reads that lay between 18 40 nt were kept. The reads of each sample were first aligned to different database by using Bowtie2 Version 2.3.4.1 count table was generated by featureCounts. Genome build: GRCz11 genome and cDNA tRNA database GtRNAdb GRCz11 | embryo | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 3’ cyclic phosphate group from the 3’end of 5’tRFls and add phosphate group to the 5’end of 3’tRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | strain:Tubingen|developmental stage:Shield stage|treatement:no | GSM5069284 | GSM5069284: Shield ncRNA seq; Danio rerio; ncRNA Seq | GSM5069284 | 1 | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 three prime cyclic phosphate group from the three primeend of five primetRFls and add phosphate group to the five primeend of three primetRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | GEO Accession:GSM5069284 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP253438 | Shield-RNA_seq.fq.gz | fastq | 3889055700.0 | 25927038.0 | GSM5069284 r1 | 0:150 1:0 | A:663037737;C:674378775;G:1956188054;T:594901111;N:550023 | 150 | 0 | 663037737 | 674378775 | 1956188054 | 594901111 | 550023 | SRX10049117 | SRS8212344 | SRA1056877 | GEO | Anming Meng Lab, School of Life Science, Tsinghua University | 1 | 0.64541 | 0.17034 | 0.79174 | 0.59714 | 150 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | nebnext | bulk | unknown | unknown | China | 2021-02-08 | Gastrula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 58544 | 58544 | SRR13652353 | SRX10049116 | SRS8212345 | SRP253438 | PRJNA613601 | five prime half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA Seq ssDRIP seq] | GSE147253 | Other | five primetRFls are small tRNA fragments derived from five prime half of mature tRNAs. However it is unknown whether five primetRFls could feed back to regulate tRNA biogenesis. Here we show that five primetRFlGly/GCC and five primetRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis dynamics of five primetRFlGly/GCC and five primetRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino mediated knockdown of five primetRFlGly/GCC or five primetRFlGlu/CTC down regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively and causes embryonic lethality that is efficiently rescued by co injection of properly refolded corresponding tRNA. In zebrafish embryos tRNA:DNA and five primetRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically unstable five primetRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes. Overall design: For small RNA sequencing total RNA were extracted respectively from wildtype zebrafish embryos Tübingen Strain of 6 chosen stages and then subjected to small RNA library preparation individually. To investigate the distribution and stability of R loop on genome we performed ssDRIP seq with S9.6 antibody which specifically recognize RNA:DNA hybrid. Two replicates from wildtype embryos of 256c sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre treated genome DNA was used as negative control which was also performed the standard ssDRIP seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation. | parent bioproject:PRJNA753013 | pubmed:34797706 | Sphere ncRNA seq | GSM5069283 | tissue:embryo|strain:Tubingen|developmental stage:Sphere stage|treatement:no | Sphere ncRNA seq | For data processing reads were quality checked by FastQCVersion 0.11.8 and adaptors were cut off by Cutadapt Version 1.16 and only reads that lay between 18 40 nt were kept. The reads of each sample were first aligned to different database by using Bowtie2 Version 2.3.4.1 count table was generated by featureCounts. Genome build: GRCz11 genome and cDNA tRNA database GtRNAdb GRCz11 | embryo | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 3’ cyclic phosphate group from the 3’end of 5’tRFls and add phosphate group to the 5’end of 3’tRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | strain:Tubingen|developmental stage:Sphere stage|treatement:no | GSM5069283 | GSM5069283: Sphere ncRNA seq; Danio rerio; ncRNA Seq | GSM5069283 | 1 | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 three prime cyclic phosphate group from the three primeend of five primetRFls and add phosphate group to the five primeend of three primetRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | GEO Accession:GSM5069283 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP253438 | Sphere-RNA_seq.fq.gz | fastq | 3717222600.0 | 24781484.0 | GSM5069283 r1 | 0:150 1:0 | A:624971961;C:648134651;G:1883560788;T:560027159;N:528041 | 150 | 0 | 624971961 | 648134651 | 1883560788 | 560027159 | 528041 | SRX10049116 | SRS8212345 | SRA1056877 | GEO | Anming Meng Lab, School of Life Science, Tsinghua University | 1 | 0.66566 | 0.17271 | 0.77378 | 0.58824 | 150 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | nebnext | bulk | unknown | unknown | China | 2021-02-08 | Blastula | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 58545 | 58545 | SRR13652352 | SRX10049115 | SRS8212343 | SRP253438 | PRJNA613601 | five prime half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA Seq ssDRIP seq] | GSE147253 | Other | five primetRFls are small tRNA fragments derived from five prime half of mature tRNAs. However it is unknown whether five primetRFls could feed back to regulate tRNA biogenesis. Here we show that five primetRFlGly/GCC and five primetRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis dynamics of five primetRFlGly/GCC and five primetRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino mediated knockdown of five primetRFlGly/GCC or five primetRFlGlu/CTC down regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively and causes embryonic lethality that is efficiently rescued by co injection of properly refolded corresponding tRNA. In zebrafish embryos tRNA:DNA and five primetRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically unstable five primetRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes. Overall design: For small RNA sequencing total RNA were extracted respectively from wildtype zebrafish embryos Tübingen Strain of 6 chosen stages and then subjected to small RNA library preparation individually. To investigate the distribution and stability of R loop on genome we performed ssDRIP seq with S9.6 antibody which specifically recognize RNA:DNA hybrid. Two replicates from wildtype embryos of 256c sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre treated genome DNA was used as negative control which was also performed the standard ssDRIP seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation. | parent bioproject:PRJNA753013 | pubmed:34797706 | 256c ncRNA seq | GSM5069282 | tissue:embryo|strain:Tubingen|developmental stage:256c stage|treatement:no | 256c ncRNA seq | For data processing reads were quality checked by FastQCVersion 0.11.8 and adaptors were cut off by Cutadapt Version 1.16 and only reads that lay between 18 40 nt were kept. The reads of each sample were first aligned to different database by using Bowtie2 Version 2.3.4.1 count table was generated by featureCounts. Genome build: GRCz11 genome and cDNA tRNA database GtRNAdb GRCz11 | embryo | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 3’ cyclic phosphate group from the 3’end of 5’tRFls and add phosphate group to the 5’end of 3’tRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | strain:Tubingen|developmental stage:256c stage|treatement:no | GSM5069282 | GSM5069282: 256c ncRNA seq; Danio rerio; ncRNA Seq | GSM5069282 | 1 | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 three prime cyclic phosphate group from the three primeend of five primetRFls and add phosphate group to the five primeend of three primetRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | GEO Accession:GSM5069282 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP253438 | 256c-RNA_seq.fq.gz | fastq | 4634985600.0 | 30899904.0 | GSM5069282 r1 | 0:150 1:0 | A:815670917;C:820280105;G:2237895473;T:760861465;N:277640 | 150 | 0 | 815670917 | 820280105 | 2237895473 | 760861465 | 277640 | SRX10049115 | SRS8212343 | SRA1056877 | GEO | Anming Meng Lab, School of Life Science, Tsinghua University | 1 | 0.67611 | 0.16429 | 0.8076 | 0.58827 | 150 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | nebnext | bulk | unknown | unknown | China | 2021-02-08 | Undetermined | Embryo | Embryo Imprecise | All anatomical structures | |||||||||||||||||
| 58546 | 58546 | SRR13652351 | SRX10049114 | SRS8212341 | SRP253438 | PRJNA613601 | five prime half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA Seq ssDRIP seq] | GSE147253 | Other | five primetRFls are small tRNA fragments derived from five prime half of mature tRNAs. However it is unknown whether five primetRFls could feed back to regulate tRNA biogenesis. Here we show that five primetRFlGly/GCC and five primetRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis dynamics of five primetRFlGly/GCC and five primetRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino mediated knockdown of five primetRFlGly/GCC or five primetRFlGlu/CTC down regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively and causes embryonic lethality that is efficiently rescued by co injection of properly refolded corresponding tRNA. In zebrafish embryos tRNA:DNA and five primetRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically unstable five primetRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes. Overall design: For small RNA sequencing total RNA were extracted respectively from wildtype zebrafish embryos Tübingen Strain of 6 chosen stages and then subjected to small RNA library preparation individually. To investigate the distribution and stability of R loop on genome we performed ssDRIP seq with S9.6 antibody which specifically recognize RNA:DNA hybrid. Two replicates from wildtype embryos of 256c sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre treated genome DNA was used as negative control which was also performed the standard ssDRIP seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation. | parent bioproject:PRJNA753013 | pubmed:34797706 | 1cell ncRNA seq | GSM5069281 | tissue:embryo|strain:Tubingen|developmental stage:1cell stage|treatement:no | 1cell ncRNA seq | For data processing reads were quality checked by FastQCVersion 0.11.8 and adaptors were cut off by Cutadapt Version 1.16 and only reads that lay between 18 40 nt were kept. The reads of each sample were first aligned to different database by using Bowtie2 Version 2.3.4.1 count table was generated by featureCounts. Genome build: GRCz11 genome and cDNA tRNA database GtRNAdb GRCz11 | embryo | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 3’ cyclic phosphate group from the 3’end of 5’tRFls and add phosphate group to the 5’end of 3’tRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | strain:Tubingen|developmental stage:1cell stage|treatement:no | GSM5069281 | GSM5069281: 1cell ncRNA seq; Danio rerio; ncRNA Seq | GSM5069281 | 1 | For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific 15596018. The lysate was centrifuged at 12 000 rpm for 10 min and the supernatant was collected and mixed with 200 μl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4℃ the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at 80℃ until all samples were collected. Two pretreatment steps were included: First purified total RNAs were treated with T4 Polynucleotide Kinase NEB M0201S with ATP for 30 min at 37℃ then purified by phenol: chloroform extraction. The aim of this step is removing the 2 three prime cyclic phosphate group from the three primeend of five primetRFls and add phosphate group to the five primeend of three primetRFs. In the second step total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing: Small RNA libraries using 1 μg RNA each were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research then bands of 135 160 bp about the length of 15 40 nt RNA ligated with both adaptors were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc pH 4.5 followed by precipitation by adding 2.5 volumes of ethanol. | GEO Accession:GSM5069281 | ncRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP253438 | 1cell-RNA_seq.fq.gz | fastq | 4393191750.0 | 29287945.0 | GSM5069281 r1 | 0:150 1:0 | A:767598671;C:783490468;G:2110419912;T:731062034;N:620665 | 150 | 0 | 767598671 | 783490468 | 2110419912 | 731062034 | 620665 | SRX10049114 | SRS8212341 | SRA1056877 | GEO | Anming Meng Lab, School of Life Science, Tsinghua University | 1 | 0.68353 | 0.17141 | 0.80338 | 0.63249 | 150 | B | usable mapping rate | illumina | novaseq_era | 5prime | size_fractionation | nebnext | bulk | unknown | unknown | China | 2021-02-08 | Zygote | Embryo | Embryo Imprecise | All anatomical structures |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;