{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Larval\" and experiment.library_strategy = \"miRNA-Seq\"", "rows": [[32541, "SRR29303120", "SRX24820197", "SRS21534299", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L6H 1 miRNA", null, "breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 10|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L6H 1", "L6H 1", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "L6H_1.fq.gz", "fastq", 619966455.0, 12156205.0, "L6H 1.fq.gz", "0:51", 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10 05|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L1H 2", "L1H 2", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "L1H_2.fq.gz", "fastq", 541697163.0, 10621513.0, "L1H 2.fq.gz", "0:51", "A:126751483;C:135818134;G:141122995;T:137953543;N:51008", 51, null, null, null, 126751483, 135818134, 141122995, 137953543, 51008, "SRX24820192", "SRS21534294", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.33438, null, 0.08101, null, 0.98238, null, 0.53337, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32547, "SRR29303126", "SRX24820191", "SRS21534293", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L1H 1 miRNA", null, "breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 04|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L1H 1", "L1H 1", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "L1H_1.fq.gz", "fastq", 930096282.0, 18237182.0, "L1H 1.fq.gz", "0:51", "A:212568445;C:243497911;G:260145458;T:213851032;N:33436", 51, null, null, null, 212568445, 243497911, 260145458, 213851032, 33436, "SRX24820191", "SRS21534293", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.64143, null, 0.02683, null, 0.98683, null, 0.5342, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32548, "SRR29303127", "SRX24820190", "SRS21534292", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "DD 3 miRNA", null, "breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 03|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "DD 3", "DD 3", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "DD_3.fq.gz", "fastq", 667459389.0, 13087439.0, "DD 3.fq.gz", "0:51", 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null, null, "miRNA seq of zebrafish larvae", "L6H 3", "L6H 3", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "L6H_3.fq.gz", "fastq", 551181072.0, 10807472.0, "L6H 3.fq.gz", "0:51", "A:126813056;C:141881980;G:147676363;T:134665008;N:144665", 51, null, null, null, 126813056, 141881980, 147676363, 134665008, 144665, "SRX24820189", "SRS21534291", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.09301, null, 0.01507, null, 0.99042, null, 0.54323, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32550, "SRR29303129", "SRX24820188", "SRS21534290", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "L6H 2 miRNA", null, "breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 11|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "L6H 2", "L6H 2", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "L6H_2.fq.gz", "fastq", 571762632.0, 11211032.0, "L6H 2.fq.gz", "0:51", "A:138521192;C:148068464;G:150615597;T:134408189;N:149190", 51, null, null, null, 138521192, 148068464, 150615597, 134408189, 149190, "SRX24820188", "SRS21534290", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.01523, null, 0.00336, null, 0.9933, null, 0.57685, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32551, "SRR29303130", "SRX24820187", "SRS21534289", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "DD 2 miRNA", null, "breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 02|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "DD 2", "DD 2", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "DD_2.fq.gz", "fastq", 706940937.0, 13861587.0, "DD 2.fq.gz", "0:51", "A:162899595;C:189209828;G:187422113;T:167222837;N:186564", 51, null, null, null, 162899595, 189209828, 187422113, 167222837, 186564, "SRX24820187", "SRS21534289", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.02266, null, 0.00566, null, 0.99334, null, 0.56959, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [32552, "SRR29303131", "SRX24820186", "SRS21534288", "SRP512097", "PRJNA1120592", "Light induce Zebrafish larvae", "PRJNA1120592", "Other", "Light induce Zebrafish larvae miRNA", null, null, null, null, "DD 1 miRNA", null, "breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 01|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA seq of zebrafish larvae", "DD 1", "DD 1", "miRNA seq", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM PCR", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP512097", null, null, "DD_1.fq.gz", "fastq", 540332862.0, 10594762.0, "DD 1.fq.gz", "0:51", "A:127336994;C:143901414;G:142437491;T:126515166;N:141797", 51, null, null, null, 127336994, 143901414, 142437491, 126515166, 141797, "SRX24820186", "SRS21534288", "SRA1890590", "Lanzhou University|College of Life Science", "Lanzhou University", 1, 0.01404, null, 0.00313, null, 0.99484, null, 0.56573, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-06-06", "Larval", "Larval", "Trunk", "Surface Structure"], [34282, "SRR31640757", "SRX27004210", "SRS23468967", "SRP550004", "PRJNA1195374", "Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2", "PRJNA1195374", "Other", "Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.", null, null, null, null, "CD1", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "microRNA seq of Danio rerio: Experiment group", "BXP 1", "BXP 1", null, null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550004", null, null, "BXP_1.fq.gz", "fastq", 816499035.0, 16009785.0, "BXP 1.fq.gz", "0:51", "A:191280900;C:189440771;G:247005615;T:188686493;N:85256", 51, null, null, null, 191280900, 189440771, 247005615, 188686493, 85256, "SRX27004210", "SRS23468967", "SRA2029520", "Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine", "Heilongjiang University of Chinese Medicine", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-12-07", "Undetermined", "Larval", "Undetermined", "Undetermined"], [34283, "SRR31640758", "SRX27004209", "SRS23468966", "SRP550004", "PRJNA1195374", "Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2", "PRJNA1195374", "Other", "Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.", null, null, null, null, "Control3", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "microRNA seq of Danio rerio: Control group", "Control 3", "Control 3", null, null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550004", null, null, "Control_3.fq.gz", "fastq", 662560023.0, 12991373.0, "Control 3.fq.gz", "0:51", "A:151053320;C:152811933;G:203340354;T:155283230;N:71186", 51, null, null, null, 151053320, 152811933, 203340354, 155283230, 71186, "SRX27004209", "SRS23468966", "SRA2029520", "Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine", "Heilongjiang University of Chinese Medicine", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-12-07", "Undetermined", "Larval", "Undetermined", "Undetermined"], [34284, "SRR31640759", "SRX27004208", "SRS23468963", "SRP550004", "PRJNA1195374", "Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2", "PRJNA1195374", "Other", "Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.", null, null, null, null, "Control2", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "microRNA seq of Danio rerio: Control group", "Control 2", "Control 2", null, null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550004", null, null, "Control_2.fq.gz", "fastq", 648856119.0, 12722669.0, "Control 2.fq.gz", "0:51", "A:149869576;C:151844056;G:195830503;T:151241215;N:70769", 51, null, null, null, 149869576, 151844056, 195830503, 151241215, 70769, "SRX27004208", "SRS23468963", "SRA2029520", "Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine", "Heilongjiang University of Chinese Medicine", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-12-07", "Undetermined", "Larval", "Undetermined", "Undetermined"], [34285, "SRR31640760", "SRX27004207", "SRS23468962", "SRP550004", "PRJNA1195374", "Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2", "PRJNA1195374", "Other", "Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.", null, null, null, null, "Control1", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "microRNA seq of Danio rerio: Control group", "Control 1", "Control 1", null, null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550004", null, null, "Control_1.fq.gz", "fastq", 835887501.0, 16389951.0, "Control 1.fq.gz", "0:51", "A:193253330;C:196900031;G:252690178;T:192797500;N:246462", 51, null, null, null, 193253330, 196900031, 252690178, 192797500, 246462, "SRX27004207", "SRS23468962", "SRA2029520", "Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine", "Heilongjiang University of Chinese Medicine", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-12-07", "Undetermined", "Larval", "Undetermined", "Undetermined"], [34290, "SRR31640765", "SRX27004202", "SRS23468965", "SRP550004", "PRJNA1195374", "Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2", "PRJNA1195374", "Other", "Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.", null, null, null, null, "CD3", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "microRNA seq of Danio rerio: Experiment group", "BXP 3", "BXP 3", null, null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550004", null, null, "BXP_3.fq.gz", "fastq", 656139327.0, 12865477.0, "BXP 3.fq.gz", "0:51", "A:152349522;C:156353407;G:196379918;T:150985088;N:71392", 51, null, null, null, 152349522, 156353407, 196379918, 150985088, 71392, "SRX27004202", "SRS23468965", "SRA2029520", "Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine", "Heilongjiang University of Chinese Medicine", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-12-07", "Undetermined", "Larval", "Undetermined", "Undetermined"], [34291, "SRR31640766", "SRX27004201", "SRS23468964", "SRP550004", "PRJNA1195374", "Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2", "PRJNA1195374", "Other", "Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected treated with CD and evaluated for migration invasion malondialdehyde level superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression alleviate HT22 cell injury and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.", null, null, null, null, "CD2", null, "strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "microRNA seq of Danio rerio: Experiment group", "BXP 2", "BXP 2", null, null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP550004", null, null, "BXP_2.fq.gz", "fastq", 644434827.0, 12635977.0, "BXP 2.fq.gz", "0:51", "A:151820167;C:153674905;G:190467723;T:148402934;N:69098", 51, null, null, null, 151820167, 153674905, 190467723, 148402934, 69098, "SRX27004201", "SRS23468964", "SRA2029520", "Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine", "Heilongjiang University of Chinese Medicine", null, null, null, null, null, null, null, null, null, null, null, "T", null, "under 1.2% mapping rate", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-12-07", "Undetermined", "Larval", "Undetermined", "Undetermined"], [39617, "SRR1873563", "SRX915243", "SRS870231", "SRP056014", "PRJNA277780", "Identification of small non coding RNAs in zebrafish", "GSE66718", "Transcriptome Analysis", "MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.", null, "pubmed:26694924", null, "5dpf", "GSM1630507", null, "source name:5 dpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:5dpf", "5dpf", "Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005 19:1288 1293 and a miRNA expression profile using identical number of reads for each sample was generated. The number of reads between samples was normalized as indicated below: Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs sequences and respective raw counts post data processing for each sample.", "5 dpf embryos", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter \"Nelson's linker\" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37\u00b0C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37\u00b0C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.", "Wild type AB zebrafish strain was maintained at 28\u00baC on a 14 h light/10 h dark cycle.", "strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:5dpf", "GSM1630507", "GSM1630507: 5dpf; Danio rerio; miRNA Seq", "GSM1630507", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter \"Nelson's linker\" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37\u00b0C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37\u00b0C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.", "GEO Accession:GSM1630507", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "LS454", "454 GS FLX", null, "SRP056014", null, null, null, null, 168981.0, 3060.0, "GSM1630507 r1", "0:4 1:51.22", "A:51895;C:42870;G:40864;T:32741;N:611", 4, 51, null, null, 51895, 42870, 40864, 32741, 611, "SRX915243", "SRS870231", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 50, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "Portugal", "2015-03-09", "Larval", "Larval", "Trunk", "Surface Structure"], [39618, "SRR1873562", "SRX915242", "SRS870232", "SRP056014", "PRJNA277780", "Identification of small non coding RNAs in zebrafish", "GSE66718", "Transcriptome Analysis", "MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.", null, "pubmed:26694924", null, "96hpf", "GSM1630506", null, "source name:96 hpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:96hpf", "96hpf", "Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005 19:1288 1293 and a miRNA expression profile using identical number of reads for each sample was generated. The number of reads between samples was normalized as indicated below: Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs sequences and respective raw counts post data processing for each sample.", "96 hpf embryos", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter \"Nelson's linker\" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37\u00b0C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37\u00b0C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.", "Wild type AB zebrafish strain was maintained at 28\u00baC on a 14 h light/10 h dark cycle.", "strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:96hpf", "GSM1630506", "GSM1630506: 96hpf; Danio rerio; miRNA Seq", "GSM1630506", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter \"Nelson's linker\" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37\u00b0C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37\u00b0C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.", "GEO Accession:GSM1630506", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "LS454", "454 GS FLX", null, "SRP056014", null, null, null, null, 61235.0, 1109.0, "GSM1630506 r1", "0:4 1:51.22", "A:18594;C:15084;G:15091;T:12247;N:219", 4, 51, null, null, 18594, 15084, 15091, 12247, 219, "SRX915242", "SRS870232", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 52, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "Portugal", "2015-03-09", "Larval", "Larval", "Trunk", "Surface Structure"], [39619, "SRR1873561", "SRX915241", "SRS870233", "SRP056014", "PRJNA277780", "Identification of small non coding RNAs in zebrafish", "GSE66718", "Transcriptome Analysis", "MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.", null, "pubmed:26694924", null, "72hpf", "GSM1630505", null, "source name:72 hpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:72hpf", "72hpf", "Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005 19:1288 1293 and a miRNA expression profile using identical number of reads for each sample was generated. The number of reads between samples was normalized as indicated below: Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs sequences and respective raw counts post data processing for each sample.", "72 hpf embryos", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter \"Nelson's linker\" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37\u00b0C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37\u00b0C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.", "Wild type AB zebrafish strain was maintained at 28\u00baC on a 14 h light/10 h dark cycle.", "strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:72hpf", "GSM1630505", "GSM1630505: 72hpf; Danio rerio; miRNA Seq", "GSM1630505", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter \"Nelson's linker\" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37\u00b0C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37\u00b0C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing.", "GEO Accession:GSM1630505", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "LS454", "454 GS FLX", null, "SRP056014", null, null, null, null, 778415.0, 14183.0, "GSM1630505 r1", "0:4 1:50.88", "A:231211;C:186354;G:190297;T:169348;N:1205", 4, 50, null, null, 231211, 186354, 190297, 169348, 1205, "SRX915241", "SRS870233", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 48, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "Portugal", "2015-03-09", "Larval", "Larval", "Trunk", "Surface Structure"], [39627, "SRR1931774", "SRX970023", "SRS885229", "SRP056603", "PRJNA279522", "tRNA sequencing in Danio rerio", "PRJNA279522", "Other", "Small RNA sequencing to look for disruption of CCA nucleotidyltransferase activity post TRNT1 knockdown.", null, null, null, "WT Danio rerio", "tRNAseq000 WT", null, "breed:not collected|age:5 day|sex:not collected|tissue:whole|phenotype:normal morphology|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRNA sequencing WT", "tRNA sequencing WT", "WT", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", "1500Application ReadForward1", "SRP056603", null, null, "2-WT_S1_L001_R1_001.fastq.gz", "fastq", 1588656656.0, 10577741.0, "tRNA sequencing WT", "0:150.19 1:0", "A:478698865;C:376122807;G:338649726;T:395185202;N:56", 150, 0, null, null, 478698865, 376122807, 338649726, 395185202, 56, "SRX970023", "SRS885229", "SRA248889", "University of Iowa|Stephen A. Wynn Institute for Vision Research", "University of Iowa", 1, 3e-05, null, 0.0, null, 0.99989, null, 0.4, null, 151, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-08-09", "Larval", "Larval", "Undetermined", "Undetermined"], [39628, "SRR1931761", "SRX970012", "SRS885221", "SRP056603", "PRJNA279522", "tRNA sequencing in Danio rerio", "PRJNA279522", "Other", "Small RNA sequencing to look for disruption of CCA nucleotidyltransferase activity post TRNT1 knockdown.", null, null, null, "TRNT1 KD", "tRNAseq000 MO", null, "breed:not collected|age:5 day|sex:not collected|tissue:whole|phenotype:normal morphology|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRNA sequencing of TRNT1 KD", "tRNA sequencing of TRNT1 KD", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", "1500Application ReadForward1", "SRP056603", null, null, "3-mutant1-TRNT-M0_S2_L001_R1_001.fastq.gz", "fastq", 1355519463.0, 9025087.0, "tRNA sequencing of TRNT1 KD", "0:150.19 1:0", "A:399052503;C:312898077;G:288848586;T:354720282;N:15", 150, 0, null, null, 399052503, 312898077, 288848586, 354720282, 15, "SRX970012", "SRS885221", "SRA248889", "University of Iowa|Stephen A. Wynn Institute for Vision Research", "University of Iowa", 1, 0.00012, null, 0.0, null, 0.99965, null, 0.78947, null, 151, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2015-08-09", "Larval", "Larval", "Undetermined", "Undetermined"], [39671, "SRR2043046", "SRX1041307", "SRS947739", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 200nM sample3", "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3", "HBCD 200nM 3", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3", "Sample HBCD 200nM 3", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "360Application ReadForward1", "SRP058729", null, null, "Sample_HBCD_200nM-3.fastq.tar.gz", "fastq", 549695784.0, 16657448.0, "Sample HBCD 200nM 3", "0:33", "A:120885057;C:120386921;G:146939259;T:161323403;N:161144", 33, null, null, null, 120885057, 120386921, 146939259, 161323403, 161144, "SRX1041307", "SRS947739", "SRA269780", "MG", "Xiamen University", 1, 0.13819, null, 0.03714, null, 0.94968, null, 0.52004, null, 33, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-09-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39672, "SRR2043044", "SRX1041306", "SRS947738", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 200nM sample2", "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep2", "HBCD 200nM 2", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2", "Sample HBCD 200nM 2", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "360Application ReadForward1", "SRP058729", null, null, "Sample_HBCD_200nM-2.fastq.tar.gz", "fastq", 566585217.0, 17169249.0, "Sample HBCD 200nM 2", "0:33", "A:119904892;C:129504656;G:159539041;T:157545273;N:91355", 33, null, null, null, 119904892, 129504656, 159539041, 157545273, 91355, "SRX1041306", "SRS947738", "SRA269780", "MG", "Xiamen University", 1, 0.07072, null, 0.01837, null, 0.96246, null, 0.52439, null, 33, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39673, "SRR2043035", "SRX1041305", "SRS947737", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 200nM sample1", "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep1", "HBCD 200nM 1", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep1", "Sample HBCD 200nM 1", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "360Application ReadForward1", "SRP058729", null, null, "Sample_HBCD_200nM-1.fastq.tar.gz", "fastq", 636936228.0, 17692673.0, "Sample HBCD 200nM 1", "0:36", "A:138321201;C:126054708;G:184822056;T:187709777;N:28486", 36, null, null, null, 138321201, 126054708, 184822056, 187709777, 28486, "SRX1041305", "SRS947737", "SRA269780", "MG", "Xiamen University", 1, 0.04374, null, 0.0115, null, 0.97839, null, 0.29573, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-09-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39674, "SRR2043030", "SRX1041276", "SRS947712", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 2nM sample3", "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep3", "HBCD 2nM 3", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3", "Sample HBCD 2nM 3", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "360Application ReadForward1", "SRP058729", null, null, "Sample_HBCD_2nM-3.fastq.tar.gz", "fastq", 636936228.0, 17692673.0, "Sample HBCD 2nM 3", "0:36", "A:138321201;C:126054708;G:184822056;T:187709777;N:28486", 36, null, null, null, 138321201, 126054708, 184822056, 187709777, 28486, "SRX1041276", "SRS947712", "SRA269780", "MG", "Xiamen University", 1, 0.04377, null, 0.01174, null, 0.97812, null, 0.30675, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39675, "SRR2042999", "SRX1041271", "SRS947707", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 2nM sample2", "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2", "HBCD 2nM 2", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2", "Sample HBCD 2nM 2", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "360Application ReadForward1", "SRP058729", null, null, "Sample_HBCD_2nM-2.fastq.tar.gz", "fastq", 482176476.0, 13393791.0, "Sample HBCD 2nM 2", "0:36", "A:104565872;C:92998014;G:137403437;T:147164823;N:44330", 36, null, null, null, 104565872, 92998014, 137403437, 147164823, 44330, "SRX1041271", "SRS947707", "SRA269780", "MG", "Xiamen University", 1, 0.0759, null, 0.02077, null, 0.97025, null, 0.33489, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-09-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39676, "SRR2040574", "SRX1038901", "SRS945650", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 2nM sample1", "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep1", "HBCD 2nM 1", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep1", "Sample HBCD 2nM 1", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "360Application ReadForward1", "SRP058729", null, null, "Sample_HBCD_2nM-1.fastq.tar.gz", "fastq", 327925620.0, 9109045.0, "Sample HBCD 2nM 1", "0:36", "A:71167117;C:63917852;G:94874537;T:97936051;N:30063", 36, null, null, null, 71167117, 63917852, 94874537, 97936051, 30063, "SRX1038901", "SRS945650", "SRA269780", "MG", "Xiamen University", 1, 0.06484, null, 0.01622, null, 0.97459, null, 0.35746, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39677, "SRR2040573", "SRX1038898", "SRS945648", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. 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Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. 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Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", "zebrafish at normal developmental age of 72hpf in the control rep1", "control 1", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:control 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the control rep1", "Sample control 1", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "330Application ReadForward1", "SRP058729", null, null, "Sample_control-1.fastq.tar.gz", "fastq", 398024253.0, 12061341.0, "Sample control 1", "0:33", "A:90133666;C:86672655;G:103932053;T:117192591;N:93288", 33, null, null, null, 90133666, 86672655, 103932053, 117192591, 93288, "SRX1038887", "SRS945623", "SRA269780", "MG", "Xiamen University", 1, 0.08082, null, 0.02367, null, 0.96106, null, 0.52033, null, 33, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [40972, "SRR3498294", "SRX1756840", "SRS1433371", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 72hpf E2", "GSM2150819", null, "source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP", "NoEndo 72hpf E2", "Illumina Casava1.7 software used for basecalling. 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Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 72hpf E1", "GSM2150818", null, "source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP", "NoEndo 72hpf E1", "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 Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. 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Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 6dpf E1", "GSM2150817", null, "source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP", "NoEndo 6dpf E1", "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 Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. 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Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 72hpf E2", "GSM2150813", null, "source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP", "Endo 72hpf E2", "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 Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. 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Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 72hpf E1", "GSM2150812", null, "source name:Endothelial cell|developmental stage:72hpf|tissue:Endothelial|stain:GFP", "Endo 72hpf E1", "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 Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. 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Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 6dpf E1", "GSM2150811", null, "source name:Endothelial cell|developmental stage:6dpf|tissue:Endothelial|stain:GFP", "Endo 6dpf E1", "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 Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:6dpf|tissue:Endothelial|stain:GFP", "GSM2150811", "GSM2150811: Endo 6dpf E1; Danio rerio; miRNA Seq", "GSM2150811", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150811", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "Endo_6dpf_E1.fastq.gz", "fastq", 890474824.0, 11716774.0, "GSM2150811 r1", "0:76", "A:230419087;C:212029155;G:232306960;T:215672618;N:47004", 76, null, null, null, 230419087, 212029155, 232306960, 215672618, 47004, "SRX1756832", "SRS1433363", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 2e-05, null, 1e-05, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [41244, "SRR3953261", "SRX1977497", "SRS1585138", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "500 \u03bcg/l BDE47 treatment miRNA", "GSM2252184", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "500 \u03bcg/l BDE47 treatment miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252184", "GSM2252184: 500 \u03bcg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq", "GSM2252184", null, "1", "Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252184", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_500_1_filtered.fastq.gz", "fastq", 427211416.0, 18037304.0, "GSM2252184 r1", "0:23.68 1:0", "A:104654735;C:95575450;G:107353019;T:119612667;N:15545", 23, 0, null, null, 104654735, 95575450, 107353019, 119612667, 15545, "SRX1977497", "SRS1585138", "SRA444471", "GEO", "Tongji University", 1, 0.85356, null, 0.06282, null, 0.88609, null, 0.63407, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41245, "SRR3953260", "SRX1977496", "SRS1585141", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "5 \u03bcg/l BDE47 treatment miRNA", "GSM2252183", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "5 \u03bcg/l BDE47 treatment miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252183", "GSM2252183: 5 \u03bcg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq", "GSM2252183", null, "1", "Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252183", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_5_1_filtered.fastq.gz", "fastq", 450698842.0, 19202408.0, "GSM2252183 r1", "0:23.47 1:0", "A:112159775;C:101086362;G:111723361;T:125713845;N:15499", 23, 0, null, null, 112159775, 101086362, 111723361, 125713845, 15499, "SRX1977496", "SRS1585141", "SRA444471", "GEO", "Tongji University", 1, 0.84838, null, 0.06014, null, 0.88637, null, 0.6441, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41246, "SRR3953259", "SRX1977495", "SRS1585136", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "s DMSO vehicle miRNA", "GSM2252182", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "s DMSO vehicle miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252182", "GSM2252182: s DMSO vehicle miRNA; Danio rerio; miRNA Seq", "GSM2252182", null, "1", "Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252182", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_s_1_filtered.fq.gz", "fastq", 383701320.0, 16988819.0, "GSM2252182 r1", "0:22.59 1:0", "A:97700155;C:85144858;G:93319367;T:107531046;N:5894", 22, 0, null, null, 97700155, 85144858, 93319367, 107531046, 5894, "SRX1977495", "SRS1585136", "SRA444471", "GEO", "Tongji University", 1, 0.86023, null, 0.05501, null, 0.89534, null, 0.59715, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41247, "SRR3953258", "SRX1977494", "SRS1585137", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "c Wildtype miRNA", "GSM2252181", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "c Wildtype miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252181", "GSM2252181: c Wildtype miRNA; Danio rerio; miRNA Seq", "GSM2252181", null, "1", "Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252181", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_c_1_filtered.fastq.gz", "fastq", 413922462.0, 17365113.0, "GSM2252181 r1", "0:23.84 1:0", "A:102173642;C:93233248;G:103684592;T:114815345;N:15635", 23, 0, null, null, 102173642, 93233248, 103684592, 114815345, 15635, "SRX1977494", "SRS1585137", "SRA444471", "GEO", "Tongji University", 1, 0.85083, null, 0.06831, null, 0.88152, null, 0.63274, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41408, "SRR4423128", "SRX2245312", "SRS1745850", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 12 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:protruding mouth stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: protruding mouth stage72 hpf", "348 12", "348 12", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S12small.fastq", "fastq", 186817590.0, 3062463.0, "S12small.fastq", "0:61.00", "A:42863072;C:49941244;G:49513828;T:44499446;N:0", 61, null, null, null, 42863072, 49941244, 49513828, 44499446, 0, "SRX2245312", "SRS1745850", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.77668, null, 0.17381, null, 0.8915, null, 0.54189, null, 36, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [53033, "SRR9674344", "SRX6434730", "SRS5089289", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "rnpc3 WT 1 [miRNA seq]", "GSM3938561", null, "source name:Wildtype siblings of rnpc3 mutants repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of rnpc3 mutants|Stage:7 dpf|tissue:whole fish embryos", "rnpc3 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Wildtype siblings of rnpc3 mutants repeat 1", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of rnpc3 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938561", "GSM3938561: rnpc3 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938561", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938561", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Rpc3_1Ctrl.fastq.gz", "fastq", 1129597674.0, 22148974.0, "GSM3938561 r1", "0:51", "A:255811479;C:280511308;G:313965625;T:279284342;N:24920", 51, null, null, null, 255811479, 280511308, 313965625, 279284342, 24920, "SRX6434730", "SRS5089289", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00979, null, 0.00166, null, 0.99588, null, 0.63728, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53034, "SRR9674343", "SRX6434729", "SRS5089288", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 WT 1 [miRNA seq]", "GSM3938560", null, "source name:Wildtype siblings of smn1 mutants repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Wildtype siblings of smn1 mutants repeat 1", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938560", "GSM3938560: smn1 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938560", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938560", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_1Ctrl.fastq.gz", "fastq", 1381751976.0, 27093176.0, "GSM3938560 r1", "0:51", "A:323091185;C:348663819;G:380517013;T:329446099;N:33860", 51, null, null, null, 323091185, 348663819, 380517013, 329446099, 33860, "SRX6434729", "SRS5089288", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00712, null, 0.00142, null, 0.99642, null, 0.66315, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53035, "SRR9674342", "SRX6434728", "SRS5089287", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 WT 1 [miRNA seq]", "GSM3938559", null, "source name:Wildtype siblings of germin5 mutants repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of germin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Wildtype siblings of germin5 mutants repeat 1", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of germin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938559", "GSM3938559: gemin5 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938559", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938559", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_1Ctrl.fastq.gz", "fastq", 1347630171.0, 26424121.0, "GSM3938559 r1", "0:51", "A:307019777;C:335315873;G:378259746;T:327002846;N:31929", 51, null, null, null, 307019777, 335315873, 378259746, 327002846, 31929, "SRX6434728", "SRS5089287", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00723, null, 0.00127, null, 0.99582, null, 0.63934, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53036, "SRR9674341", "SRX6434727", "SRS5089286", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 3 [miRNA seq]", "GSM3938558", null, "source name:Homozygous smn1 mutants repeat 3|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous smn1 mutants repeat 3", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938558", "GSM3938558: smn1 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938558", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938558", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_3hom.fastq.gz", "fastq", 1269172638.0, 24885738.0, "GSM3938558 r1", "0:51", "A:290351922;C:320656517;G:354834895;T:303300306;N:28998", 51, null, null, null, 290351922, 320656517, 354834895, 303300306, 28998, "SRX6434727", "SRS5089286", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.0061, null, 0.00111, null, 0.9962, null, 0.5917, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53037, "SRR9674340", "SRX6434726", "SRS5089285", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 2 [miRNA seq]", "GSM3938557", null, "source name:Homozygous smn1 mutants repeat 2|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous smn1 mutants repeat 2", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938557", "GSM3938557: smn1 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938557", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938557", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_2hom.fastq.gz", "fastq", 1625802786.0, 31878486.0, "GSM3938557 r1", "0:51", "A:376836190;C:399950981;G:453572869;T:395403783;N:38963", 51, null, null, null, 376836190, 399950981, 453572869, 395403783, 38963, "SRX6434726", "SRS5089285", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00609, null, 0.00111, null, 0.99638, null, 0.63347, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53038, "SRR9674339", "SRX6434725", "SRS5089284", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 1 [miRNA seq]", "GSM3938556", null, "source name:Homozygous smn1 mutants repeat 1|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous smn1 mutants repeat 1", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938556", "GSM3938556: smn1 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938556", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938556", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_1hom.fastq.gz", "fastq", 1553527320.0, 30461320.0, "GSM3938556 r1", "0:51", "A:360279409;C:388795394;G:432335873;T:372080058;N:36586", 51, null, null, null, 360279409, 388795394, 432335873, 372080058, 36586, "SRX6434725", "SRS5089284", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00691, null, 0.00137, null, 0.99638, null, 0.61909, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53039, "SRR9674338", "SRX6434724", "SRS5089283", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 3 [miRNA seq]", "GSM3938555", null, "source name:Homozygous gemin5 mutants repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin5 mutants repeat 3", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938555", "GSM3938555: gemin5 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938555", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938555", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_3hom.fastq.gz", "fastq", 1162857936.0, 22801136.0, "GSM3938555 r1", "0:51", "A:267576310;C:282684680;G:327841913;T:284728561;N:26472", 51, null, null, null, 267576310, 282684680, 327841913, 284728561, 26472, "SRX6434724", "SRS5089283", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00597, null, 0.00114, null, 0.99618, null, 0.62386, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53040, "SRR9674337", "SRX6434723", "SRS5089282", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 2 [miRNA seq]", "GSM3938554", null, "source name:Homozygous gemin5 mutants repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin5 mutants repeat 2", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938554", "GSM3938554: gemin5 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938554", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938554", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_2hom.fastq.gz", "fastq", 1612392846.0, 31615546.0, "GSM3938554 r1", "0:51", "A:360634123;C:389619637;G:457463377;T:404638471;N:37238", 51, null, null, null, 360634123, 389619637, 457463377, 404638471, 37238, "SRX6434723", "SRS5089282", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00538, null, 0.00085, null, 0.99677, null, 0.62726, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53041, "SRR9674336", "SRX6434722", "SRS5089281", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 1 [miRNA seq]", "GSM3938553", null, "source name:Homozygous gemin5 mutants repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin5 mutants repeat 1", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938553", "GSM3938553: gemin5 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938553", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938553", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_1hom.fastq.gz", "fastq", 1734523362.0, 34010262.0, "GSM3938553 r1", "0:51", "A:400823854;C:428868747;G:484830308;T:419961177;N:39276", 51, null, null, null, 400823854, 428868747, 484830308, 419961177, 39276, "SRX6434722", "SRS5089281", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00485, null, 0.00098, null, 0.99636, null, 0.65384, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53042, "SRR9674335", "SRX6434721", "SRS5089280", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 3 [miRNA seq]", "GSM3938552", null, "source name:Homozygous gemin6 mutants repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin6 mutants repeat 3", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938552", "GSM3938552: gemin6 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938552", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938552", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_3.fastq.gz", "fastq", 3450343851.0, 67653801.0, "GSM3938552 r1", "0:51", "A:777873635;C:888116741;G:969513398;T:814785464;N:54613", 51, null, null, null, 777873635, 888116741, 969513398, 814785464, 54613, "SRX6434721", "SRS5089280", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01435, null, 0.00222, null, 0.99486, null, 0.71333, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53043, "SRR9674334", "SRX6434720", "SRS5089279", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 2 [miRNA seq]", "GSM3938551", null, "source name:Homozygous gemin6 mutants repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin6 mutants repeat 2", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938551", "GSM3938551: gemin6 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938551", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938551", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_2.fastq.gz", "fastq", 1586876781.0, 31115231.0, "GSM3938551 r1", "0:51", "A:373921059;C:393906222;G:435371208;T:383652895;N:25397", 51, null, null, null, 373921059, 393906222, 435371208, 383652895, 25397, "SRX6434720", "SRS5089279", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01456, null, 0.00199, null, 0.99488, null, 0.65884, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53044, "SRR9674333", "SRX6434719", "SRS5089278", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 1 [miRNA seq]", "GSM3938550", null, "source name:Homozygous gemin6 mutants repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin6 mutants repeat 1", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938550", "GSM3938550: gemin6 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938550", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938550", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_1.fastq.gz", "fastq", 1632291159.0, 32005709.0, "GSM3938550 r1", "0:51", "A:387703621;C:405051941;G:452019824;T:387489473;N:26300", 51, null, null, null, 387703621, 405051941, 452019824, 387489473, 26300, "SRX6434719", "SRS5089278", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01378, null, 0.00168, null, 0.99482, null, 0.66266, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53045, "SRR9674332", "SRX6434718", "SRS5089277", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 3 [miRNA seq]", "GSM3938549", null, "source name:Homozygous gemin4 mutants repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin4 mutants repeat 3", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938549", "GSM3938549: gemin4 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938549", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938549", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_3.fastq.gz", "fastq", 1079490837.0, 21166487.0, "GSM3938549 r1", "0:51", "A:247548301;C:266526237;G:295997407;T:269401582;N:17310", 51, null, null, null, 247548301, 266526237, 295997407, 269401582, 17310, "SRX6434718", "SRS5089277", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01616, null, 0.00211, null, 0.99486, null, 0.65494, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53046, "SRR9674331", "SRX6434717", "SRS5089276", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 2 [miRNA seq]", "GSM3938548", null, "source name:Homozygous gemin4 mutants repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin4 mutants repeat 2", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938548", "GSM3938548: gemin4 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938548", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938548", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_2.fastq.gz", "fastq", 6427925862.0, 126037762.0, "GSM3938548 r1", "0:51", "A:1491339645;C:1560095279;G:1804953332;T:1571434430;N:103176", 51, null, null, null, 1491339645, 1560095279, 1804953332, 1571434430, 103176, "SRX6434717", "SRS5089276", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01032, null, 0.00157, null, 0.99504, null, 0.70577, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53047, "SRR9674330", "SRX6434716", "SRS5089275", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 1 [miRNA seq]", "GSM3938547", null, "source name:Homozygous gemin4 mutants repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0 no softclip no spliced alignment rna strandness R new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression paired end forward prob 0.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output\" for mRNA Seq \"rsem calculate expression forward prob 1.0 alignments p 16 seed 987347 calc ci calc pme estimate rspd time no bam output fragment length mean 22 fragment length sd 10 seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output gene abundance", "Homozygous gemin4 mutants repeat 1", null, "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938547", "GSM3938547: gemin4 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938547", null, "1", "Embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample pool all libraries load pool on HiSeq 2500 run as indexed 50 base single end reads. embryos were placed in Qiazol and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938547", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_1.fastq.gz", "fastq", 3063591624.0, 60070424.0, "GSM3938547 r1", "0:51", "A:710248035;C:750319193;G:848095316;T:754879685;N:49395", 51, null, null, null, 710248035, 750319193, 848095316, 754879685, 49395, "SRX6434716", "SRS5089275", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01137, null, 0.00151, null, 0.99527, null, 0.69096, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [71643, "SRR21869762", "SRX17856938", "SRS15377982", "SRP402080", "PRJNA889683", "miRNA mRNA sequencing of zebrafish embryos", "PRJNA889683", "Other", "miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE", null, null, null, null, "BHEE H 3", null, "replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 15|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish larvae", "AT20221124", "AT20221124", "miRNA Seq of zebrafish larvae", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP402080", null, "loader:fastq load.py", "BHEE_H_3.fq.gz", "fastq", 533428889.0, 23211223.0, "BHEE H 3.fq.gz", "0:22.98", "A:120057830;C:104713991;G:142506271;T:166150296;N:501", 22, null, null, null, 120057830, 104713991, 142506271, 166150296, 501, "SRX17856938", "SRS15377982", "SRA1518395", "Jiangsu University|School of Environment and Safety Engineering", "Jiangsu University", 1, 0.79272, null, 0.10596, null, 0.92431, null, 0.52918, null, 22, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-10-12", "Larval", "Larval", "Trunk", "Surface Structure"], [71644, "SRR21869763", "SRX17856937", "SRS15377981", "SRP402080", "PRJNA889683", "miRNA mRNA sequencing of zebrafish embryos", "PRJNA889683", "Other", "miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE", null, null, null, null, "BHEE H 2", null, "replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 14|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish larvae", "AT20221123", "AT20221123", "miRNA Seq of zebrafish larvae", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP402080", null, "loader:fastq load.py", "BHEE_H_2.fq.gz", "fastq", 542237520.0, 23757627.0, "BHEE H 2.fq.gz", "0:22.82", "A:118608004;C:107602147;G:146341292;T:169685803;N:274", 22, null, null, null, 118608004, 107602147, 146341292, 169685803, 274, "SRX17856937", "SRS15377981", "SRA1518395", "Jiangsu University|School of Environment and Safety Engineering", "Jiangsu University", 1, 0.78829, null, 0.10064, null, 0.91346, null, 0.52625, null, 22, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-10-12", "Larval", "Larval", "Trunk", "Surface Structure"], [71645, "SRR21869764", "SRX17856936", "SRS15377980", "SRP402080", "PRJNA889683", "miRNA mRNA sequencing of zebrafish embryos", "PRJNA889683", "Other", "miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE", null, null, null, null, "BHEE H 1", null, 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[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 from run_metadata where \"devstage_curation_coarse\" = :p0 and \"experiment.library_strategy\" = :p1 order by rowid limit 101", "params": {"p0": "Larval", "p1": "miRNA-Seq"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq", "results": [{"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 73, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval", "selected": true}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 73, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": 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"toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&experiment.library_selection=RANDOM", "selected": false}, {"value": "cDNA", "label": "cDNA", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 73, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 54, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&experiment.platform=BGISEQ", "selected": false}, {"value": "LS454", "label": "LS454", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&experiment.platform=LS454", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&experiment.platform=ION_TORRENT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Larval", "label": "Larval", "count": 73, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=miRNA-Seq", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Larval", "label": "Larval", "count": 67, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&devstage_curation=Larval", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Surface Structure", "label": "Surface Structure", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&tissue_curation_coarse=Surface+Structure", "selected": false}, {"value": "All anatomical structures", 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"/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Trunk", "label": "Trunk", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&tissue_curation=Trunk", "selected": false}, {"value": "Whole Organism", "label": "Whole Organism", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&tissue_curation=Whole+Organism", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&tissue_curation=Undetermined", "selected": false}, {"value": "Endothelium", "label": "Endothelium", "count": 6, "toggle_url": 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"http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&technology=bulk", "selected": false}, {"value": "454", "label": "454", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Larval&experiment.library_strategy=miRNA-Seq&technology=454", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 117.87284699676093}