{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"RANDOM\", experiment.platform = \"ILLUMINA\" and tissue_curation_coarse = \"Undetermined\"", "rows": [[41, "DRR408245", "DRX393851", "DRS407176", "DRP012042", "PRJDB14275", "Zebrafish EN/ENCDC RNA seq", "DRP012042", "Transcriptome Analysis", "A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 3", "zebrafish EN replicate 3", "SAMD00529465", null, "sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529465", "DRX393851", "190326ENvsNC N703 5day;EntericNeuron;rep3", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "NextSeq 550", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012042", "NextSeq 550 paired end sequencing of SAMD00529465", null, null, null, 3729799291.0, 23985772.0, "DRR408245", "0:77.75 1:77.75", "A:978752781;C:879988139;G:903976580;T:962122970;N:4958821", 77, 77, null, null, 978752781, 879988139, 903976580, 962122970, 4958821, "DRX393851", "DRS407176", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [42, "DRR408244", "DRX393850", "DRS407175", "DRP012042", "PRJDB14275", "Zebrafish EN/ENCDC RNA seq", "DRP012042", "Transcriptome Analysis", "A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 2", "zebrafish EN replicate 2", "SAMD00529464", null, "sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529464", "DRX393850", "190326ENvsNC N702 5day;EntericNeuron;rep2", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "NextSeq 550", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012042", "NextSeq 550 paired end sequencing of SAMD00529464", null, null, null, 3315994810.0, 21477755.0, "DRR408244", "0:77.19 1:77.20", "A:873970427;C:778042505;G:798459853;T:859611841;N:5910184", 77, 77, null, null, 873970427, 778042505, 798459853, 859611841, 5910184, "DRX393850", "DRS407175", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [43, "DRR408243", "DRX393849", "DRS407174", "DRP012042", "PRJDB14275", "Zebrafish EN/ENCDC RNA seq", "DRP012042", "Transcriptome Analysis", "A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.", null, null, "zebrafish 5 day GFP positive enteric neurons replicate 1", "zebrafish EN replicate 1", "SAMD00529463", null, "sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp", null, null, null, null, null, null, null, null, "NextSeq 550 paired end sequencing of SAMD00529463", "DRX393849", "190326ENvsNC N701 5day;EntericNeuron;rep1", "1", "1", null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "NextSeq 550", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "DRP012042", "NextSeq 550 paired end sequencing of SAMD00529463", null, null, null, 2999501518.0, 19455440.0, "DRR408243", "0:77.08 1:77.09", "A:788053541;C:705895776;G:724185148;T:775760738;N:5606315", 77, 77, null, null, 788053541, 705895776, 724185148, 775760738, 5606315, "DRX393849", "DRS407174", "DRA014886", "NIBB|NIBB core research facilities, National Institute for Basic Biology", "University of Hyogo", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Japan", "2024-09-22", "Undetermined", "Larval", "Undetermined", "Undetermined"], [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"], [48909, "SRR7615221", "SRX4479802", "SRS3604791", "SRP155604", "PRJNA479418", "Lariat intronic RNAs in the cytoplasm of vertebrate cells", "PRJNA479418", "Other", "Introns are non coding DNA sequences interspersed among the coding sequences of genes. Shortly post transcription  the intronic sequences are spliced out of the primary RNA transcript as lariat RNAs circular molecules with a short tail. Most of these lariats are destroyed within minutes in the cell nucleus. We report here that many such intronic RNAs are  in fact  exported to the cytoplasm  where they remain as stable circular molecules. These cytoplasmic introns are derived from hundreds of different genes of widely different functions. We find them in cells of human  mouse  chicken  frog  and zebrafish. The widespread occurrence of so many stable lariat RNAs in the cytoplasm suggests that they play some as yet unexpected role in cell metabolism.", null, null, null, null, "zebrafish eggs plusRNaseR", null, "strain:AB strain|dev stage:Germline|sex:female|tissue:Egg|treatment:n1|rna treatment:rRNA depletion and RNase R|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Zebrafish egg plus RNaseR", "Zf pR", "Zf pR", "rRNA depletion ribozero fellowed by TruSeq Stranded Total RNA illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP155604", null, null, "150112_Zebrafish_egg_plusRNaseR_50bp.fastq", "fastq", 1453087900.0, 29061758.0, "150112 Zebrafish egg plusRNaseR 50bp.fastq", "0:50", "A:316388483;C:426462939;G:363020331;T:347178488;N:37659", 50, null, null, null, 316388483, 426462939, 363020331, 347178488, 37659, "SRX4479802", "SRS3604791", "SRA746415", "Carnegie Institution for Science|Department of Embryology", "Carnegie Institution for Science", 1, 0.83263, null, 0.31979, null, 0.81592, null, 0.51542, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2018-07-28", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [48910, "SRR7615223", "SRX4479800", "SRS3604789", "SRP155604", "PRJNA479418", "Lariat intronic RNAs in the cytoplasm of vertebrate cells", "PRJNA479418", "Other", "Introns are non coding DNA sequences interspersed among the coding sequences of genes. Shortly post transcription  the intronic sequences are spliced out of the primary RNA transcript as lariat RNAs circular molecules with a short tail. Most of these lariats are destroyed within minutes in the cell nucleus. We report here that many such intronic RNAs are  in fact  exported to the cytoplasm  where they remain as stable circular molecules. These cytoplasmic introns are derived from hundreds of different genes of widely different functions. We find them in cells of human  mouse  chicken  frog  and zebrafish. The widespread occurrence of so many stable lariat RNAs in the cytoplasm suggests that they play some as yet unexpected role in cell metabolism.", null, null, null, null, "zebrafish eggs minusRNaseR", null, "strain:AB strain|dev stage:Germline|sex:female|tissue:Egg|treatment:n1|rna treatment:rRNA depletion|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Zebrafish egg minus RNaseR", "Zf mR", "Zf mR", "rRNA depletion ribozero fellowed by TruSeq Stranded Total RNA illumina", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP155604", null, null, "150112_Zebrafish_egg_minusRNaseR_50bp.fastq", "fastq", 2440809700.0, 48816194.0, "150112 Zebrafish egg minusRNaseR 50bp.fastq", "0:50", "A:588729472;C:623954878;G:556893764;T:671166713;N:64873", 50, null, null, null, 588729472, 623954878, 556893764, 671166713, 64873, "SRX4479800", "SRS3604789", "SRA746415", "Carnegie Institution for Science|Department of Embryology", "Carnegie Institution for Science", 1, 0.92096, null, 0.07705, null, 0.72861, null, 0.50081, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "ribozero", "bulk", "unknown", "unknown", null, "United States", "2018-07-28", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [60827, "SRR12536650", "SRX9026395", "SRS7277845", "SRP279118", "PRJNA659812", "Defects in the zonule in loxl1 knock out zebrafish", "PRJNA659812", "Other", "Purposes: To investigate the roles of lysyl oxidase like 1 loxl1 in zebrafish eye development and the potency of loxl1 knock out in mimicking the ocular manifestations of Exfoliation Syndrome.Methods: CRISPR/Cas9 technology was used to generate a frameshift deletion shifting code deletion in zebrafish loxl1. Expression profiles and ocular manifestations of wildtype WT  heterozygous mutant loxl1+/  and homozygous mutant loxl1 /  zebrafish were analyzed in a range of developmental stages from whole zebrafish larvae to dissected adult zebrafish eyes using western blot  immunofluorescence  real time RT PCR and transcriptome resequencing analysis RNA seq. Scanning electron microscopy SEM was used to study the zonular structure and corneal fiber organization of adult zebrafish eyes.Results: The loxl1 mutation caused zonular bundling disorders in juvenile zebrafish and accumulation of pearl like particles adhering to the adult zebrafish zonule. SEM revealed more numerous particles  but of smaller size in loxl1 /  zebrafish compared with those in loxl1+/   although light microscopy showed that the overall staining of the zonule in loxl1+/  was darker than that in loxl1 / . Expression of transforming growth factor b tgfb pathway related proteins changed at the protein level  but not the mRNA level. The phosphorylated Smad3 pSmad3 level was locally activated in the iris side trabecular meshwork and ciliary body of loxl1 /  adults.Conclusions: Defects in the zonular bundling found in loxl1 knock out zebrafish indicate dysplasia. Compared with adult loxl1+/  zebrafish  more numerous but smaller pearl like particles adhered to the zonule in adult loxl1 /  zebrafish. loxl1 /  zebrafish is a promising animal model of XFS zonular pathology.", null, null, null, null, "3 larvae loxl1 / ", null, "strain:AB|dev stage:7 dpf|sex:male|tissue:larvae|source material id:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "7dpf ko", "loxl1 zebrafish3", "loxl1 zebrafish3", "materials and methods", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP279118", null, null, "larvae_ko_20190920NA_ATAGCGAC_S101_L001_R1_001.fastq.gz larvae_ko_20190920NA_ATAGCGAC_S101_L001_R2_001.fastq.gz", "fastq fastq", 8570236936.0, 28378268.0, "larvae ko 20190920NA ATAGCGAC S101 L001 R1 001.fastq.gz", "0:151 1:151", "A:2291363400;C:1985315062;G:2023225375;T:2269717794;N:615305", 151, 151, null, null, 2291363400, 1985315062, 2023225375, 2269717794, 615305, "SRX9026395", "SRS7277845", "SRA1118248", "Eye and ENT Hospital of Fudan University|Ophthalmology and Vision Science", "Eye and ENT Hospital of Fudan University", 2, 0.95641, 0.95018, 0.09997, 0.0968, 0.68436, 0.68627, 0.45419, 0.45754, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-08-27", "Larval", "Larval", "Undetermined", "Undetermined"], [60828, "SRR12536651", "SRX9026394", "SRS7277844", "SRP279118", "PRJNA659812", "Defects in the zonule in loxl1 knock out zebrafish", "PRJNA659812", "Other", "Purposes: To investigate the roles of lysyl oxidase like 1 loxl1 in zebrafish eye development and the potency of loxl1 knock out in mimicking the ocular manifestations of Exfoliation Syndrome.Methods: CRISPR/Cas9 technology was used to generate a frameshift deletion shifting code deletion in zebrafish loxl1. Expression profiles and ocular manifestations of wildtype WT  heterozygous mutant loxl1+/  and homozygous mutant loxl1 /  zebrafish were analyzed in a range of developmental stages from whole zebrafish larvae to dissected adult zebrafish eyes using western blot  immunofluorescence  real time RT PCR and transcriptome resequencing analysis RNA seq. Scanning electron microscopy SEM was used to study the zonular structure and corneal fiber organization of adult zebrafish eyes.Results: The loxl1 mutation caused zonular bundling disorders in juvenile zebrafish and accumulation of pearl like particles adhering to the adult zebrafish zonule. SEM revealed more numerous particles  but of smaller size in loxl1 /  zebrafish compared with those in loxl1+/   although light microscopy showed that the overall staining of the zonule in loxl1+/  was darker than that in loxl1 / . Expression of transforming growth factor b tgfb pathway related proteins changed at the protein level  but not the mRNA level. The phosphorylated Smad3 pSmad3 level was locally activated in the iris side trabecular meshwork and ciliary body of loxl1 /  adults.Conclusions: Defects in the zonular bundling found in loxl1 knock out zebrafish indicate dysplasia. Compared with adult loxl1+/  zebrafish  more numerous but smaller pearl like particles adhered to the zonule in adult loxl1 /  zebrafish. loxl1 /  zebrafish is a promising animal model of XFS zonular pathology.", null, null, null, null, "2 larvae loxl1+/ ", null, "strain:AB|dev stage:7 dpf|sex:male|tissue:larvae|source material id:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "7dpf het", "loxl1 zebrafish2", "loxl1 zebrafish2", "materials and methods", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP279118", null, null, "larvae_het_20190930N_CGGATTGC_S300_L003_R1_001.fastq.gz larvae_het_20190930N_CGGATTGC_S300_L003_R2_001.fastq.gz", "fastq fastq", 5856779318.0, 19393309.0, "larvae het 20190930N CGGATTGC S300 L003 R1 001.fastq.gz", "0:151 1:151", "A:1552921599;C:1369101147;G:1376867518;T:1557750473;N:138581", 151, 151, null, null, 1552921599, 1369101147, 1376867518, 1557750473, 138581, "SRX9026394", "SRS7277844", "SRA1118248", "Eye and ENT Hospital of Fudan University|Ophthalmology and Vision Science", "Eye and ENT Hospital of Fudan University", 2, 0.95845, 0.95108, 0.0757, 0.07156, 0.6551, 0.65644, 0.47472, 0.47519, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-08-27", "Larval", "Larval", "Undetermined", "Undetermined"], [60829, "SRR12536652", "SRX9026393", "SRS7277843", "SRP279118", "PRJNA659812", "Defects in the zonule in loxl1 knock out zebrafish", "PRJNA659812", "Other", "Purposes: To investigate the roles of lysyl oxidase like 1 loxl1 in zebrafish eye development and the potency of loxl1 knock out in mimicking the ocular manifestations of Exfoliation Syndrome.Methods: CRISPR/Cas9 technology was used to generate a frameshift deletion shifting code deletion in zebrafish loxl1. Expression profiles and ocular manifestations of wildtype WT  heterozygous mutant loxl1+/  and homozygous mutant loxl1 /  zebrafish were analyzed in a range of developmental stages from whole zebrafish larvae to dissected adult zebrafish eyes using western blot  immunofluorescence  real time RT PCR and transcriptome resequencing analysis RNA seq. Scanning electron microscopy SEM was used to study the zonular structure and corneal fiber organization of adult zebrafish eyes.Results: The loxl1 mutation caused zonular bundling disorders in juvenile zebrafish and accumulation of pearl like particles adhering to the adult zebrafish zonule. SEM revealed more numerous particles  but of smaller size in loxl1 /  zebrafish compared with those in loxl1+/   although light microscopy showed that the overall staining of the zonule in loxl1+/  was darker than that in loxl1 / . Expression of transforming growth factor b tgfb pathway related proteins changed at the protein level  but not the mRNA level. The phosphorylated Smad3 pSmad3 level was locally activated in the iris side trabecular meshwork and ciliary body of loxl1 /  adults.Conclusions: Defects in the zonular bundling found in loxl1 knock out zebrafish indicate dysplasia. Compared with adult loxl1+/  zebrafish  more numerous but smaller pearl like particles adhered to the zonule in adult loxl1 /  zebrafish. loxl1 /  zebrafish is a promising animal model of XFS zonular pathology.", null, null, null, null, "1 larvae wildtype", null, "strain:AB|dev stage:7 dpf|sex:male|tissue:larvae|source material id:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "7dpf wt", "loxl1 zebrafish1", "loxl1 zebrafish1", "materials and methods", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP279118", null, null, "larvae_AB_20190930N_CGACACAC_S299_L003_R1_001.fastq.gz larvae_AB_20190930N_CGACACAC_S299_L003_R2_001.fastq.gz", "fastq fastq", 6190673236.0, 20498918.0, "larvae AB 20190930N CGACACAC S299 L003 R1 001.fastq.gz", "0:151 1:151", "A:1650586924;C:1439612857;G:1445758759;T:1654565514;N:149182", 151, 151, null, null, 1650586924, 1439612857, 1445758759, 1654565514, 149182, "SRX9026393", "SRS7277843", "SRA1118248", "Eye and ENT Hospital of Fudan University|Ophthalmology and Vision Science", "Eye and ENT Hospital of Fudan University", 2, 0.95643, 0.95006, 0.08333, 0.07911, 0.64747, 0.649, 0.47878, 0.4805, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-08-27", "Larval", "Larval", "Undetermined", "Undetermined"], [65842, "SRR15646741", "SRX11943797", "SRS9954428", "SRP334349", "PRJNA758122", "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "PRJNA758122", "Other", "To explore Pathological Features of Klebsiella pneumonia", null, null, null, null, "KP C", null, "isolate:Fresh tea leaves|age:13 day post budding|sex:neuter|tissue:zebrafish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "KP C", "KP C", "zebrafish larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334349", null, null, "KP-C_1.fq.gz KP-C_2.fq.gz", "fastq fastq", 15119561100.0, 50398537.0, "KP C 1.fq.gz", "0:150 1:150", "A:4199977746;C:3373965332;G:3340795484;T:4199564734;N:5257804", 150, 150, null, null, 4199977746, 3373965332, 3340795484, 4199564734, 5257804, "SRX11943797", "SRS9954428", "SRA1284498", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University|Department of Laboratory Medicine", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University", 2, 0.94575, 0.93866, 0.11928, 0.11816, 0.6578, 0.66188, 0.46916, 0.46929, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Larval", "Larval", "Undetermined", "Undetermined"], [65843, "SRR15646742", "SRX11943796", "SRS9954427", "SRP334349", "PRJNA758122", "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "PRJNA758122", "Other", "To explore Pathological Features of Klebsiella pneumonia", null, null, null, null, "KP B", null, "isolate:Fresh tea leaves|age:12 day post budding|sex:neuter|tissue:zebrafish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "KP B", "KP B", "zebrafish larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334349", null, null, "KP-B_1.fq.gz KP-B_2.fq.gz", "fastq fastq", 15136008000.0, 50453360.0, "KP B 1.fq.gz", "0:150 1:150", "A:4207311279;C:3372650612;G:3329889166;T:4220543122;N:5613821", 150, 150, null, null, 4207311279, 3372650612, 3329889166, 4220543122, 5613821, "SRX11943796", "SRS9954427", "SRA1284498", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University|Department of Laboratory Medicine", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University", 2, 0.94501, 0.93639, 0.13097, 0.12966, 0.66011, 0.66324, 0.47057, 0.46916, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Larval", "Larval", "Undetermined", "Undetermined"], [65844, "SRR15646743", "SRX11943795", "SRS9954426", "SRP334349", "PRJNA758122", "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "PRJNA758122", "Other", "To explore Pathological Features of Klebsiella pneumonia", null, null, null, null, "KP A", null, "isolate:Fresh tea leaves|age:11 day post budding|sex:neuter|tissue:zebrafish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "KP A", "KP A", "zebrafish larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334349", null, null, "KP-A_1.fq.gz KP-A_2.fq.gz", "fastq fastq", 15101107800.0, 50337026.0, "KP A 1.fq.gz", "0:150 1:150", "A:4230648761;C:3333194101;G:3286438045;T:4245689507;N:5137386", 150, 150, null, null, 4230648761, 3333194101, 3286438045, 4245689507, 5137386, "SRX11943795", "SRS9954426", "SRA1284498", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University|Department of Laboratory Medicine", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University", 2, 0.94262, 0.93382, 0.12796, 0.12632, 0.66044, 0.66413, 0.46665, 0.46809, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Larval", "Larval", "Undetermined", "Undetermined"], [65845, "SRR15646744", "SRX11943794", "SRS9954425", "SRP334349", "PRJNA758122", "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "PRJNA758122", "Other", "To explore Pathological Features of Klebsiella pneumonia", null, null, null, null, "Control", null, "isolate:Fresh tea leaves|age:10 day post budding|sex:neuter|tissue:zebrafish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "Control", "Control", "zebrafish larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334349", null, null, "Control_1.fq.gz Control_2.fq.gz", "fastq fastq", 15162870900.0, 50542903.0, "Control 1.fq.gz", "0:150 1:150", "A:4201431091;C:3391463446;G:3336650829;T:4228305627;N:5019907", 150, 150, null, null, 4201431091, 3391463446, 3336650829, 4228305627, 5019907, "SRX11943794", "SRS9954425", "SRA1284498", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University|Department of Laboratory Medicine", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University", 2, 0.94591, 0.93718, 0.12576, 0.12432, 0.65303, 0.65764, 0.47398, 0.4772, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Larval", "Larval", "Undetermined", "Undetermined"], [65846, "SRR15646745", "SRX11943793", "SRS9954424", "SRP334349", "PRJNA758122", "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "PRJNA758122", "Other", "To explore Pathological Features of Klebsiella pneumonia", null, null, null, null, "WT8dpf", null, "isolate:Fresh tea leaves|age:19 day post budding|sex:neuter|tissue:zebrafish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "WT8dpf", "WT8dpf", "zebrafish larvae", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP334349", null, null, "WT8dpf_2.fq.gz WT8dpf_1.fq.gz", "fastq fastq", 14960604900.0, 49868683.0, "WT8dpf 1.fq.gz", "0:150 1:150", "A:4116429948;C:3366634041;G:3311720522;T:4161497787;N:4322602", 150, 150, null, null, 4116429948, 3366634041, 3311720522, 4161497787, 4322602, "SRX11943793", "SRS9954424", "SRA1284498", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University|Department of Laboratory Medicine", "The Affiliated Wuxi No. 2 Peoples Hospital of Nanjing Medical University", 2, 0.94296, 0.93434, 0.13087, 0.12937, 0.66093, 0.66458, 0.4602, 0.46456, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-08-27", "Larval", "Larval", "Undetermined", "Undetermined"], [65847, "SRR15646746", "SRX11943792", "SRS9954423", "SRP334349", "PRJNA758122", "Use of Zebrafish Larvae as Host Model to Evaluate Different Virulence Traits and Pathological Features of Klebsiella pneumonia", "PRJNA758122", "Other", "To explore Pathological Features of Klebsiella pneumonia", null, null, null, null, "WT5dpf", null, "isolate:Fresh tea leaves|age:18 day post budding|sex:neuter|tissue:zebrafish|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Use of Zebrafish Larvae as Host Model to 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