rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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.,,,,,CD1,,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,,,,,,,,,microRNA seq of Danio rerio: Experiment group,BXP 1,BXP 1,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,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,,,,191280900,189440771,247005615,188686493,85256,SRX27004210,SRS23468967,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,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.,,,,,Control3,,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,,,,,,,,,microRNA seq of Danio rerio: Control group,Control 3,Control 3,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,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,,,,151053320,152811933,203340354,155283230,71186,SRX27004209,SRS23468966,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,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.,,,,,Control2,,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,,,,,,,,,microRNA seq of Danio rerio: Control group,Control 2,Control 2,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,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,,,,149869576,151844056,195830503,151241215,70769,SRX27004208,SRS23468963,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,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.,,,,,Control1,,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,,,,,,,,,microRNA seq of Danio rerio: Control group,Control 1,Control 1,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,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,,,,193253330,196900031,252690178,192797500,246462,SRX27004207,SRS23468962,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,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.,,,,,CD3,,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,,,,,,,,,microRNA seq of Danio rerio: Experiment group,BXP 3,BXP 3,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,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,,,,152349522,156353407,196379918,150985088,71392,SRX27004202,SRS23468965,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,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.,,,,,CD2,,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,,,,,,,,,microRNA seq of Danio rerio: Experiment group,BXP 2,BXP 2,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,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,,,,151820167,153674905,190467723,148402934,69098,SRX27004201,SRS23468964,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
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.,,,,WT Danio rerio,tRNAseq000 WT,,breed:not collected|age:5 day|sex:not collected|tissue:whole|phenotype:normal morphology|BioSampleModel:Model organism or animal,,,,,,,,,tRNA sequencing WT,tRNA sequencing WT,WT,1,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP056603,,,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,,,478698865,376122807,338649726,395185202,56,SRX970023,SRS885229,SRA248889,University of Iowa|Stephen A. Wynn Institute for Vision Research,University of Iowa,1,3e-05,,0.0,,0.99989,,0.4,,151,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,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.,,,,TRNT1 KD,tRNAseq000 MO,,breed:not collected|age:5 day|sex:not collected|tissue:whole|phenotype:normal morphology|BioSampleModel:Model organism or animal,,,,,,,,,tRNA sequencing of TRNT1 KD,tRNA sequencing of TRNT1 KD,1,1,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP056603,,,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,,,399052503,312898077,288848586,354720282,15,SRX970012,SRS885221,SRA248889,University of Iowa|Stephen A. Wynn Institute for Vision Research,University of Iowa,1,0.00012,,0.0,,0.99965,,0.78947,,151,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United States,2015-08-09,Larval,Larval,Undetermined,Undetermined