metadata: run_metadata: 8 rows where experiment.library_selection = "RANDOM", experiment.library_strategy = "miRNA-Seq" and technology = "unknown"

8 rows where experiment.library_selection = "RANDOM", experiment.library_strategy = "miRNA-Seq" and technology = "unknown"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
34282	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	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	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	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	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	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
51852	51852	SRR10358701	SRX7068102	SRS5584514	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	Model organism or animal sample from Danio rerio	miRNA WT SVCV	strain:Wild type\|age:6 month\|sex:pooled male and female\|tissue:kidney\|BioSampleModel:Model organism or animal	miRNA WT SVCV	miRNA WT SVCV	miRNA WT SVCV	Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.	miRNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP192333	WT-SVCV_1.fastq.gz	fastq	1316699181.0	25817631.0	WT SVCV 1.fastq.gz	0:51	A:276414308;C:338128957;G:380963712;T:321185951;N:6253	51	276414308	338128957	380963712	321185951	6253	SRX7068102	SRS5584514	SRA986546	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	1	0.12679	0.0134	0.9931	0.63608	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System
51853	51853	SRR10358540	SRX7067941	SRS5584353	SRP192333	PRJNA532380	Danio rerio SVCV infection	PRJNA532380	Other	Zebrafish Danio rerio is a model fish species for genomic developmental biomedical and pharmacological studies among other areas of inquiry. The existence of numerous zebrafish mutant lines is a wonderful tool to study diverse biological aspects in this teleost. This is the case of the zebrafish mutant line rag1. VDJ recombination carried out by the combined endonuclease activity of recombination activating gene 1 RAG1 and RAG2 assembles the vast diversity of immunoglobulins and T cell receptor TCR genes. A point mutation of the rag1 gene in zebrafish causes a premature stop codon in the rag1 catalytic domain; therefore this mutation presumably abolishes the adaptive immune system. The use of heterogygous rag1 zebrafish could help us to discover compensatory mechanisms in these animals which are partially deficient in Rag1 protein to effectively fisght an infection. We were interested in the long non coding RNAs lncRNAs differentially modulated in both lines post infection with spring viraemia of carp virus SVCV.For this we conducted Illumina sequencing of wild type WT and heterozygous rag1 mutant rag1+/ zebrafish at 24 h post the infection with SVCV. Kidney samples were taken from infected and uninfected fish for transcriptome sequencing. Transcriptome de novo aseembly generated 198 540 contigs among which 58 805 contigs represented coding sequences and 12 165 were putative lncRNA sequences Differential expression analysis of lncRNAs modulated post SVCV in both zebrafish lines helped us to to identify lncRNAs involved in the adaptive immune response.	Model organism or animal sample from Danio rerio	miRNA WT Control	strain:Wild type\|age:6 month\|sex:pooled male and female\|tissue:kidney\|BioSampleModel:Model organism or animal	miRNA WT Control	miRNA WT Control	miRNA WT Control	Total RNA was isolated from a pools containing kidney from uninfected adult zebrafish. RNA quality was confirmed in the Agilent 2100 Bioanalyzer Agilent Technologies Inc. Santa Clara CA USA according to the manufacturers instructions. miRNA library was constructed with the TruSeq small RNA Library Preparation Kit Illumina San Diego CA USA was used and sequencing was conducted with HiSeq 2500 technology.	miRNA-Seq	TRANSCRIPTOMIC	RANDOM	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP192333	WT-C_1.fastq.gz	fastq	1391330184.0	27280984.0	WT C 1.fastq.gz	0:51	A:252097427;C:365291036;G:426841004;T:347094254;N:6463	51	252097427	365291036	426841004	347094254	6463	SRX7067941	SRS5584353	SRA986495	IIM - CSIC\|Biotechnology and Aquaculture	IIM - CSIC	1	0.01783	0.00242	0.99411	0.61368	51	B	usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown	Spain	2019-10-29	Adult	Adult	Kidney	Renal System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;