metadata: run_metadata: 30 rows where devstage_curation_coarse = "Undetermined" and experiment.library

30 rows where devstage_curation_coarse = "Undetermined" and experiment.library_strategy = "miRNA-Seq"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	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.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.r2_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
28470	28470	SRR26253203	SRX21963295	SRS19039869	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA IFN4 2	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 22\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA IFND2	Small RNA IFND2	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	IFN4-2.deadaptor.fq.gz	fastq	278362309.0	11056139.0	IFN4 2.deadaptor.fq.gz	0:25.18	A:71944968;C:54562141;G:73333701;T:78511075;N:10424	25		71944968	54562141	73333701	78511075	10424	SRX21963295	SRS19039869	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.93133	0.07401	0.96181	0.74558	31	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28471	28471	SRR26253204	SRX21963294	SRS19039868	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA IFN4 1	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 21\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA IFND1	Small RNA IFND1	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	IFN4-1.deadaptor.fq.gz	fastq	289362334.0	11048590.0	IFN4 1.deadaptor.fq.gz	0:26.19	A:73933649;C:59386039;G:76847534;T:79184583;N:10529	26		73933649	59386039	76847534	79184583	10529	SRX21963294	SRS19039868	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.91683	0.07099	0.96132	0.64882	25	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28472	28472	SRR26253205	SRX21963293	SRS19039867	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA IFN1 4	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 20\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA IFNA4	Small RNA IFNA4	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	IFN1-4.deadaptor.fq.gz	fastq	270529395.0	11070360.0	IFN1 4.deadaptor.fq.gz	0:24.44	A:69759888;C:54924667;G:71358091;T:74470720;N:16029	24		69759888	54924667	71358091	74470720	16029	SRX21963293	SRS19039867	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.88469	0.06696	0.96664	0.74853	22	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28473	28473	SRR26253206	SRX21963292	SRS19039866	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA IFN1 3	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 19\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA IFNA3	Small RNA IFNA3	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	IFN1-3.deadaptor.fq.gz	fastq	353291957.0	11740560.0	IFN1 3.deadaptor.fq.gz	0:30.09	A:89026549;C:76490337;G:94719420;T:93036955;N:18696	30		89026549	76490337	94719420	93036955	18696	SRX21963292	SRS19039866	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.83151	0.07199	0.96471	0.71641	22	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28474	28474	SRR26253207	SRX21963291	SRS19039865	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA IFN1 2	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 18\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA IFNA2	Small RNA IFNA2	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	IFN1-2.deadaptor.fq.gz	fastq	257949577.0	11213774.0	IFN1 2.deadaptor.fq.gz	0:23.00	A:67371681;C:51128621;G:67605590;T:71826657;N:17028	23		67371681	51128621	67605590	71826657	17028	SRX21963291	SRS19039865	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.91396	0.06536	0.97197	0.76269	23	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28475	28475	SRR26253208	SRX21963290	SRS19039864	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA IFN1 1	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 17\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA IFNA1	Small RNA IFNA1	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	IFN1-1.deadaptor.fq.gz	fastq	329358383.0	11799176.0	IFN1 1.deadaptor.fq.gz	0:27.91	A:84093681;C:68961271;G:86502739;T:89779605;N:21087	27		84093681	68961271	86502739	89779605	21087	SRX21963290	SRS19039864	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.92116	0.07483	0.96796	0.75179	22	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28476	28476	SRR26253209	SRX21963289	SRS19039863	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA Control 4	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 16\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA C4	Small RNA C4	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	Control-4.deadaptor.fq.gz	fastq	251577736.0	10951659.0	Control 4.deadaptor.fq.gz	0:22.97	A:65382449;C:50041232;G:66038625;T:70106464;N:8966	22		65382449	50041232	66038625	70106464	8966	SRX21963289	SRS19039863	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.89744	0.06821	0.96607	0.63829	22	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28477	28477	SRR26253210	SRX21963288	SRS19039862	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA Control 3	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 15\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA C3	Small RNA C3	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	Control-3.deadaptor.fq.gz	fastq	252164979.0	11004167.0	Control 3.deadaptor.fq.gz	0:22.92	A:65850899;C:48466665;G:66708038;T:71130786;N:8591	22		65850899	48466665	66708038	71130786	8591	SRX21963288	SRS19039862	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.91567	0.06804	0.96278	0.75579	22	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28478	28478	SRR26253211	SRX21963287	SRS19039861	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA IFN4 4	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 24\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA IFND4	Small RNA IFND4	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	IFN4-4.deadaptor.fq.gz	fastq	291708053.0	11503883.0	IFN4 4.deadaptor.fq.gz	0:25.36	A:74079231;C:61368459;G:76898572;T:79351225;N:10566	25		74079231	61368459	76898572	79351225	10566	SRX21963287	SRS19039861	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.88888	0.0633	0.97305	0.74862	23	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28479	28479	SRR26253212	SRX21963286	SRS19039860	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA IFN4 3	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 23\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA IFND3	Small RNA IFND3	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	IFN4-3.deadaptor.fq.gz	fastq	349995495.0	11885662.0	IFN4 3.deadaptor.fq.gz	0:29.45	A:87443709;C:76373108;G:92741296;T:93425866;N:11516	29		87443709	76373108	92741296	93425866	11516	SRX21963286	SRS19039860	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.92619	0.06843	0.9709	0.74977	73	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28480	28480	SRR26253213	SRX21963285	SRS19039859	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA Control 2	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 14\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA C2	Small RNA C2	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	Control-2.deadaptor.fq.gz	fastq	254163676.0	10744164.0	Control 2.deadaptor.fq.gz	0:23.66	A:66003417;C:49309846;G:67463940;T:71377644;N:8829	23		66003417	49309846	67463940	71377644	8829	SRX21963285	SRS19039859	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.93068	0.06626	0.96441	0.7492	22	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
28481	28481	SRR26253214	SRX21963284	SRS19039858	SRP464138	PRJNA1022587	Danio rerio Raw sequence reads	PRJNA1022587	Whole Genome Sequencing	In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis of the small RNA.				Small RNA Control 1	strain:not collected\|age:not collected\|collection date:2023 08 20\|geo loc name:not collected\|sex:not collected\|tissue:not collected\|cell line:ZF4\|replicate:biological replicate 13\|BioSampleModel:Model organism or animal							Small RNAseq of zebrafish	Small RNA C1	Small RNA C1	small RNA seq of zebrafish			miRNA-Seq	TRANSCRIPTOMIC	PCR	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP464138	Control-1.deadaptor.fq.gz	fastq	267090429.0	11027241.0	Control 1.deadaptor.fq.gz	0:24.22	A:70162511;C:50705437;G:69872659;T:76339682;N:10140	24		70162511	50705437	69872659	76339682	10140	SRX21963284	SRS19039858	SRA1724093	Shanghai Ocean University\|College of Fisheries and Life Science	Shanghai Ocean University	1	0.93267	0.07189	0.96735	0.75447	21	B	usable mapping rate	illumina	novaseq_era	unknown	random_priming	unknown	bulk	unknown	unknown	China	2023-10-02	Undetermined	Undetermined	Cell Line	Cell Line
41420	41420	SRR4423116	SRX2245300	SRS1745858	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development		egg pools from three different mothers		Egg pool Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Egg\|sex:not applicable\|tissue:eggs\|BioSampleModel:Model organism or animal							miRNA Seq of Zebrafish: Egg pool	94 4	94 4	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	eggRID0094BC04smallZF.fastq	fastq	1392075126.0	18333358.0	eggRID0094BC04smallZF.fastq	0:75.93	A:323480979;C:386272283;G:377777594;T:304544270;N:0	75		323480979	386272283	377777594	304544270	0	SRX2245300	SRS1745858	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.68028	0.1685	0.89982	0.84521	83	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Undetermined	Undetermined	Undetermined	Undetermined
41424	41424	SRR4423112	SRX2245296	SRS1745858	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development		egg pools from three different mothers		Egg pool Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Egg\|sex:not applicable\|tissue:eggs\|BioSampleModel:Model organism or animal							miRNA Seq of Zebrafish: Egg pool	88 4	88 4	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	eggRID0088BC04smallZF.fastq	fastq	1063934659.0	14422089.0	eggRID0088BC04smallZF.fastq	0:73.77	A:248885216;C:293368431;G:288043879;T:233637133;N:0	73		248885216	293368431	288043879	233637133	0	SRX2245296	SRS1745858	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.66115	0.18031	0.89546	0.78468	72	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Undetermined	Undetermined	Undetermined	Undetermined
41426	41426	SRR4423110	SRX2245294	SRS1745858	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development		egg pools from three different mothers		Egg pool Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:Egg\|sex:not applicable\|tissue:eggs\|BioSampleModel:Model organism or animal							miRNA Seq of Zebrafish: Egg pool	93 4	93 4	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	eggRID0093BC04smallZF.fastq	fastq	1382951404.0	18190154.0	eggRID0093BC04smallZF.fastq	0:76.03	A:322536095;C:383176934;G:374216039;T:303022336;N:0	76		322536095	383176934	374216039	303022336	0	SRX2245294	SRS1745858	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.66399	0.17461	0.90134	0.82432	156	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Undetermined	Undetermined	Undetermined	Undetermined
50795	50795	SRR8305648	SRX5120118	SRS4121998	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.	pubmed:30597924	Replicate 3		14dpi#3	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#3\|BioSampleModel:Model organism or animal							14dpi rep3 miRNA	6011	6011	miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP173044	SID6011_S15_L003_R1_001.fastq.gz	fastq	578164050.0	11563281.0	SID6011 S15 L003 R1 001.fastq.gz	0:50	A:109934197;C:149003532;G:179264553;T:139924815;N:36953	50		109934197	149003532	179264553	139924815	36953	SRX5120118	SRS4121998	SRA822004	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	1	0.0225	0.00372	0.9906	0.61747	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	unknown	unknown	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
50796	50796	SRR8305649	SRX5120117	SRS4121996	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.	pubmed:30597924	Replicate 2		14dpi#2	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#2\|BioSampleModel:Model organism or animal							14dpi rep2 miRNA	6010	6010	miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP173044	SID6010_S14_L003_R1_001.fastq.gz	fastq	682820200.0	13656404.0	SID6010 S14 L003 R1 001.fastq.gz	0:50	A:132413613;C:177691857;G:213067602;T:159602931;N:44197	50		132413613	177691857	213067602	159602931	44197	SRX5120117	SRS4121996	SRA822004	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	1	0.02361	0.00321	0.99281	0.46548	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	unknown	unknown	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
50797	50797	SRR8305650	SRX5120116	SRS4121997	SRP173044	PRJNA509429	Delineating the transcriptomic response during Zebrafish heart regeneration	PRJNA509429	Other	Sequencing data of both mRNA and microRNA were obtained to study the transcriptomic response during zebrafish heart regeneration. Samples were utilised in triplicates for each time point up to 160 xxx post injury. Furthermore mRNA and miRNA were obtained from the same biological samples to allow correlation analysis.	pubmed:30597924	Replicate 1		14dpi#1	breed:zebrafish\|age:NA\|sex:missing\|tissue:whole heart\|time point:14 dpi\|time replicate:14dpi#1\|BioSampleModel:Model organism or animal							14dpi rep1 miRNA	6009	6009	miRNAs were extracted using miRNeasy Mini Kit Qiagen #217004 and used for library preparation with the TruSeq Small RNA Library Prep Illumina #20005613			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP173044	SID6009_S5_L006_R1_001.fastq.gz	fastq	645018650.0	12900373.0	SID6009 S5 L006 R1 001.fastq.gz	0:50	A:121217579;C:170403284;G:199790376;T:153583951;N:23460	50		121217579	170403284	199790376	153583951	23460	SRX5120116	SRS4121997	SRA822004	University of Freiburg\|Institute of Molecular Medicine and Cell Research	University of Freiburg DeCaRe	1	0.02637	0.00359	0.99095	0.50364	50	B	usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	unknown	unknown	Germany	2019-04-30	Undetermined	Undetermined	Heart	Cardiovascular System
52326	52326	SRR9119512	SRX5893495	SRS4815090	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIb 3	GSM3816534	source name:stage IIIb follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	IIIb 3	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIb follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	GSM3816534	GSM3816534: IIIb 3; Danio rerio; miRNA Seq	GSM3816534		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816534	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.005.RPI10.IIIb_3_R1.fastq.gz	fastq	1449340900.0	28986818.0	GSM3816534 r1	0:50 1:0	A:351029701;C:324452324;G:401722902;T:371889768;N:246205	50	0	351029701	324452324	401722902	371889768	246205	SRX5893495	SRS4815090	SRA890399	GEO	Biology, YorkU	1	0.08662	0.01333	0.96213	0.83838	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52327	52327	SRR9119513	SRX5893495	SRS4815090	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIb 3	GSM3816534	source name:stage IIIb follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	IIIb 3	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIb follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	GSM3816534	GSM3816534: IIIb 3; Danio rerio; miRNA Seq	GSM3816534		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816534	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.006.RPI10.IIIb_3_R1.fastq	fastq	1447621100.0	28952422.0	GSM3816534 r2	0:50 1:0	A:350650304;C:324162528;G:401055729;T:371582418;N:170121	50	0	350650304	324162528	401055729	371582418	170121	SRX5893495	SRS4815090	SRA890399	GEO	Biology, YorkU	1	0.08676	0.01312	0.96282	0.84604	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52328	52328	SRR9119510	SRX5893494	SRS4815089	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIb 2	GSM3816533	source name:stage IIIb follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	IIIb 2	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIb follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	GSM3816533	GSM3816533: IIIb 2; Danio rerio; miRNA Seq	GSM3816533		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816533	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.005.RPI9.IIIb_2_R1.fastq.gz	fastq	1012538750.0	20250775.0	GSM3816533 r1	0:50 1:0	A:242873339;C:228078637;G:287889366;T:253526026;N:171382	50	0	242873339	228078637	287889366	253526026	171382	SRX5893494	SRS4815089	SRA890399	GEO	Biology, YorkU	1	0.04745	0.00802	0.968	0.75298	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52329	52329	SRR9119511	SRX5893494	SRS4815089	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIb 2	GSM3816533	source name:stage IIIb follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	IIIb 2	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIb follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	GSM3816533	GSM3816533: IIIb 2; Danio rerio; miRNA Seq	GSM3816533		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816533	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.006.RPI9.IIIb_2_R1.fastq	fastq	1010559400.0	20211188.0	GSM3816533 r2	0:50 1:0	A:242471282;C:227664296;G:287157957;T:253147388;N:118477	50	0	242471282	227664296	287157957	253147388	118477	SRX5893494	SRS4815089	SRA890399	GEO	Biology, YorkU	1	0.04679	0.008	0.96946	0.71268	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52330	52330	SRR9119508	SRX5893493	SRS4815088	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIb 1	GSM3816532	source name:stage IIIb follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	IIIb 1	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIb follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	GSM3816532	GSM3816532: IIIb 1; Danio rerio; miRNA Seq	GSM3816532		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816532	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.005.RPI8.IIIb_1_R1.fastq.gz	fastq	1443846950.0	28876939.0	GSM3816532 r1	0:50 1:0	A:350805103;C:319766230;G:407583206;T:365448522;N:243889	50	0	350805103	319766230	407583206	365448522	243889	SRX5893493	SRS4815088	SRA890399	GEO	Biology, YorkU	1	0.02559	0.00389	0.98407	0.82023	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52331	52331	SRR9119509	SRX5893493	SRS4815088	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIb 1	GSM3816532	source name:stage IIIb follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	IIIb 1	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIb follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIb	GSM3816532	GSM3816532: IIIb 1; Danio rerio; miRNA Seq	GSM3816532		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816532	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.006.RPI8.IIIb_1_R1.fastq	fastq	1442694250.0	28853885.0	GSM3816532 r2	0:50 1:0	A:350607715;C:319569609;G:407049947;T:365297986;N:168993	50	0	350607715	319569609	407049947	365297986	168993	SRX5893493	SRS4815088	SRA890399	GEO	Biology, YorkU	1	0.02565	0.00409	0.98417	0.81633	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52332	52332	SRR9119506	SRX5893492	SRS4815087	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIa 3	GSM3816531	source name:stage IIIa follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	IIIa 3	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIa follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	GSM3816531	GSM3816531: IIIa 3; Danio rerio; miRNA Seq	GSM3816531		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816531	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.005.RPI4.IIIa_3_R1.fastq.gz	fastq	1324489100.0	26489782.0	GSM3816531 r1	0:50 1:0	A:333465386;C:289207984;G:364882545;T:336711699;N:221486	50	0	333465386	289207984	364882545	336711699	221486	SRX5893492	SRS4815087	SRA890399	GEO	Biology, YorkU	1	0.02703	0.00432	0.98313	0.75385	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52333	52333	SRR9119507	SRX5893492	SRS4815087	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIa 3	GSM3816531	source name:stage IIIa follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	IIIa 3	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIa follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	GSM3816531	GSM3816531: IIIa 3; Danio rerio; miRNA Seq	GSM3816531		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816531	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.006.RPI4.IIIa_3_R1.fastq	fastq	1322554650.0	26451093.0	GSM3816531 r2	0:50 1:0	A:333031673;C:288843797;G:364209143;T:336315522;N:154515	50	0	333031673	288843797	364209143	336315522	154515	SRX5893492	SRS4815087	SRA890399	GEO	Biology, YorkU	1	0.02671	0.00422	0.98283	0.76748	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52334	52334	SRR9119504	SRX5893491	SRS4815086	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIa 2	GSM3816530	source name:stage IIIa follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	IIIa 2	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIa follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	GSM3816530	GSM3816530: IIIa 2; Danio rerio; miRNA Seq	GSM3816530		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816530	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.005.RPI3.IIIa_2_R1.fastq.gz	fastq	1382308600.0	27646172.0	GSM3816530 r1	0:50 1:0	A:342206537;C:301597185;G:385756857;T:352517232;N:230789	50	0	342206537	301597185	385756857	352517232	230789	SRX5893491	SRS4815086	SRA890399	GEO	Biology, YorkU	1	0.05315	0.00892	0.9643	0.79967	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52335	52335	SRR9119505	SRX5893491	SRS4815086	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIa 2	GSM3816530	source name:stage IIIa follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	IIIa 2	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIa follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	GSM3816530	GSM3816530: IIIa 2; Danio rerio; miRNA Seq	GSM3816530		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816530	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.006.RPI3.IIIa_2_R1.fastq	fastq	1383050750.0	27661015.0	GSM3816530 r2	0:50 1:0	A:342441286;C:301828080;G:385820344;T:352800933;N:160107	50	0	342441286	301828080	385820344	352800933	160107	SRX5893491	SRS4815086	SRA890399	GEO	Biology, YorkU	1	0.0533	0.00892	0.96323	0.81292	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52336	52336	SRR9119502	SRX5893490	SRS4815085	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIa 1	GSM3816529	source name:stage IIIa follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	IIIa 1	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIa follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	GSM3816529	GSM3816529: IIIa 1; Danio rerio; miRNA Seq	GSM3816529		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816529	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.005.RPI2.IIIa_1_R1.fastq.gz	fastq	1333818450.0	26676369.0	GSM3816529 r1	0:50 1:0	A:320039883;C:296663387;G:380656068;T:336233800;N:225312	50	0	320039883	296663387	380656068	336233800	225312	SRX5893490	SRS4815085	SRA890399	GEO	Biology, YorkU	1	0.0976	0.019	0.93718	0.75404	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive System
52337	52337	SRR9119503	SRX5893490	SRS4815085	SRP199448	PRJNA544696	Identification of novel microRNAs and characterization of microRNA expression profiles in zebrafish ovarian follicular cells	GSE131759	Transcriptome Analysis	MicroRNAs miRNAs are small noncoding RNAs that regulate gene expression primarily at the post transcriptional levels and thereby play important roles in regulating many physiological and developmental processes. Oocyte maturation in fish is induced by hormones produced from the hypothalamus pituitary and ovary. Gonadotropin releasing hormone GnRH stimulates the secretion of luteinizing hormone LH which in turn induces the secretion of maturation inducing hormone MIH from the ovary. It is documented that small early vitellogenic or stage IIIa follicles are unable to undergo oocyte maturation whereas oocytes in mid to late vitellogenic stage IIIb follicles can be induced by LH and MIH to become mature. To determine whether miRNAs may be involved in the growth and acquisition of maturational competency of ovarian follicles we determined the miRNA expression profiles in follicular cells collected from stage IIIa and IIIb follicles using next generation sequencing. It was found that miRNAs are abundantly expressed in the follicular cells from both stages IIIa and IIIb follicles. Furthermore bioinformatics analysis revealed the presence of 214 known 31 conserved novel and 44 novel miRNAs in zebrafish vitellogenic ovarian follicular cells. Most mature miRNAs in follicular cells were found to be in the length of 22 nucleotides. Differential expression analysis revealed that 11 miRNAs were significantly up regulated and 13 miRNAs were significantly down regulated in the stage IIIb follicular cells as compared with stage IIIa follicular cells. The expression of four of the significantly regulated miRNAs dre miR 22a 3p dre miR 16a dre miR 181a 3p and dre miR 29a was validated by real time PCR. Finally gene enrichment and pathway analyses of the predicted targets of the significantly regulated miRNAs supported the involvement of several key signaling pathways in regulating ovarian function including oocyte maturation. Taken together this study identifies novel zebrafish miRNAs and characterizes miRNA expr…	pubmed:31417497		IIIa 1	GSM3816529	source name:stage IIIa follicular cells\|tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	IIIa 1	LC Sciences in house program ACGT101 miR program was used to process the raw sequencing data allowing for 1 mismatch Raw sequencing reads were processed using the ACGT101 miR program LC Sciences Houston Texas USA. Adaptor dimers junk low complexity common RNA families and repeats were removed and only unique sequences of 18 26 nucleotides nt in length were retained and compared to known zebrafish miRNAs in miRBase. Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre miRNA and such pre miRNA is able to form a hairpin structure whose genomic coordinates should not overlap with known pre miRNAs included in this analysis were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample Genome build: GRCz11 Supplementary files format and content: tab delimited text files include mature miRNA sequence and normalized values for each Sample	stage IIIa follicular cells	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	tissue:ovary\|cell type:follicular cells\|developmental stage:IIIa	GSM3816529	GSM3816529: IIIa 1; Danio rerio; miRNA Seq	GSM3816529		1	Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA Seq Illumina Massively Parallel Sequencing. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3816529	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP199448	HI.2030.006.RPI2.IIIa_1_R1.fastq	fastq	1334152750.0	26683055.0	GSM3816529 r2	0:50 1:0	A:320194547;C:296827909;G:380547854;T:336424243;N:158197	50	0	320194547	296827909	380547854	336424243	158197	SRX5893490	SRS4815085	SRA890399	GEO	Biology, YorkU	1	0.09727	0.01947	0.93866	0.76527	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	Canada	2019-05-24	Undetermined	Undetermined	Gonad	Reproductive 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");;