metadata: run_metadata: 28 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "miRNA-Seq" and tissue_curation

28 rows where experiment.library_selection = "size fractionation", experiment.library_strategy = "miRNA-Seq" and tissue_curation_coarse = "Reproductive System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.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
37997	37997	SRR1265760	SRX529154	SRS598851	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Testis Replicate 3 sRNAseq	GSM1376643	source name:Testis\|gender:male\|tissue:Testis\|genetic background:Wild type Singapore strain	Testis Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Testis	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Testis\|genetic background:Wild type Singapore strain	GSM1376643	GSM1376643: Testis Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376643		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376643	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZT004_GCCAAT_L004_R1.fastq.gz	fastq	1096387628.0	14426153.0	GSM1376643 r1	0:76	A:268706118;C:286539627;G:262643519;T:278353167;N:145197	76		268706118	286539627	262643519	278353167	145197	SRX529154	SRS598851	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00659	0.00333	0.99845	0.7331	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
37998	37998	SRR1265759	SRX529153	SRS598850	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Testis Replicate 2 sRNAseq	GSM1376642	source name:Testis\|gender:male\|tissue:Testis\|genetic background:Wild type Singapore strain	Testis Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Testis	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Testis\|genetic background:Wild type Singapore strain	GSM1376642	GSM1376642: Testis Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376642		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376642	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZT003_ACAGTG_L004_R1.fastq.gz	fastq	1562745896.0	20562446.0	GSM1376642 r1	0:76	A:381752411;C:387452090;G:395892335;T:397438930;N:210130	76		381752411	387452090	395892335	397438930	210130	SRX529153	SRS598850	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.01222	0.00651	0.99788	0.69591	76	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
37999	37999	SRR1265758	SRX529152	SRS598849	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Testis Replicate 1 sRNAseq	GSM1376641	source name:Testis\|gender:male\|tissue:Testis\|genetic background:Wild type Singapore strain	Testis Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Testis	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Male\|tissue:Testis\|genetic background:Wild type Singapore strain	GSM1376641	GSM1376641: Testis Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376641		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376641	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZT001_TGACCA_L004_R1.fastq.gz	fastq	1368892316.0	18011741.0	GSM1376641 r1	0:76	A:335715713;C:358829703;G:326742789;T:347419137;N:184974	76		335715713	358829703	326742789	347419137	184974	SRX529152	SRS598849	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00032	3e-05	0.99943	0.69387	76	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
38000	38000	SRR1265757	SRX529151	SRS598848	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Ovary Replicate 3 sRNAseq	GSM1376640	source name:Ovary\|gender:female\|tissue:Ovary\|genetic background:Wild type Singapore strain	Ovary Replicate 3 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Ovary	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Ovary\|genetic background:Wild type Singapore strain	GSM1376640	GSM1376640: Ovary Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376640		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376640	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZO006_GATCAG_L008_R1.fastq.gz	fastq	1411005984.0	27666784.0	GSM1376640 r1	0:51	A:326542153;C:314421825;G:411019622;T:358847379;N:175005	51		326542153	314421825	411019622	358847379	175005	SRX529151	SRS598848	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00638	0.00068	0.99513	0.75483	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
38001	38001	SRR1265756	SRX529150	SRS598847	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Ovary Replicate 2 sRNAseq	GSM1376639	source name:Ovary\|gender:female\|tissue:Ovary\|genetic background:Wild type Singapore strain	Ovary Replicate 2 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Ovary	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Ovary\|genetic background:Wild type Singapore strain	GSM1376639	GSM1376639: Ovary Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376639		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376639	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZO005_ACTTGA_L008_R1.fastq.gz	fastq	765419424.0	15008224.0	GSM1376639 r1	0:51	A:179455664;C:170237021;G:221342071;T:194287721;N:96947	51		179455664	170237021	221342071	194287721	96947	SRX529150	SRS598847	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.02512	0.00355	0.98212	0.67744	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
38002	38002	SRR1265755	SRX529149	SRS598846	SRP041544	PRJNA245824	Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish	GSE57169	Transcriptome Analysis	The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain gut liver ovary testis eye heart and embryo of zebrafish. In brain gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2 we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0% with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.	pubmed:26574018	Ovary Replicate 1 sRNAseq	GSM1376638	source name:Ovary\|gender:female\|tissue:Ovary\|genetic background:Wild type Singapore strain	Ovary Replicate 1 sRNAseq	Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedländer et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl p <zebrafish precursor miRNA fasta file> m <zebrafish mature miRNA fasta file> r <unique reads fasta file> t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.	Ovary	N/A	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	Fishes were purchased from a local supplier and acclimatized before tissue extraction.	gender:Female\|tissue:Ovary\|genetic background:Wild type Singapore strain	GSM1376638	GSM1376638: Ovary Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376638		1	Total RNA were extracted using mirVana™ miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana™ miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit RS 200 0012 Illumina Inc.. Libraries were prepared according to manufacturer instructions. Briefly 1µg of good quality Total RNA per sample was used as starting material. 5’ and 3’ RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.	GEO Accession:GSM1376638	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZO004_CAGATC_L008_R1.fastq.gz	fastq	487558674.0	9559974.0	GSM1376638 r1	0:51	A:114833813;C:108951811;G:140408702;T:123302557;N:61791	51		114833813	108951811	140408702	123302557	61791	SRX529149	SRS598846	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.00298	0.0004	0.99644	0.84584	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Gonad	Reproductive System
38256	38256	SRR1596061	SRX719267	SRS715451	SRP048591	PRJNA262865	Identification and Characterization of MicroRNAs in Zebrafish Spermatozoa by Illumina Sequencing	GSE61984	Other	MicroRNAs miRNAs are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA rRNA snRNA snoRNA and miRNA. By mapping to the zebrafish genome we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families including zebrafish specific families such as mir 731 mir 724 mir 725 mir 729 and mir 2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate. Overall design: Examination of small RNA populations in zebrafish spermatozoa	pubmed:26418264	zebrafish sperm	GSM1517943	tissue:Zebrafish Spermatozoa\|cell type:Spermatozoa\|strain:AB wild type	zebrafish sperm	The sequencing data were analyzed as described previously by Xu et al 2014. The low quality reads were filtered to remove reads without xxx 3’ adaptor 5’ adaptor contaminant reads reads without xxx insert fragment reads containing polyA stretches and reads of less than 18 nt. Next the remaining sequences clean reads were mapped to the zebrafish genome using SOAP with a tolerance of one mismatch to analyze their distribution The sequences were aligned against known miRNA precursors and mature miRNAs deposited in the miRBase 20.0 to identify conserved miRNAs. The clean reads were compared against the sRNAs rRNAs tRNAs snRNAs snoRNA miRNA deposited in the GenBank and Rfam http://www.sanger.ac.uk/resources/databases/rfam.html databases to annotate the sRNA sequences. Because some sRNA tags might map to more than one category we used priority rules to ensure that every unique sRNA was mapped to only one annotation as follows: rRNA etc. GenBank >Rfam >known miRNA >repeat >exon >intron. Genome build: miRBase 20.0 Supplementary files format and content: zebrafish miRNA count.txt include RPKM values of each known miRNA in this sample	Zebrafish Spermatozoa		Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.		cell type:Spermatozoa\|strain:AB wild type	GSM1517943	GSM1517943: zebrafish sperm; Danio rerio; miRNA Seq	GSM1517943		1	Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform.	GEO Accession:GSM1517943	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP048591	zebrafish-sperm5.fq.bz2	fastq	588000000.0	12000000.0	GSM1517943 r1	0:49	A:122673394;C:136175879;G:140377184;T:188702650;N:70893	49		122673394	136175879	140377184	188702650	70893	SRX719267	SRS715451	SRA188511	GEO	SUN YAT-SEN UNIVERSITY	1	2e-05	0.0	0.99997	1.0	49	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2014-10-02	Zygote	Embryo	Oocyte	Reproductive 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
60887	60887	SRR12628234	SRX9110497	SRS7353480	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs	pubmed:33506864	h24 2: PGCs 24hpf repeat2	GSM4777194	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h24 2: PGCs 24hpf repeat2	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs		PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777194	GSM4777194: h24 2: PGCs 24hpf repeat2; Danio rerio; miRNA Seq	GSM4777194		1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777194	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h24_2.fastq	fastq	4024398750.0	26829325.0	GSM4777194 r1	0:150 1:0	A:1030703487;C:1025857271;G:1004392553;T:963376583;N:68856	150	0	1030703487	1025857271	1004392553	963376583	68856	SRX9110497	SRS7353480	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.00025	0.0	0.99997	1.0	150	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Pharyngula	Embryo	Gonad	Reproductive System
60888	60888	SRR12628233	SRX9110496	SRS7353479	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs	pubmed:33506864	h24 1: PGCs 24hpf repeat1	GSM4777193	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h24 1: PGCs 24hpf repeat1	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs		PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777193	GSM4777193: h24 1: PGCs 24hpf repeat1; Danio rerio; miRNA Seq	GSM4777193		1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777193	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h24_1.fastq	fastq	2223111450.0	14820743.0	GSM4777193 r1	0:150 1:0	A:510125618;C:561938103;G:577742482;T:573267493;N:37754	150	0	510125618	561938103	577742482	573267493	37754	SRX9110496	SRS7353479	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.0004	0.0	0.99993	1.0	150	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Pharyngula	Embryo	Gonad	Reproductive System
60889	60889	SRR12628232	SRX9110495	SRS7353478	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs	pubmed:33506864	h11 2: PGCs 11hpf repeat2	GSM4777192	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h11 2: PGCs 11hpf repeat2	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs		PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777192	GSM4777192: h11 2: PGCs 11hpf repeat2; Danio rerio; miRNA Seq	GSM4777192		1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777192	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h11_2.fastq	fastq	1725506100.0	11503374.0	GSM4777192 r1	0:150 1:0	A:419294958;C:415643261;G:432730446;T:457808038;N:29397	150	0	419294958	415643261	432730446	457808038	29397	SRX9110495	SRS7353478	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.00062	0.0	0.99991	1.0	150	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Segmentation	Embryo	Gonad	Reproductive System
60890	60890	SRR12628231	SRX9110494	SRS7353477	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs	pubmed:33506864	h11 1: PGCs 11hpf repeat1	GSM4777191	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h11 1: PGCs 11hpf repeat1	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs		PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777191	GSM4777191: h11 1: PGCs 11hpf repeat1; Danio rerio; miRNA Seq	GSM4777191		1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777191	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h11_1.fastq	fastq	2690366550.0	17935777.0	GSM4777191 r1	0:150 1:0	A:722881530;C:687611993;G:633563837;T:646263376;N:45814	150	0	722881530	687611993	633563837	646263376	45814	SRX9110494	SRS7353477	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.0006	0.0	0.99991	1.0	150	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Segmentation	Embryo	Gonad	Reproductive System
60891	60891	SRR12628230	SRX9110493	SRS7353476	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs	pubmed:33506864	h6 2: PGCs 6hpf repeat2	GSM4777190	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h6 2: PGCs 6hpf repeat2	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs		PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777190	GSM4777190: h6 2: PGCs 6hpf repeat2; Danio rerio; miRNA Seq	GSM4777190		1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777190	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h6_2.fastq	fastq	2330922150.0	15539481.0	GSM4777190 r1	0:150 1:0	A:563758043;C:619336180;G:552040747;T:595747277;N:39903	150	0	563758043	619336180	552040747	595747277	39903	SRX9110493	SRS7353476	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.00014	0.0	0.99997	1.0	150	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Gastrula	Embryo	Gonad	Reproductive System
60892	60892	SRR12628229	SRX9110492	SRS7353475	SRP282187	PRJNA663091	Characterization of small RNAs in early zebrafish PGCs	GSE157865	Transcriptome Analysis	Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf shield stage 11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs	pubmed:33506864	h6 1: PGCs 6hpf repeat1	GSM4777189	source name:PGCs\|cell type:primordial germ cells\|strain:AB\|tissue:gonad	h6 1: PGCs 6hpf repeat1	Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample …	PGCs		PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.		cell type:primordial germ cells\|strain:AB\|tissue:gonad	GSM4777189	GSM4777189: h6 1: PGCs 6hpf repeat1; Danio rerio; miRNA Seq	GSM4777189		1	PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.	GEO Accession:GSM4777189	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	HiSeq X Ten	SRP282187	h6_1.fastq	fastq	1979588400.0	13197256.0	GSM4777189 r1	0:150 1:0	A:453046525;C:471873747;G:495904656;T:558729697;N:33775	150	0	453046525	471873747	495904656	558729697	33775	SRX9110492	SRS7353475	SRA1124474	GEO	Shanghai Institute of Biochemistry and Cell Biology,CAS	1	0.00028	0.0	0.99997	1.0	150	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2020-09-12	Gastrula	Embryo	Gonad	Reproductive System
69435	69435	SRR18685198	SRX14786396	SRS12545301	SRP368241	PRJNA824784	Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes	GSE200470	Other	We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species except mouse. We found endo siRNAs resulted from the truncated Dicer isoform were mouse specific and os piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2' three prime O methylation. The sequences of many highly expressed piRNA clusters are fast evolving compared with their syntenic genomic locations and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.	pubmed:38532500	small RNA zebrafish 3	GSM6034594	source name:oocyte\|tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|molecule subtype:small RNA\|geo loc name:missing\|collection date:missing	small RNA zebrafish 3	We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs tsRNA tRNA derived small non coding RNA rsRNA rRNA derived small non coding RNA small snoRNAs lncRNA and mRNA successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others. We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM transcripts per kilobase of exon model per million mapped reads by StringTie. Assembly: GRCh38 GRCm38 Supplementary files format and content: tab delimited text files include TPM values or raw counts for each Sample	oocyte		Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|molecule subtype:small RNA	GSM6034594	GSM6034594: small RNA zebrafish 3; Danio rerio; miRNA Seq	GSM6034594 r1	GSM6034594	1	Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP368241	Zebrafish3_combined_R1.fastq.gz	fastq	687816450.0	4585443.0	GSM6034594 r1	0:150 1:0	A:94948683;C:106096224;G:367933691;T:118821697;N:16155	150	0	94948683	106096224	367933691	118821697	16155	SRX14786396	SRS12545301	SRA1400916	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	1	2e-05	0.0	0.99993	0.66666	150	T	under 1.2% mapping rate	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2022-04-08	Zygote	Embryo	Oocyte	Reproductive System
69436	69436	SRR18685199	SRX14786395	SRS12545300	SRP368241	PRJNA824784	Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes	GSE200470	Other	We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species except mouse. We found endo siRNAs resulted from the truncated Dicer isoform were mouse specific and os piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2' three prime O methylation. The sequences of many highly expressed piRNA clusters are fast evolving compared with their syntenic genomic locations and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.	pubmed:38532500	small RNA zebrafish 2	GSM6034593	source name:oocyte\|tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|molecule subtype:small RNA\|geo loc name:missing\|collection date:missing	small RNA zebrafish 2	We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs tsRNA tRNA derived small non coding RNA rsRNA rRNA derived small non coding RNA small snoRNAs lncRNA and mRNA successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others. We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM transcripts per kilobase of exon model per million mapped reads by StringTie. Assembly: GRCh38 GRCm38 Supplementary files format and content: tab delimited text files include TPM values or raw counts for each Sample	oocyte		Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|molecule subtype:small RNA	GSM6034593	GSM6034593: small RNA zebrafish 2; Danio rerio; miRNA Seq	GSM6034593 r1	GSM6034593	1	Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP368241	Zebrafish2_combined_R1.fastq.gz	fastq	354830850.0	2365539.0	GSM6034593 r1	0:150 1:0	A:48935028;C:57418354;G:192263153;T:56206000;N:8315	150	0	48935028	57418354	192263153	56206000	8315	SRX14786395	SRS12545300	SRA1400916	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	1	0.00026	0.0	0.99967	1.0	150	T	under 1.2% mapping rate	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2022-04-08	Zygote	Embryo	Oocyte	Reproductive System
69437	69437	SRR18685200	SRX14786394	SRS12545299	SRP368241	PRJNA824784	Divergent composition and transposon silencing activity of small RNAs in mammalian oocytes	GSE200470	Other	We found piRNAs with different lengths represented the predominant small RNA species in oocytes from the 12 explored species except mouse. We found endo siRNAs resulted from the truncated Dicer isoform were mouse specific and os piRNAs associating with PIWIL3 in human oocytes are widespread in mammals and are typically with low levels of the 2' three prime O methylation. The sequences of many highly expressed piRNA clusters are fast evolving compared with their syntenic genomic locations and the TE families distributing in the conserved piRNA clusters are various between species. Overall design: Profiling small RNAs and mRNA in oocytes from 12 animals.	pubmed:38532500	small RNA zebrafish 1	GSM6034592	source name:oocyte\|tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|molecule subtype:small RNA\|geo loc name:missing\|collection date:missing	small RNA zebrafish 1	We used cutadapt to clip adaptor and filter low quality reads. Reads failing to match the adaptor or reads with lengths shorter than 17 nt were discarded. Redundant sequences were collapsed as useful reads and mapped to reference sequences by bowite. The useful reads were assigned to known miRNAs tsRNA tRNA derived small non coding RNA rsRNA rRNA derived small non coding RNA small snoRNAs lncRNA and mRNA successively. The reads that could not be mapped to these known small RNAs were used to predict piRNAs and endo siRNAs successively. Sequences that were not annotated with any of the RNA categories above were classified as others. We used trimmomatic to clip adaptor and filter low quality reads. The high quality reads were mapped to reference genomes by STAR. The expressed levels of genes were caculated in TPM transcripts per kilobase of exon model per million mapped reads by StringTie. Assembly: GRCh38 GRCm38 Supplementary files format and content: tab delimited text files include TPM values or raw counts for each Sample	oocyte		Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		tissue:oocyte\|Sex:female\|Stage:MII\|genotype:wild type\|molecule subtype:small RNA	GSM6034592	GSM6034592: small RNA zebrafish 1; Danio rerio; miRNA Seq	GSM6034592 r1	GSM6034592	1	Total RNA from oocytes of different species were extracted with TRIzol Reagent Ambion USA respectively. Small RNA library construction. Briefly the single oocytes were incubated at 72 °C for 3 min then cooled in ice. post 3′ adapter ligation the samples were incubated with 5 U of lambda exonuclease and 25 U of 5′ de adenylates. Small RNAs were reverse transcribed post 5′ adapter ligation. Two rounds of amplification were conducted to get the libraries and the libraries were recovered with 6% polyacrylamide gel. mRNA library construction. In brief single oocytes were incubated at 72 °C for 3 min and then cooled on ice. For every single oocyte 1 μl of a 1/500 000 1/50 000 dilution of the ERCC RNA Spike In Mix Invitrogen 4456740 was added. post reverse transcription and PCR pre amplification cDNAs were purified and 3 ng of purified cDNA was used for a tagmentation reaction with Tn5 transposase.		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP368241	Zebrafish1_combined_R1.fastq.gz	fastq	1096131600.0	7307544.0	GSM6034592 r1	0:150 1:0	A:172547981;C:159060763;G:590708513;T:173788947;N:25396	150	0	172547981	159060763	590708513	173788947	25396	SRX14786394	SRS12545299	SRA1400916	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences	1	0.00016	0.0	0.99965	0.96551	150	T	under 1.2% mapping rate	illumina	novaseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2022-04-08	Zygote	Embryo	Oocyte	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");;