metadata: run_metadata: 45 rows where experiment.library_strategy = "miRNA-Seq" and tissue

45 rows where experiment.library_strategy = "miRNA-Seq" and tissue_curation = "Embryo Imprecise"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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
38020	38020	SRR1265736	SRX529131	SRS598827	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	Embryo Replicate 3 sRNAseq	GSM1376619	source name:Embryo\|tissue:Embryo\|genetic background:Wild type Singapore strain	Embryo 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.	Embryo	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.	tissue:Embryo\|genetic background:Wild type Singapore strain	GSM1376619	GSM1376619: Embryo Replicate 3 sRNAseq; Danio rerio; miRNA Seq	GSM1376619		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:GSM1376619	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZE006_CTTGTA_L008_R1.fastq.gz	fastq	1714180635.0	33611385.0	GSM1376619 r1	0:51	A:338559677;C:431494863;G:537012008;T:406904091;N:209996	51		338559677	431494863	537012008	406904091	209996	SRX529131	SRS598827	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.09044	0.01776	0.97782	0.77023	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38021	38021	SRR1265735	SRX529130	SRS598828	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	Embryo Replicate 2 sRNAseq	GSM1376618	source name:Embryo\|tissue:Embryo\|genetic background:Wild type Singapore strain	Embryo 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.	Embryo	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.	tissue:Embryo\|genetic background:Wild type Singapore strain	GSM1376618	GSM1376618: Embryo Replicate 2 sRNAseq; Danio rerio; miRNA Seq	GSM1376618		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:GSM1376618	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZE005_GGCTAC_L008_R1.fastq.gz	fastq	736486002.0	14440902.0	GSM1376618 r1	0:51	A:145757737;C:194417932;G:231157927;T:165060763;N:91643	51		145757737	194417932	231157927	165060763	91643	SRX529130	SRS598828	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.01133	0.00234	0.99515	0.73854	51	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38022	38022	SRR1265734	SRX529129	SRS598825	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	Embryo Replicate 1 sRNAseq	GSM1376617	source name:Embryo\|tissue:Embryo\|genetic background:Wild type Singapore strain	Embryo 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.	Embryo	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.	tissue:Embryo\|genetic background:Wild type Singapore strain	GSM1376617	GSM1376617: Embryo Replicate 1 sRNAseq; Danio rerio; miRNA Seq	GSM1376617		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:GSM1376617	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP041544	MZE004_TAGCTT_L008_R1.fastq.gz	fastq	477426912.0	9361312.0	GSM1376617 r1	0:51	A:93534991;C:123428376;G:148877677;T:111524753;N:61115	51		93534991	123428376	148877677	111524753	61115	SRX529129	SRS598825	SRA160430	GEO	Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore	1	0.02061	0.00461	0.99379	0.8448	51	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Singapore	2014-04-29	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38042	38042	SRR1371226	SRX585640	SRS631986	SRP043064	PRJNA252044	Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond Blackfan Anemia from RPL5 Deficiency [miRNA Seq]	GSE58344	Transcriptome Analysis	In this study we generated a zebrafish model of DBA with RPL5 morphants and implemented high throughput RNA seq and miRNA seq to identify key genes lncRNAs and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a noc2l tars and nol6 and miRNAs such as dre miR 10a* dre miR 722 dre miR 737 and dre miR 142a 3p were significantly deregulated and these changes may play a crucial role in hematopoiesis ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network we identified central node genes in the network connected to the P53 pathway almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5 deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5 mediated DBA and other ribosomopathies. Overall design: Determine the differences of miRNome between RPL5 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5 mediated human diseases	parent bioproject:PRJNA252043	pubmed:26961822	RPL5 MO [miRNA]	GSM1408095	tissue:embryo\|genotype/variation:RPL5 morpholino knockdown\|developmental stage:48hpf	RPL5 MO [miRNA]	FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9	embryo	Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration.	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf	genotype/variation:RPL5 morpholino knockdown\|developmental stage:48hpf	GSM1408095	GSM1408095: RPL5 MO [miRNA]; Danio rerio; miRNA Seq	GSM1408095		1	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	GEO Accession:GSM1408095	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP043064	s_7_IDX19_1.fq	fastq	1093234725.0	13496725.0	GSM1408095 r1	0:81	A:263908052;C:257987133;G:278889068;T:292410262;N:40210	81		263908052	257987133	278889068	292410262	40210	SRX585640	SRS631986	SRA169796	GEO	Beijing Institute of Genomics	1	3e-05	0.0	0.99991	0.5	81	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2014-06-10	Hatching	Embryo	Embryo Imprecise	All anatomical structures
38043	38043	SRR1371225	SRX585639	SRS631982	SRP043064	PRJNA252044	Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond Blackfan Anemia from RPL5 Deficiency [miRNA Seq]	GSE58344	Transcriptome Analysis	In this study we generated a zebrafish model of DBA with RPL5 morphants and implemented high throughput RNA seq and miRNA seq to identify key genes lncRNAs and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a noc2l tars and nol6 and miRNAs such as dre miR 10a* dre miR 722 dre miR 737 and dre miR 142a 3p were significantly deregulated and these changes may play a crucial role in hematopoiesis ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network we identified central node genes in the network connected to the P53 pathway almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5 deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5 mediated DBA and other ribosomopathies. Overall design: Determine the differences of miRNome between RPL5 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5 mediated human diseases	parent bioproject:PRJNA252043	pubmed:26961822	morpholino control [miRNA]	GSM1408094	tissue:embryo\|genotype/variation:control morpholino\|developmental stage:48hpf	morpholino control [miRNA]	FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9	embryo	Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration.	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf	genotype/variation:control morpholino\|developmental stage:48hpf	GSM1408094	GSM1408094: morpholino control [miRNA]; Danio rerio; miRNA Seq	GSM1408094		1	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	GEO Accession:GSM1408094	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP043064			308681847.0	3810887.0	GSM1408094 r1	0:81	A:63686404;C:75263287;G:80056961;T:89650625;N:24570	81		63686404	75263287	80056961	89650625	24570	SRX585639	SRS631982	SRA169796	GEO	Beijing Institute of Genomics	1	8e-05	2e-05	0.99991	0.42857	81	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2014-06-10	Hatching	Embryo	Embryo Imprecise	All anatomical structures
38252	38252	SRR1593717	SRX718003	SRS713863	SRP048545	PRJNA262696	Adenylation of maternally inherited microRNAs by Wispy	GSE61931	Other	Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing		pubmed:25454948	Zeb fish Emb t 24h	GSM1517418	tissue:embryo\|genotype/variation:WT\|developmental stage:embryo 24h	Zeb fish Emb t 24h	The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.	embryo		Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.		genotype/variation:WT\|developmental stage:embryo 24h	GSM1517418	GSM1517418: Zeb fish Emb t 24h; Danio rerio; miRNA Seq	GSM1517418		1	Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.	GEO Accession:GSM1517418	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP048545	Zeb_fish_Emb_t_24h_1.fastq.gz	fastq	2747798604.0	53878404.0	GSM1517418 r1	0:51	A:675086979;C:579211488;G:812576920;T:680856005;N:67212	51		675086979	579211488	812576920	680856005	67212	SRX718003	SRS713863	SRA188351	GEO	Narry Kim Lab, School of Biological Sciences, Seoul National University	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	size_fractionation	trueseq	bulk	unknown	unknown	South Korea	2014-09-30	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
38253	38253	SRR1593716	SRX718002	SRS713862	SRP048545	PRJNA262696	Adenylation of maternally inherited microRNAs by Wispy	GSE61931	Other	Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing		pubmed:25454948	Zeb fish Emb t 30m	GSM1517417	tissue:embryo\|genotype/variation:WT\|developmental stage:embryo 30m	Zeb fish Emb t 30m	The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.	embryo		Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.		genotype/variation:WT\|developmental stage:embryo 30m	GSM1517417	GSM1517417: Zeb fish Emb t 30m; Danio rerio; miRNA Seq	GSM1517417		1	Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.	GEO Accession:GSM1517417	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP048545	Zeb_fish_Emb_t_30m_1.fastq.gz	fastq	3380715591.0	66288541.0	GSM1517417 r1	0:51	A:854040134;C:726173965;G:952338238;T:848081062;N:82192	51		854040134	726173965	952338238	848081062	82192	SRX718002	SRS713862	SRA188351	GEO	Narry Kim Lab, School of Biological Sciences, Seoul National University	1	1e-05	0.0	0.99997	1.0	51	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	size_fractionation	trueseq	bulk	unknown	unknown	South Korea	2014-09-30	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38254	38254	SRR1593715	SRX718001	SRS713861	SRP048545	PRJNA262696	Adenylation of maternally inherited microRNAs by Wispy	GSE61931	Other	Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing		pubmed:25454948	Zeb fish Emb t 10m	GSM1517416	tissue:embryo\|genotype/variation:WT\|developmental stage:embryo 10m	Zeb fish Emb t 10m	The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.	embryo		Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.		genotype/variation:WT\|developmental stage:embryo 10m	GSM1517416	GSM1517416: Zeb fish Emb t 10m; Danio rerio; miRNA Seq	GSM1517416		1	Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.	GEO Accession:GSM1517416	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP048545	Zeb_fish_Emb_t_10m_1.fastq.gz	fastq	3339395697.0	65478347.0	GSM1517416 r1	0:51	A:847877403;C:714050198;G:934084609;T:843302102;N:81385	51		847877403	714050198	934084609	843302102	81385	SRX718001	SRS713861	SRA188351	GEO	Narry Kim Lab, School of Biological Sciences, Seoul National University	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	size_fractionation	trueseq	bulk	unknown	unknown	South Korea	2014-09-30	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38255	38255	SRR1593714	SRX718000	SRS713860	SRP048545	PRJNA262696	Adenylation of maternally inherited microRNAs by Wispy	GSE61931	Other	Early development depends heavily on accurate control of maternally inherited mRNAs and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly sea urchin and mouse indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction which may allow the effective and selective adenylation of miRNAs. Thus adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing		pubmed:25454948	Zeb fish Emb t 0m	GSM1517415	tissue:egg\|genotype/variation:WT\|developmental stage:embryo 0m	Zeb fish Emb t 0m	The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3′ adaptor sequences starting with “TGGAATTC” were removed and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC respectively. The BWA short read aligner Li and Durbin 2009 version 0.7.5a r405 was used for the alignment with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall 2010 with annotations retrieved from RefSeq GtRNAdb FlyBase RepeatMasker Rfam and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack 2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA. Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.	egg		Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.		genotype/variation:WT\|developmental stage:embryo 0m	GSM1517415	GSM1517415: Zeb fish Emb t 0m; Danio rerio; miRNA Seq	GSM1517415		1	Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer’s guide. For each library 10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3’ adaptor ligated RNA the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.	GEO Accession:GSM1517415	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP048545	Zeb_fish_Emb_t_0m_1.fastq.gz	fastq	3135589293.0	61482143.0	GSM1517415 r1	0:51	A:800912828;C:671516191;G:883139862;T:779944407;N:76005	51		800912828	671516191	883139862	779944407	76005	SRX718000	SRS713860	SRA188351	GEO	Narry Kim Lab, School of Biological Sciences, Seoul National University	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	3prime	size_fractionation	trueseq	bulk	unknown	unknown	South Korea	2014-09-30	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
38321	38321	SRR1732707	SRX822003	SRS801698	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727	Emb MO Ct 48hpf	GSM1571860	source name:Embryos MO Ct 48hpf\|tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:48hpf	Emb MO Ct 48hpf	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Ct 48hpf	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:48hpf	GSM1571860	GSM1571860: Emb MO Ct 48hpf; Danio rerio; miRNA Seq	GSM1571860		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571860	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP051503	L.T.fq.gz	fastq	338322717.0	11175516.0	GSM1571860 r1	0:30.27 1:0	A:72708202;C:91561004;G:102921744;T:71122135;N:9632	30	0	72708202	91561004	102921744	71122135	9632	SRX822003	SRS801698	SRA221043	GEO	IIT, CNR	1	0.86712	0.22408	0.92725	0.50365	23	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Hatching	Embryo	Embryo Imprecise	All anatomical structures
38322	38322	SRR1732706	SRX822002	SRS801697	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727	Emb MO Tbx5a 48hpf	GSM1571859	source name:Embryos MO Tbx5a 48hpf\|tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:48hpf	Emb MO Tbx5a 48hpf	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Tbx5a 48hpf	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:48hpf	GSM1571859	GSM1571859: Emb MO Tbx5a 48hpf; Danio rerio; miRNA Seq	GSM1571859		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571859	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP051503	I.T.fq.gz	fastq	262219132.0	10137926.0	GSM1571859 r1	0:25.87 1:0	A:60415193;C:62111082;G:75168882;T:64515539;N:8436	25	0	60415193	62111082	75168882	64515539	8436	SRX822002	SRS801697	SRA221043	GEO	IIT, CNR	1	0.52287	0.13984	0.8788	0.6354	30	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Hatching	Embryo	Embryo Imprecise	All anatomical structures
38323	38323	SRR1732705	SRX822001	SRS801696	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727	Emb MO Ct 24hpf rep2	GSM1571858	source name:Embryos MO Ct 24hpf replicate2\|tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:24hpf	Emb MO Ct 24hpf rep2	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Ct 24hpf replicate2	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:24hpf	GSM1571858	GSM1571858: Emb MO Ct 24hpf rep2; Danio rerio; miRNA Seq	GSM1571858		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571858	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP051503	H.T.fq.gz	fastq	281909951.0	10806197.0	GSM1571858 r1	0:26.09 1:0	A:66055828;C:65184020;G:81768559;T:68892445;N:9099	26	0	66055828	65184020	81768559	68892445	9099	SRX822001	SRS801696	SRA221043	GEO	IIT, CNR	1	0.56084	0.23499	0.86819	0.64638	22	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
38324	38324	SRR1732704	SRX822000	SRS801695	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727	Emb MO Ct 24hpf rep1	GSM1571857	source name:Embryos MO Ct 24hpf replicate1\|tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:24hpf	Emb MO Ct 24hpf rep1	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Ct 24hpf replicate1	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo Ct injection\|developmental stage:24hpf	GSM1571857	GSM1571857: Emb MO Ct 24hpf rep1; Danio rerio; miRNA Seq	GSM1571857		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571857	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP051503	G.T.fq.gz	fastq	541546124.0	19319535.0	GSM1571857 r1	0:28.03 1:0	A:126881333;C:133281439;G:163930613;T:117435553;N:17186	28	0	126881333	133281439	163930613	117435553	17186	SRX822000	SRS801695	SRA221043	GEO	IIT, CNR	1	0.53436	0.20796	0.9009	0.55394	34	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
38325	38325	SRR1732703	SRX821999	SRS801694	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727	Emb MO Tbx5a 24hpf rep2	GSM1571856	source name:Embryos MO Tbx5a 24hpf replicate2\|tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:24hpf	Emb MO Tbx5a 24hpf rep2	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Tbx5a 24hpf replicate2	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:24hpf	GSM1571856	GSM1571856: Emb MO Tbx5a 24hpf rep2; Danio rerio; miRNA Seq	GSM1571856		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571856	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP051503	F.T.fq.gz	fastq	362513460.0	13684345.0	GSM1571856 r1	0:26.49 1:0	A:82709386;C:83987865;G:107681867;T:88122760;N:11582	26	0	82709386	83987865	107681867	88122760	11582	SRX821999	SRS801694	SRA221043	GEO	IIT, CNR	1	0.58925	0.2498	0.86821	0.65549	30	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
38326	38326	SRR1732702	SRX821998	SRS801693	SRP051503	PRJNA271079	Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]	GSE64465	Transcriptome Analysis	To investigate the complex regulatory networks disrupted in Holt Oram Syndrome we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points 24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA271069	pubmed:27471727	Emb MO Tbx5a 24hpf rep1	GSM1571855	source name:Embryos MO Tbx5a 24hpf replicate1\|tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:24hpf	Emb MO Tbx5a 24hpf rep1	Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Tbx5a 24hpf replicate1	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	tissue:embryo\|strain:AB\|treatment:Mo MOTbx5a injection\|developmental stage:24hpf	GSM1571855	GSM1571855: Emb MO Tbx5a 24hpf rep1; Danio rerio; miRNA Seq	GSM1571855		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1571855	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP051503	E.T.fq.gz	fastq	399134579.0	13766109.0	GSM1571855 r1	0:28.99 1:0	A:88725326;C:102855219;G:121123717;T:86418155;N:12162	28	0	88725326	102855219	121123717	86418155	12162	SRX821998	SRS801693	SRA221043	GEO	IIT, CNR	1	0.66472	0.25948	0.89623	0.54913	34	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2014-12-23	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
39703	39703	SRR2057604	SRX1054376	SRS957216	SRP059278	PRJNA286201	MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome [miRNA seq]	GSE69690	Transcriptome Analysis	The regulative role of miRNAs in Holt Oram Syndrome is investigated in a zebrafish model. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT sample. 1.5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxxhpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA286199	pubmed:26657204	Emb MO Ct 48hpf [miRNA seq]	GSM1707594	source name:Embryos MO Ct 48hpf\|strain background:AB\|infected with:MO C\|tissue:embryo\|developmental stage:48hpf	Emb MO Ct 48hpf [miRNA seq]	Basecalls performed using GA Pipeline v1.5 Sequenced reads were filtered for low quality and trimmed for three prime adaptor sequence. Reads were algned to mirBase v16.0 using CLC workbench Expression values were normalized to reads per million rpm Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Ct 48hpf	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	strain background:AB\|infected with:MO C\|tissue:embryo\|developmental stage:48hpf	GSM1707594	GSM1707594: Emb MO Ct 48hpf [miRNA seq]; Danio rerio; miRNA Seq	GSM1707594		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1707594	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP059278	Dre_FC_4.fq.gz	fastq	1033068440.0	25826711.0	GSM1707594 r1	0:40	A:417902194;C:195580811;G:153264728;T:266159736;N:160971	40		417902194	195580811	153264728	266159736	160971	SRX1054376	SRS957216	SRA272222	GEO	IIT, CNR	1	0.05412	0.01319	0.97693	0.22489	40	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2015-06-09	Hatching	Embryo	Embryo Imprecise	All anatomical structures
39704	39704	SRR2057603	SRX1054375	SRS957217	SRP059278	PRJNA286201	MicroRNA 19a replacement partially rescues fin and cardiac defects in zebrafish model of Holt Oram syndrome [miRNA seq]	GSE69690	Transcriptome Analysis	The regulative role of miRNAs in Holt Oram Syndrome is investigated in a zebrafish model. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT sample. 1.5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxxhpf.The Zebrafish wild type AB strain line was used.	parent bioproject:PRJNA286199	pubmed:26657204	Emb MO Tbx5a 48hpf [miRNA seq]	GSM1707593	source name:Embryos MO Tbx5a 48hpf\|strain background:AB\|infected with:MO Tbx5a\|tissue:embryo\|developmental stage:48hpf	Emb MO Tbx5a 48hpf [miRNA seq]	Basecalls performed using GA Pipeline v1.5 Sequenced reads were filtered for low quality and trimmed for three prime adaptor sequence. Reads were algned to mirBase v16.0 using CLC workbench Expression values were normalized to reads per million rpm Supplementary files format and content: tab delimited text file includes normalized read count per sample	Embryos MO Tbx5a 48hpf	1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast Varese Italy.	strain background:AB\|infected with:MO Tbx5a\|tissue:embryo\|developmental stage:48hpf	GSM1707593	GSM1707593: Emb MO Tbx5a 48hpf [miRNA seq]; Danio rerio; miRNA Seq	GSM1707593		1	For each library 1 μg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc. San Diego USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 µl elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18–33 nt.	GEO Accession:GSM1707593	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP059278	Dre_FC_3.fq.gz	fastq	1038855840.0	25971396.0	GSM1707593 r1	0:40	A:430923990;C:193052690;G:149627446;T:265119627;N:132087	40		430923990	193052690	149627446	265119627	132087	SRX1054375	SRS957217	SRA272222	GEO	IIT, CNR	1	0.01858	0.00322	0.98699	0.23156	40	B	usable mapping rate	illumina	early_illumina	unknown	size_fractionation	unknown	bulk	unknown	unknown	Italy	2015-06-09	Hatching	Embryo	Embryo Imprecise	All anatomical structures
39760	39760	SRR2127901	SRX1118699	SRS1011434	SRP061587	PRJNA290964	Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos	GSE71346	Transcriptome Analysis	To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar.		pubmed:30090366	6 48 0.5µM OTA [miRNA seq]	GSM1832841	tissue:embryo control\|strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:0.5 µM ochratoxin A from 6 hpf to 48 hpf	6 48 0.5µM OTA [miRNA seq]	Initially the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3′ adapter sequence and discarding reads shorter than 18 nucleotides before aligning reads to the Zebrafish genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome	embryo control	6 hpf embryos were treated with ochratoxin A 0.5 mM till 48 hpf.	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	zebrafish embryos were selected at 6 hph with normal development.	strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:0.5 µM ochratoxin A from 6 hpf to 48 hpf	GSM1832841	GSM1832841: 6 48 0.5µM OTA [miRNA seq]; Danio rerio; miRNA Seq	GSM1832841		1	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	GEO Accession:GSM1832841	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP061587	6_48_0.5um_OTA.fastq.gz	fastq	310077729.0	6130868.0	GSM1832841 r1	0:50.58 1:0	A:74462826;C:72958352;G:87201353;T:75455198;N:0	50	0	74462826	72958352	87201353	75455198	0	SRX1118699	SRS1011434	SRA280185	GEO	ntu	1	0.00671	0.00134	0.99594	0.39026	51	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Unknown	2015-07-25	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
39761	39761	SRR2127900	SRX1118698	SRS1011435	SRP061587	PRJNA290964	Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos	GSE71346	Transcriptome Analysis	To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar.		pubmed:30090366	6 48 control [miRNA seq]	GSM1832840	tissue:embryo control\|strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:n1 control	6 48 control [miRNA seq]	Initially the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3′ adapter sequence and discarding reads shorter than 18 nucleotides before aligning reads to the Zebrafish genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome	embryo control	6 hpf embryos were treated with ochratoxin A 0.5 mM till 48 hpf.	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	zebrafish embryos were selected at 6 hph with normal development.	strain:Wild Type AB line\|developemental stage:6 hpf embryos\|exposed to:n1 control	GSM1832840	GSM1832840: 6 48 control [miRNA seq]; Danio rerio; miRNA Seq	GSM1832840		1	Total RNA was extracted by Trizol® Reagent Invitrogen USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology USA and qualitated by using a Bioanalyzer 2100 Agilent Technology USA with RNA 6000 labchip kit Agilent Technologies USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene Taipei Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters. Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software	GEO Accession:GSM1832840	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx	SRP061587	6_48_control.fastq.gz	fastq	308947811.0	6107500.0	GSM1832840 r1	0:50.58 1:0	A:75126425;C:71798677;G:85490341;T:76532368;N:0	50	0	75126425	71798677	85490341	76532368	0	SRX1118698	SRS1011435	SRA280185	GEO	ntu	1	0.00833	0.00166	0.99476	0.42762	51	T	under 1.2% mapping rate	illumina	early_illumina	unknown	size_fractionation	trueseq	bulk	unknown	unknown	Unknown	2015-07-25	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41406	41406	SRR4423130	SRX2245314	SRS1745863	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 10 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:prim 16 stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: prim 16 stage31 hpf	348 10	348 10	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S10small.fastq	fastq	427409571.0	5026564.0	S10small.fastq	0:85.03	A:98026046;C:116630773;G:114413502;T:98339250;N:0	85		98026046	116630773	114413502	98339250	0	SRX2245314	SRS1745863	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.81583	0.17938	0.9094	0.63072	126	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
41407	41407	SRR4423129	SRX2245313	SRS1745862	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 9 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:prim 5 stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: prim 5 stage24 hpf	348 9	348 9	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S09small.fastq	fastq	516614705.0	6246071.0	S09small.fastq	0:82.71	A:117786535;C:140799134;G:139362428;T:118666608;N:0	82		117786535	140799134	139362428	118666608	0	SRX2245313	SRS1745862	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.81132	0.18952	0.88925	0.69719	17	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Pharyngula	Embryo	Embryo Imprecise	All anatomical structures
41408	41408	SRR4423128	SRX2245312	SRS1745850	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 12 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:protruding mouth stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: protruding mouth stage72 hpf	348 12	348 12	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S12small.fastq	fastq	186817590.0	3062463.0	S12small.fastq	0:61.00	A:42863072;C:49941244;G:49513828;T:44499446;N:0	61		42863072	49941244	49513828	44499446	0	SRX2245312	SRS1745850	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.77668	0.17381	0.8915	0.54189	36	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Larval	Larval	Embryo Imprecise	All anatomical structures
41409	41409	SRR4423127	SRX2245311	SRS1745851	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 11 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:long pec stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: long pec stage48 hpf	348 11	348 11	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S11small.fastq	fastq	405003101.0	5197273.0	S11small.fastq	0:77.93	A:93494059;C:109265919;G:106696649;T:95546474;N:0	77		93494059	109265919	106696649	95546474	0	SRX2245311	SRS1745851	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.78244	0.17047	0.93379	0.6272	30	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Hatching	Embryo	Embryo Imprecise	All anatomical structures
41428	41428	SRR4423108	SRX2245292	SRS1745857	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 5 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:90% epiboly stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: 90% epiboly stage 9 hpf	348 5	348 5	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S05small.fastq	fastq	412237561.0	3386443.0	S05small.fastq	0:121.73	A:91644321;C:118905395;G:115070912;T:86616933;N:0	121		91644321	118905395	115070912	86616933	0	SRX2245292	SRS1745857	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.81233	0.06309	0.93385	0.93973	163	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41429	41429	SRR4423107	SRX2245291	SRS1745856	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 6 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:4 somite stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: 4 somite stage11.3 hpf	348 6	348 6	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S06small.fastq	fastq	535288776.0	4443685.0	S06small.fastq	0:120.46	A:119322177;C:152704452;G:149509408;T:113752739;N:0	120		119322177	152704452	149509408	113752739	0	SRX2245291	SRS1745856	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.82872	0.09035	0.93194	0.81296	159	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
41430	41430	SRR4423106	SRX2245290	SRS1745854	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 3 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:zfs:0000015 stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: zfs:0000015 stage 4.7 hpf	348 3	348 3	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S03small.fastq	fastq	1025732824.0	7452991.0	S03small.fastq	0:137.63	A:225573059;C:298586545;G:288470386;T:213102834;N:0	137		225573059	298586545	288470386	213102834	0	SRX2245290	SRS1745854	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.8983	0.04271	0.95546	0.91281	159	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41431	41431	SRR4423105	SRX2245289	SRS1745855	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 4 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:70% epiboly stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: 70% epiboly stage7 hpf	348 4	348 4	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S04small.fastq	fastq	193259658.0	1840126.0	S04small.fastq	0:105.03	A:43516548;C:54669405;G:53501927;T:41571778;N:0	105		43516548	54669405	53501927	41571778	0	SRX2245289	SRS1745855	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.81053	0.16265	0.90698	0.92112	159	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Gastrula	Embryo	Embryo Imprecise	All anatomical structures
41432	41432	SRR4423104	SRX2245288	SRS1745853	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 1 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:64 cells\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: 64 cells2 hpf	348 1	348 1	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S01small.fastq	fastq	91910627.0	1396009.0	S01small.fastq	0:65.84	A:21663404;C:25661192;G:25069267;T:19516764;N:0	65		21663404	25661192	25069267	19516764	0	SRX2245288	SRS1745853	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.56828	0.1715	0.92435	0.90047	34	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Cleavage	Embryo	Embryo Imprecise	All anatomical structures
41433	41433	SRR4423103	SRX2245287	SRS1745852	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 2 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:high stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: high stage3.3 hpf	348 2	348 2	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S02small.fastq	fastq	304535574.0	3376105.0	S02small.fastq	0:90.20	A:69193719;C:84372087;G:86707481;T:64262287;N:0	90		69193719	84372087	86707481	64262287	0	SRX2245287	SRS1745852	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.56812	0.09695	0.93474	0.93654	51	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Blastula	Embryo	Embryo Imprecise	All anatomical structures
41436	41436	SRR4423100	SRX2245284	SRS1745849	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 7 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:12 somite stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: 12 somite stage15 hpf	348 7	348 7	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S07small.fastq	fastq	279201769.0	2713759.0	S07small.fastq	0:102.88	A:61655863;C:78667355;G:77702440;T:61176111;N:0	102		61655863	78667355	77702440	61176111	0	SRX2245284	SRS1745849	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.79087	0.10046	0.89221	0.77892	158	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
41437	41437	SRR4423099	SRX2245283	SRS1745848	SRP091534	PRJNA347637	Danio rerio and Xenopus laevis Raw sequence reads	PRJNA347637	Other	To study the transcriptome during development				Time course 8 Dr	strain:not applicable\|isolate:not applicable\|breed:ABTL\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:22 somite stage\|sex:not determined\|tissue:single embryo\|BioSampleModel:Model organism or animal									miRNA Seq of Zebrafish: 22 somite stage20 hpf	348 8	348 8	Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton	SRP091534	S08small.fastq	fastq	520785540.0	4495080.0	S08small.fastq	0:115.86	A:115224831;C:149325753;G:144978190;T:111256766;N:0	115		115224831	149325753	144978190	111256766	0	SRX2245283	SRS1745848	SRA485147	Universiteit van Amsterdam\|SILS	Universiteit van Amsterdam	1	0.83781	0.08976	0.92904	0.80492	183	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-19	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
49101	49101	SRR7726444	SRX4582847	SRS3697100	SRP158508	PRJNA487021	MicroRNA expression signatures for gata4/5/6 knocking down in zebrafish	GSE118850	Transcriptome Analysis	Previous works showed that gata4/5/6 lie at the hierarchical apex of the regulatory network of the hemangioblast formation and primitive myelopoiesis in zebrafish. To explore the roles of miRNAs in zebrafish primitive myelopoiesis we employed deep sequencing to analyze the difference of miRNA expression profiles between gata4/5/6 knockdown embryos gata5/6 morphants and control embryos. Overall design: The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for collected for miRNA deep sequencing.The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo.			G56 miRNA	GSM3349122	tissue:G56 embryos\|genotype:gata4/5/6 knockdown\|developmental stage:embryos\|age:14hpf	G56 miRNA	The cDNA library was sequenced using Illumina Solexa following version 8 multiplexed single read sequencing recipe. Fastx fastx toolkit 0.0.13.2 was used to preprocess the original reads of the sequence. The CLC genomics workbench5.5 was applied to match the preprocessed sequence to the Sanger miRBase database version 19.0. Genome build: Sanger miRBase database version 19.0 Supplementary files format and content: .csv file includes small RNA sequences and counts Supplementary files format and content: .xls file includes effective reads and fold changes	G56 embryos	Morpholinos MOs were purchased from Gene Tools http://www.gene tools.com. MOs were dissolved in nanopure water and microinjected into the embryos at xxx cell stages. The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo. The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for analyzing the miRNA expression changes affected by knocking down gata4/5/6.	Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The 3’ and 5’ adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp.	Zebrafish were housed in the zebrafish room of Model Animal Research Center Nanjing University in accordance with IACUC approved protocol. All methods were performed in accordance with the relevant guidelines and regulations.	genotype:gata4/5/6 knockdown\|developmental stage:embryos\|age:14hpf	GSM3349122	GSM3349122: G56 miRNA; Danio rerio; miRNA Seq	GSM3349122		1	Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The three prime and five prime adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp.	GEO Accession:GSM3349122	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina MiSeq	SRP158508			655037050.0	13100741.0	GSM3349122 r1	0:50 1:0	A:161448247;C:135821164;G:200213833;T:156824030;N:729776	50	0	161448247	135821164	200213833	156824030	729776	SRX4582847	SRS3697100	SRA761361	GEO	Nanjing University	1	0.00066	6e-05	0.99896	0.64583	50	T	under 1.2% mapping rate	illumina	miseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-08-21	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
49102	49102	SRR7726443	SRX4582846	SRS3697099	SRP158508	PRJNA487021	MicroRNA expression signatures for gata4/5/6 knocking down in zebrafish	GSE118850	Transcriptome Analysis	Previous works showed that gata4/5/6 lie at the hierarchical apex of the regulatory network of the hemangioblast formation and primitive myelopoiesis in zebrafish. To explore the roles of miRNAs in zebrafish primitive myelopoiesis we employed deep sequencing to analyze the difference of miRNA expression profiles between gata4/5/6 knockdown embryos gata5/6 morphants and control embryos. Overall design: The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for collected for miRNA deep sequencing.The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo.			WT miRNA	GSM3349121	tissue:WT embryos\|genotype:wild type\|developmental stage:embryos\|age:14hpf	WT miRNA	The cDNA library was sequenced using Illumina Solexa following version 8 multiplexed single read sequencing recipe. Fastx fastx toolkit 0.0.13.2 was used to preprocess the original reads of the sequence. The CLC genomics workbench5.5 was applied to match the preprocessed sequence to the Sanger miRBase database version 19.0. Genome build: Sanger miRBase database version 19.0 Supplementary files format and content: .csv file includes small RNA sequences and counts Supplementary files format and content: .xls file includes effective reads and fold changes	WT embryos	Morpholinos MOs were purchased from Gene Tools http://www.gene tools.com. MOs were dissolved in nanopure water and microinjected into the embryos at xxx cell stages. The microinjection amount was 1 nl solution containing 6.25 ng gata5 MO and 1.25 ng gata6 MO or 7.5 ng control MO per embryo. The embryos microinjected with control MO or gata5/6 MOs at 1 cell stage were collected at 14 hpf for analyzing the miRNA expression changes affected by knocking down gata4/5/6.	Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The 3’ and 5’ adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp.	Zebrafish were housed in the zebrafish room of Model Animal Research Center Nanjing University in accordance with IACUC approved protocol. All methods were performed in accordance with the relevant guidelines and regulations.	genotype:wild type\|developmental stage:embryos\|age:14hpf	GSM3349121	GSM3349121: WT miRNA; Danio rerio; miRNA Seq	GSM3349121		1	Total RNA was isolated from 80 of the 14 hpf embryos and its quantity was examined by electrophoresis using Agilent Bioanalyzer 2100 Agilent Technologies Santa Clara US. The miRNA was isolated using mirVana miRNA Isolation Kit Life technologies USA from the total RNA. The three prime and five prime adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98℃ 30 s 11 × 98℃ 10 s 60℃ 30 s 72 ℃ 15 s for 72 ℃ 10 min 4℃. The cDNA was separated by 6% Novex TBE PAGE Gel for collecting the fragments with 147 157 nt long. The cDNA library was constructed and the quantity was examined using a commercial kit Qubit™ dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/µl and the size of cDNA was 140 160 bp.	GEO Accession:GSM3349121	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina MiSeq	SRP158508			627151350.0	12543027.0	GSM3349121 r1	0:50 1:0	A:153340174;C:128104541;G:192611227;T:152395340;N:700068	50	0	153340174	128104541	192611227	152395340	700068	SRX4582846	SRS3697099	SRA761361	GEO	Nanjing University	1	0.0006	0.00012	0.99904	0.60759	50	T	under 1.2% mapping rate	illumina	miseq	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2018-08-21	Segmentation	Embryo	Embryo Imprecise	All anatomical structures
53169	53169	SRR9697470	SRX6455747	SRS5113424	SRP215029	PRJNA555064	Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells	GSE134399	Transcriptome Analysis	MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.		pubmed:31923196	ZF4 18 30d cold3	GSM3946004	tissue:embryonic fibroblast cells\|cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:cultured at 18 C for 30 days\|treatment:cold treatment for 30 days	ZF4 18 30d cold3	Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs	embryonic fibroblast cells	For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days.	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2.	cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:cultured at 18 C for 30 days\|treatment:cold treatment for 30 days	GSM3946004	GSM3946004: ZF4 18 30d cold3; Danio rerio; miRNA Seq	GSM3946004		1	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	GEO Accession:GSM3946004	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq X Ten	SRP215029	6.fq.gz	fastq	888718150.0	17774363.0	GSM3946004 r1	0:50	A:200112040;C:206776226;G:254640770;T:227172753;N:16361	50		200112040	206776226	254640770	227172753	16361	SRX6455747	SRS5113424	SRA922199	GEO	Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University	1	0.00546	0.00027	0.99799	0.4985	50	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2019-07-17	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
53170	53170	SRR9697469	SRX6455746	SRS5113421	SRP215029	PRJNA555064	Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells	GSE134399	Transcriptome Analysis	MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.		pubmed:31923196	ZF4 18 30d cold2	GSM3946003	tissue:embryonic fibroblast cells\|cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:cultured at 18 C for 30 days\|treatment:cold treatment for 30 days	ZF4 18 30d cold2	Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs	embryonic fibroblast cells	For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days.	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2.	cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:cultured at 18 C for 30 days\|treatment:cold treatment for 30 days	GSM3946003	GSM3946003: ZF4 18 30d cold2; Danio rerio; miRNA Seq	GSM3946003		1	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	GEO Accession:GSM3946003	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq X Ten	SRP215029	5.fq.gz	fastq	853031700.0	17060634.0	GSM3946003 r1	0:50	A:192338096;C:205750986;G:242627478;T:212299265;N:15875	50		192338096	205750986	242627478	212299265	15875	SRX6455746	SRS5113421	SRA922199	GEO	Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University	1	0.00538	0.00045	0.99738	0.47457	50	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2019-07-17	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
53171	53171	SRR9697468	SRX6455745	SRS5113422	SRP215029	PRJNA555064	Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells	GSE134399	Transcriptome Analysis	MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.		pubmed:31923196	ZF4 18 30d cold1	GSM3946002	tissue:embryonic fibroblast cells\|cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:cultured at 18 C for 30 days\|treatment:cold treatment for 30 days	ZF4 18 30d cold1	Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs	embryonic fibroblast cells	For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days.	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2.	cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:cultured at 18 C for 30 days\|treatment:cold treatment for 30 days	GSM3946002	GSM3946002: ZF4 18 30d cold1; Danio rerio; miRNA Seq	GSM3946002		1	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	GEO Accession:GSM3946002	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq X Ten	SRP215029	4.fq.gz	fastq	878731000.0	17574620.0	GSM3946002 r1	0:50	A:196907854;C:209105082;G:251308531;T:221393524;N:16009	50		196907854	209105082	251308531	221393524	16009	SRX6455745	SRS5113422	SRA922199	GEO	Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University	1	0.01219	0.00089	0.99691	0.52247	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2019-07-17	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
53172	53172	SRR9697467	SRX6455744	SRS5113420	SRP215029	PRJNA555064	Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells	GSE134399	Transcriptome Analysis	MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.		pubmed:31923196	ZF4 28 con3	GSM3946001	tissue:embryonic fibroblast cells\|cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:normal cultured 28 C\|treatment:control	ZF4 28 con3	Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs	embryonic fibroblast cells	For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days.	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2.	cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:normal cultured 28 C\|treatment:control	GSM3946001	GSM3946001: ZF4 28 con3; Danio rerio; miRNA Seq	GSM3946001		1	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	GEO Accession:GSM3946001	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq X Ten	SRP215029	3.fq.gz	fastq	908953950.0	18179079.0	GSM3946001 r1	0:50	A:206519605;C:210829105;G:259204569;T:232383846;N:16825	50		206519605	210829105	259204569	232383846	16825	SRX6455744	SRS5113420	SRA922199	GEO	Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University	1	0.00508	0.00042	0.99756	0.48	50	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2019-07-17	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
53173	53173	SRR9697466	SRX6455743	SRS5113423	SRP215029	PRJNA555064	Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells	GSE134399	Transcriptome Analysis	MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.		pubmed:31923196	ZF4 28 con2	GSM3946000	tissue:embryonic fibroblast cells\|cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:normal cultured 28 C\|treatment:control	ZF4 28 con2	Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs	embryonic fibroblast cells	For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days.	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2.	cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:normal cultured 28 C\|treatment:control	GSM3946000	GSM3946000: ZF4 28 con2; Danio rerio; miRNA Seq	GSM3946000		1	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	GEO Accession:GSM3946000	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq X Ten	SRP215029	2.fq.gz	fastq	876929500.0	17538590.0	GSM3946000 r1	0:50	A:198651931;C:204780756;G:249251465;T:224229047;N:16301	50		198651931	204780756	249251465	224229047	16301	SRX6455743	SRS5113423	SRA922199	GEO	Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University	1	0.01465	0.00237	0.99559	0.5232	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2019-07-17	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
53174	53174	SRR9697465	SRX6455742	SRS5113425	SRP215029	PRJNA555064	Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells	GSE134399	Transcriptome Analysis	MicroRNAs miRNAs play vital roles in various biological processes by leading to mRNA cleavage or translational repression and are also involved in multiple stress conditions. However the detailed roles of miRNAs in cold acclimation in fish are still unclear. In the present study high throughput sequencing was performed to identify miRNAs from 6 small RNA libraries from the zebrafish embryonic fibroblast ZF4 cells under control 28°C 30 days and cold acclimation 18°C 30 days conditions. A total of 414 miRNAs 349 known and 65 novel were identified. Among those miRNAs 24 19 known and 5 novel were up regulated and 23 9 known and 14 novel were down regulated in cold acclimated cells. The Gene Ontology GO and Kyoto Encyclopaedia of Genes and Genomes KEGG enrichment analyses indicated that the known differentially expressed miRNAs DE miRNA are involved in cold acclimation by regulation of phosphorylation cell junction intracellular signal transduction ECM receptor interaction and so on. Moreover dre miR 100 3p inhibitor or dre miR 16b mimics could protect ZF4 cells under cold stress indicating the involvement of miRNA in cold acclimation. In summary the present data show that miRNAs are closely involved in cold acclimation in fish and provide information for further understanding of the roles of miRNAs in cold acclimation. Overall design: ZF4 cells were cultured at 28 °C as control and at 18 °C for 30 days seperately. Each condition has three biological replica.		pubmed:31923196	ZF4 28 con1	GSM3945999	tissue:embryonic fibroblast cells\|cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:normal cultured 28 C\|treatment:control	ZF4 28 con1	Illumina Casava1.8 software used for basecalling. Clean reads were obtained from raw sequences post removing all low quality reads N% > 5% or with ploy A contaminants reads smaller than 17 nt or longer than 35 nt and trimming the adapters. Clean reads were mapped to zebrafish reference non coding RNA sequences danRer10 ftp://ftp.ensembl.org/pub/release 91/fasta/ danio rerio/ncrna/ using bowtie 2.3.0 To identify the miRNAs associated with cold acclimation clean reads were aligned to known zebrafish miRNAs database miRBase22 http://www.mirbase.org/ using bowtie2.3.0. The miRNAs expression levels were estimated by TPM Transcripts per million Genome build: GRCz10 Supplementary files format and content: tab delimited text files include TPM values for novel micRNAs	embryonic fibroblast cells	For cold acclimation ZF4 cells were seeded at 50% confluence and the next day transferred to an incubator at 18˚C 5% CO2 in the same medium for 30 days.	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	ZF4 cell line was from the American Type Culture Collection ATCC CRL 2050. Cells were cultured in Dulbecco's modified Eagle's medium/F12 nutrient mix SH30023.01B Hyclone Thermo Scientific supplemented with 10% fetal bovine serum 10099141 Gibco Life technologies 1% penicillin streptomycin glutamine solution SV30082.01 Hyclone Thermo Scientificat 28°C 5% CO2.	cell line:ZF4\|cell type:fibroblast cell line\|growth temperature:normal cultured 28 C\|treatment:control	GSM3945999	GSM3945999: ZF4 28 con1; Danio rerio; miRNA Seq	GSM3945999		1	Total RNA was extracted using miRNeasy Mini Kit 217004 Qiagen and purified by RNAClean XP Kit A63987 Beckman Coulter and RNase Free DNase Set 79254 Qiagen. Libraries were pooled and sequenced using the Illumina HiSeq machine as 50 bp single end sequencing reads.	GEO Accession:GSM3945999	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq X Ten	SRP215029	1.fq.gz	fastq	957098100.0	19141962.0	GSM3945999 r1	0:50	A:217645979;C:223129215;G:273039214;T:243266316;N:17376	50		217645979	223129215	273039214	243266316	17376	SRX6455742	SRS5113425	SRA922199	GEO	Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, College of Fisheries and Life Science, Shanghai Ocean University	1	0.00967	0.0007	0.99701	0.51905	50	T	under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown	China	2019-07-17	Undetermined	Embryo	Embryo Imprecise	All anatomical structures
57186	57186	SRR11263444	SRX7870077	SRS6278494	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061		miRNA of MZdgcr8 3	GSM4396432	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	miRNA of MZdgcr8 3	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo		small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	GSM4396432	GSM4396432: miRNA of MZdgcr8 3; Danio rerio; miRNA Seq	GSM4396432		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396432	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	MZ_3_miRNA.fq.gz	fastq	602855750.0	12057115.0	GSM4396432 r1	0:50 1:0	A:146678206;C:139956283;G:181049484;T:135139840;N:31937	50	0	146678206	139956283	181049484	135139840	31937	SRX7870077	SRS6278494	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.00091	0.0001	0.9987	0.73076	50	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57187	57187	SRR11263443	SRX7870076	SRS6278493	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061		miRNA of MZdgcr8 2	GSM4396431	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	miRNA of MZdgcr8 2	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo		small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	GSM4396431	GSM4396431: miRNA of MZdgcr8 2; Danio rerio; miRNA Seq	GSM4396431		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396431	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	MZ_2_miRNA.fq.gz	fastq	532605954.0	10443254.0	GSM4396431 r1	0:51 1:0	A:124901241;C:134604417;G:148078897;T:124932015;N:89384	51	0	124901241	134604417	148078897	124932015	89384	SRX7870076	SRS6278493	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.0002	2e-05	0.99935	0.51428	51	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57188	57188	SRR11263442	SRX7870075	SRS6278492	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061		miRNA of MZdgcr8 1	GSM4396430	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	miRNA of MZdgcr8 1	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo		small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:MZdgcr8	GSM4396430	GSM4396430: miRNA of MZdgcr8 1; Danio rerio; miRNA Seq	GSM4396430		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396430	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	MZ_1_miRNA.fq.gz	fastq	588374148.0	11536748.0	GSM4396430 r1	0:51 1:0	A:137533072;C:149724383;G:163915952;T:137198731;N:2010	51	0	137533072	149724383	163915952	137198731	2010	SRX7870075	SRS6278492	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.0014	0.00031	0.99795	0.62441	51	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57189	57189	SRR11263441	SRX7870074	SRS6278490	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061		miRNA of Wild type 3	GSM4396429	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	miRNA of Wild type 3	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo		small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	GSM4396429	GSM4396429: miRNA of Wild type 3; Danio rerio; miRNA Seq	GSM4396429		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396429	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	WT_3_miRNA.fq.gz	fastq	688929450.0	13778589.0	GSM4396429 r1	0:50 1:0	A:171239999;C:140558088;G:209452609;T:167641448;N:37306	50	0	171239999	140558088	209452609	167641448	37306	SRX7870074	SRS6278490	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.00247	0.00016	0.99797	0.60356	50	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57190	57190	SRR11263440	SRX7870073	SRS6278491	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061		miRNA of Wild type 2	GSM4396428	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	miRNA of Wild type 2	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo		small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	GSM4396428	GSM4396428: miRNA of Wild type 2; Danio rerio; miRNA Seq	GSM4396428		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396428	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	WT_2_miRNA.fq.gz	fastq	680017935.0	13333685.0	GSM4396428 r1	0:51 1:0	A:161673690;C:168811670;G:190321246;T:159208682;N:2647	51	0	161673690	168811670	190321246	159208682	2647	SRX7870073	SRS6278491	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.03809	0.00119	0.99318	0.59584	51	B	usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures
57191	57191	SRR11263439	SRX7870072	SRS6278489	SRP251978	PRJNA611062	Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]	GSE146605	Transcriptome Analysis	Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing in triplicate.	parent bioproject:PRJNA611061		miRNA of Wild type 1	GSM4396427	source name:Embryo\|strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	miRNA of Wild type 1	Subsequently unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both three prime and five prime ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 22.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software http://rna.tbi.univie.ac. at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem ≤12 2 number of base pairs in the stem region of the predicted hairpin ≥16 3 cutoff of free energy kCal/mol ≤ 15 4 length of hairpin up and down stems + terminal loop ≥50 5 length of hairpin loop ≤200. 6 number of nucleotides in one bulge in mature region ≤4 7 number of biased errors in one bulge in mature region ≤2 8 number of biased bulges in mature region ≤2 9 number of errors in mature region ≤4 10 number of base pairs in the mature region of the predicted hairpin ≥12 11 percent of mature in stem ≥80. Supplementary files format and content: excel expression profiles	Embryo		small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:embryo\|age:4.5hpf\|genotype:wild type	GSM4396427	GSM4396427: miRNA of Wild type 1; Danio rerio; miRNA Seq	GSM4396427		1	small RNA was extracted from MZdcgr8 and Wild type embryos 50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4396427	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP251978	WT_1_miRNA.fq.gz	fastq	606884853.0	11899703.0	GSM4396427 r1	0:51 1:0	A:144656910;C:150045615;G:169161904;T:143018153;N:2271	51	0	144656910	150045615	169161904	143018153	2271	SRX7870072	SRS6278489	SRA1052219	GEO	The Chinese University of Hong Kong	1	0.0559	0.00242	0.99064	0.54228	51	B	usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown	China	2020-03-08	Blastula	Embryo	Embryo Imprecise	All anatomical structures

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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");;