metadata: run_metadata: 134 rows where experiment.library_strategy = "miRNA-Seq", technology = "unknown" and tissue_curation

134 rows where experiment.library_strategy = "miRNA-Seq", technology = "unknown" and tissue_curation_coarse = "All anatomical structures"

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.description	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.spot_descriptor	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
39671	39671	SRR2043046	SRX1041307	SRS947739	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			HBCD 200nM sample3	zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3	HBCD 200nM 3	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:HBCD 200nM 3\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3	Sample HBCD 200nM 3	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729		Sample_HBCD_200nM-3.fastq.tar.gz	fastq	549695784.0	16657448.0	Sample HBCD 200nM 3	0:33	A:120885057;C:120386921;G:146939259;T:161323403;N:161144	33		120885057	120386921	146939259	161323403	161144	SRX1041307	SRS947739	SRA269780	MG	Xiamen University	1	0.13819	0.03714	0.94968	0.52004	33	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-09-18	Larval	Larval	Whole Organism	All anatomical structures
39672	39672	SRR2043044	SRX1041306	SRS947738	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			HBCD 200nM sample2	zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep2	HBCD 200nM 2	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:HBCD 200nM 2\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2	Sample HBCD 200nM 2	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729		Sample_HBCD_200nM-2.fastq.tar.gz	fastq	566585217.0	17169249.0	Sample HBCD 200nM 2	0:33	A:119904892;C:129504656;G:159539041;T:157545273;N:91355	33		119904892	129504656	159539041	157545273	91355	SRX1041306	SRS947738	SRA269780	MG	Xiamen University	1	0.07072	0.01837	0.96246	0.52439	33	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-05-27	Larval	Larval	Whole Organism	All anatomical structures
39673	39673	SRR2043035	SRX1041305	SRS947737	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			HBCD 200nM sample1	zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep1	HBCD 200nM 1	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:HBCD 200nM 1\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep1	Sample HBCD 200nM 1	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729		Sample_HBCD_200nM-1.fastq.tar.gz	fastq	636936228.0	17692673.0	Sample HBCD 200nM 1	0:36	A:138321201;C:126054708;G:184822056;T:187709777;N:28486	36		138321201	126054708	184822056	187709777	28486	SRX1041305	SRS947737	SRA269780	MG	Xiamen University	1	0.04374	0.0115	0.97839	0.29573	36	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-09-18	Larval	Larval	Whole Organism	All anatomical structures
39674	39674	SRR2043030	SRX1041276	SRS947712	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			HBCD 2nM sample3	zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep3	HBCD 2nM 3	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:HBCD 2nM 3\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3	Sample HBCD 2nM 3	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729		Sample_HBCD_2nM-3.fastq.tar.gz	fastq	636936228.0	17692673.0	Sample HBCD 2nM 3	0:36	A:138321201;C:126054708;G:184822056;T:187709777;N:28486	36		138321201	126054708	184822056	187709777	28486	SRX1041276	SRS947712	SRA269780	MG	Xiamen University	1	0.04377	0.01174	0.97812	0.30675	36	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-05-27	Larval	Larval	Whole Organism	All anatomical structures
39675	39675	SRR2042999	SRX1041271	SRS947707	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			HBCD 2nM sample2	zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2	HBCD 2nM 2	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:HBCD 2nM 2\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2	Sample HBCD 2nM 2	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729		Sample_HBCD_2nM-2.fastq.tar.gz	fastq	482176476.0	13393791.0	Sample HBCD 2nM 2	0:36	A:104565872;C:92998014;G:137403437;T:147164823;N:44330	36		104565872	92998014	137403437	147164823	44330	SRX1041271	SRS947707	SRA269780	MG	Xiamen University	1	0.0759	0.02077	0.97025	0.33489	36	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-09-18	Larval	Larval	Whole Organism	All anatomical structures
39676	39676	SRR2040574	SRX1038901	SRS945650	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			HBCD 2nM sample1	zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep1	HBCD 2nM 1	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:HBCD 2nM 1\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep1	Sample HBCD 2nM 1	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729		Sample_HBCD_2nM-1.fastq.tar.gz	fastq	327925620.0	9109045.0	Sample HBCD 2nM 1	0:36	A:71167117;C:63917852;G:94874537;T:97936051;N:30063	36		71167117	63917852	94874537	97936051	30063	SRX1038901	SRS945650	SRA269780	MG	Xiamen University	1	0.06484	0.01622	0.97459	0.35746	36	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-05-27	Larval	Larval	Whole Organism	All anatomical structures
39677	39677	SRR2040573	SRX1038898	SRS945648	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			HBCD 0nM sample3	zebrafish at normal developmental age of 72hpf in the control rep3	control 3	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:control 3\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the control rep3	Sample control 3	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729		Sample_control-3.fastq.tar.gz	fastq	456812301.0	13842797.0	Sample control 3	0:33	A:99424011;C:100923631;G:121758068;T:134398048;N:308543	33		99424011	100923631	121758068	134398048	308543	SRX1038898	SRS945648	SRA269780	MG	Xiamen University	1	0.14866	0.03878	0.95079	0.53781	33	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-09-18	Larval	Larval	Whole Organism	All anatomical structures
39678	39678	SRR2040572	SRX1038893	SRS945643	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			HBCD 0nM sample2	zebrafish at normal developmental age of 72hpf in the control rep2	control 2	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:control 2\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the control rep2	Sample control 2	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729				451846230.0	13692310.0	Sample control 2	0:33	A:100056403;C:97812076;G:121442936;T:132449348;N:85467	33		100056403	97812076	121442936	132449348	85467	SRX1038893	SRS945643	SRA269780	MG	Xiamen University	1	0.06007	0.01901	0.96794	0.4743	33	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-05-27	Larval	Larval	Whole Organism	All anatomical structures
39679	39679	SRR2040562	SRX1038887	SRS945623	SRP058729	PRJNA284830	MicroRNA expression changes during zebrafish Danio rerio development induced by hexabromocyclododecane	PRJNA284830	Whole Genome Sequencing	Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 and 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.			Hexabromocyclododecane HBCD one of the most widely used brominated flame retardants has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 200 nM. Subsequently RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.	zebrafish at normal developmental age of 72hpf in the control rep1	control 1	breed:zebrafish\|strain:Wild type TU strain\|age:72 hpf£¨hpf stage:embryo\|sex:pooled male and female\|tissue:whole zebrafish\|treatment:control 1\|BioSampleModel:Model organism or animal									zebrafish at normal developmental age of 72hpf in the control rep1	Sample control 1	1	1			miRNA-Seq	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP058729		Sample_control-1.fastq.tar.gz	fastq	398024253.0	12061341.0	Sample control 1	0:33	A:90133666;C:86672655;G:103932053;T:117192591;N:93288	33		90133666	86672655	103932053	117192591	93288	SRX1038887	SRS945623	SRA269780	MG	Xiamen University	1	0.08082	0.02367	0.96106	0.52033	33	B	usable mapping rate	illumina	early_illumina	unknown	small_rna	unknown	bulk	unknown	unknown	China	2015-05-27	Larval	Larval	Whole Organism	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
41244	41244	SRR3953261	SRX1977497	SRS1585138	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		500 μg/l BDE47 treatment miRNA	GSM2252184	source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	500 μg/l BDE47 treatment miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252184	GSM2252184: 500 μg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq	GSM2252184		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252184	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896		Sample_500_1_filtered.fastq.gz	fastq	427211416.0	18037304.0	GSM2252184 r1	0:23.68 1:0	A:104654735;C:95575450;G:107353019;T:119612667;N:15545	23	0	104654735	95575450	107353019	119612667	15545	SRX1977497	SRS1585138	SRA444471	GEO	Tongji University	1	0.85356	0.06282	0.88609	0.63407	21	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41245	41245	SRR3953260	SRX1977496	SRS1585141	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		5 μg/l BDE47 treatment miRNA	GSM2252183	source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	5 μg/l BDE47 treatment miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252183	GSM2252183: 5 μg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq	GSM2252183		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252183	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896		Sample_5_1_filtered.fastq.gz	fastq	450698842.0	19202408.0	GSM2252183 r1	0:23.47 1:0	A:112159775;C:101086362;G:111723361;T:125713845;N:15499	23	0	112159775	101086362	111723361	125713845	15499	SRX1977496	SRS1585141	SRA444471	GEO	Tongji University	1	0.84838	0.06014	0.88637	0.6441	23	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41246	41246	SRR3953259	SRX1977495	SRS1585136	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		s DMSO vehicle miRNA	GSM2252182	source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	s DMSO vehicle miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252182	GSM2252182: s DMSO vehicle miRNA; Danio rerio; miRNA Seq	GSM2252182		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252182	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896		Sample_s_1_filtered.fq.gz	fastq	383701320.0	16988819.0	GSM2252182 r1	0:22.59 1:0	A:97700155;C:85144858;G:93319367;T:107531046;N:5894	22	0	97700155	85144858	93319367	107531046	5894	SRX1977495	SRS1585136	SRA444471	GEO	Tongji University	1	0.86023	0.05501	0.89534	0.59715	22	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	All anatomical structures
41247	41247	SRR3953258	SRX1977494	SRS1585137	SRP079896	PRJNA335352	Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment	GSE84845	Transcriptome Analysis	Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control a dozen of validated zebrafish miRNAs including dre miR 142a 3p dre miR 142b 5p dre miR 144 3p dre miR 146a dre miR 190a dre miR 219 5p dre miR 301b 3p dre miR 459 5p rno miR 33 5p dre miR 735 3p and dre miR 735 5p significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank vehicle and 2 different concentrations of BDE47 treatments.		pubmed:28072866		c Wildtype miRNA	GSM2252181	source name:6 dpf larvae\|strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	c Wildtype miRNA	Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al. Nucleic Acids Research 2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.	6 dpf larvae		Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.		strain:Tuebingen\|tissue:whole larvae\|age:6 dpf	GSM2252181	GSM2252181: c Wildtype miRNA; Danio rerio; miRNA Seq	GSM2252181		1	Zebrafish larvae were homogenized and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 μg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2252181	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP079896		Sample_c_1_filtered.fastq.gz	fastq	413922462.0	17365113.0	GSM2252181 r1	0:23.84 1:0	A:102173642;C:93233248;G:103684592;T:114815345;N:15635	23	0	102173642	93233248	103684592	114815345	15635	SRX1977494	SRS1585137	SRA444471	GEO	Tongji University	1	0.85083	0.06831	0.88152	0.63274	27	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown	China	2016-07-26	Larval	Larval	Whole Organism	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
41457	41457	SRR4449278	SRX2267734	SRS1758938	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S09 RID0445	strain:ABTL\|dev stage:54% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S09	S09 RID0445	S09 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_009_rawlib.basecaller.bam	bam	56886794.0	2186951.0	IonXpressRNA 009 rawlib.basecaller.bam	0:26.01	A:15763527;C:12934017;G:13233004;T:14956246;N:0	26		15763527	12934017	13233004	14956246	0	SRX2267734	SRS1758938	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.6501	0.44849	0.83465	0.59625	26	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2016-10-25	Gastrula	Embryo	Whole Organism	All anatomical structures
41458	41458	SRR4449277	SRX2267733	SRS1758937	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S10 RID0445	strain:ABTL\|dev stage:51% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S10	S10 RID0445	S10 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_010_rawlib.basecaller.bam	bam	63108712.0	2361941.0	IonXpressRNA 010 rawlib.basecaller.bam	0:26.72	A:16956361;C:14496251;G:15049416;T:16606684;N:0	26		16956361	14496251	15049416	16606684	0	SRX2267733	SRS1758937	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.64387	0.42592	0.81091	0.58276	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41459	41459	SRR4449276	SRX2267732	SRS1758936	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S07 RID0445	strain:ABTL\|dev stage:47% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S07	S07 RID0445	S07 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_007_rawlib.basecaller.bam	bam	50356775.0	1885340.0	IonXpressRNA 007 rawlib.basecaller.bam	0:26.71	A:13603929;C:11508700;G:12096780;T:13147366;N:0	26		13603929	11508700	12096780	13147366	0	SRX2267732	SRS1758936	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.63582	0.39586	0.79839	0.56846	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41460	41460	SRR4449275	SRX2267731	SRS1758935	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S08 RID0445	strain:ABTL\|dev stage:53% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S08	S08 RID0445	S08 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_008_rawlib.basecaller.bam	bam	63655011.0	2486240.0	IonXpressRNA 008 rawlib.basecaller.bam	0:25.60	A:17274215;C:14286496;G:15277222;T:16817078;N:0	25		17274215	14286496	15277222	16817078	0	SRX2267731	SRS1758935	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.64165	0.41617	0.79931	0.56754	34	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41461	41461	SRR4449274	SRX2267730	SRS1758933	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S05 RID0445	strain:ABTL\|dev stage:58% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S05	S05 RID0445	S05 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_005_rawlib.basecaller.bam	bam	36352941.0	1403002.0	IonXpressRNA 005 rawlib.basecaller.bam	0:25.91	A:10088289;C:8176923;G:8667822;T:9419907;N:0	25		10088289	8176923	8667822	9419907	0	SRX2267730	SRS1758933	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.59289	0.36407	0.80213	0.57695	26	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41462	41462	SRR4449273	SRX2267729	SRS1758934	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S06 RID0445	strain:ABTL\|dev stage:43% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S06	S06 RID0445	S06 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_006_rawlib.basecaller.bam	bam	41157611.0	1592351.0	IonXpressRNA 006 rawlib.basecaller.bam	0:25.85	A:11322629;C:9228187;G:9750979;T:10855816;N:0	25		11322629	9228187	9750979	10855816	0	SRX2267729	SRS1758934	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.63095	0.40683	0.8003	0.56985	29	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41463	41463	SRR4449272	SRX2267728	SRS1758932	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S03 RID0445	strain:ABTL\|dev stage:55% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S03	S03 RID0445	S03 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_003_rawlib.basecaller.bam	bam	60356442.0	2057592.0	IonXpressRNA 003 rawlib.basecaller.bam	0:29.33	A:17060096;C:13661341;G:13721228;T:15913777;N:0	29		17060096	13661341	13721228	15913777	0	SRX2267728	SRS1758932	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.73029	0.49935	0.8225	0.56029	30	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41464	41464	SRR4449271	SRX2267727	SRS1758931	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S04 RID0445	strain:ABTL\|dev stage:54% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S04	S04 RID0445	S04 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_004_rawlib.basecaller.bam	bam	55705225.0	2055064.0	IonXpressRNA 004 rawlib.basecaller.bam	0:27.11	A:15806355;C:12308008;G:12579212;T:15011650;N:0	27		15806355	12308008	12579212	15011650	0	SRX2267727	SRS1758931	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.70796	0.49815	0.81444	0.54452	41	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41465	41465	SRR4449270	SRX2267726	SRS1758930	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S01 RID0445	strain:ABTL\|dev stage:50% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S01	S01 RID0445	S01 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_001_rawlib.basecaller.bam	bam	35407241.0	1342552.0	IonXpressRNA 001 rawlib.basecaller.bam	0:26.37	A:9988109;C:7841340;G:8187069;T:9390723;N:0	26		9988109	7841340	8187069	9390723	0	SRX2267726	SRS1758930	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.63621	0.43661	0.80992	0.53899	31	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41466	41466	SRR4449269	SRX2267725	SRS1758928	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S02 RID0445	strain:ABTL\|dev stage:55% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S02	S02 RID0445	S02 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_002_rawlib.basecaller.bam	bam	40875445.0	1512601.0	IonXpressRNA 002 rawlib.basecaller.bam	0:27.02	A:11593378;C:9124451;G:9444184;T:10713432;N:0	27		11593378	9124451	9444184	10713432	0	SRX2267725	SRS1758928	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.66621	0.45417	0.8127	0.55033	21	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41467	41467	SRR4449267	SRX2267724	SRS1758927	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S15 RID0445	strain:ABTL\|dev stage:52% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S15	S15 RID0445	S15 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_015_rawlib.basecaller.bam	bam	58421266.0	2091074.0	IonXpressRNA 015 rawlib.basecaller.bam	0:27.94	A:16715618;C:13019609;G:13014639;T:15671400;N:0	27		16715618	13019609	13014639	15671400	0	SRX2267724	SRS1758927	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.71786	0.51457	0.83863	0.53442	29	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41468	41468	SRR4449266	SRX2267723	SRS1758929	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S16 RID0445	strain:ABTL\|dev stage:54% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S16	S16 RID0445	S16 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_016_rawlib.basecaller.bam	bam	55022551.0	2073507.0	IonXpressRNA 016 rawlib.basecaller.bam	0:26.54	A:15319738;C:12288588;G:12653066;T:14761159;N:0	26		15319738	12288588	12653066	14761159	0	SRX2267723	SRS1758929	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.68905	0.46941	0.80306	0.55981	26	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41469	41469	SRR4449265	SRX2267722	SRS1758926	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S13 RID0445	strain:ABTL\|dev stage:55% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S13	S13 RID0445	S13 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_013_rawlib.basecaller.bam	bam	49641484.0	2028008.0	IonXpressRNA 013 rawlib.basecaller.bam	0:24.48	A:13840820;C:11016762;G:11715475;T:13068427;N:0	24		13840820	11016762	11715475	13068427	0	SRX2267722	SRS1758926	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.55355	0.3659	0.81576	0.55987	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41470	41470	SRR4449264	SRX2267721	SRS1758925	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S14 RID0445	strain:ABTL\|dev stage:56% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S14	S14 RID0445	S14 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_014_rawlib.basecaller.bam	bam	52969826.0	2019609.0	IonXpressRNA 014 rawlib.basecaller.bam	0:26.23	A:14762618;C:11847782;G:12164393;T:14195033;N:0	26		14762618	11847782	12164393	14195033	0	SRX2267721	SRS1758925	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.65926	0.45113	0.80515	0.56221	22	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41471	41471	SRR4449263	SRX2267720	SRS1758923	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S11 RID0445	strain:ABTL\|dev stage:56% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S11	S11 RID0445	S11 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_011_rawlib.basecaller.bam	bam	54877334.0	2122171.0	IonXpressRNA 011 rawlib.basecaller.bam	0:25.86	A:14884144;C:12539815;G:13173981;T:14279394;N:0	25		14884144	12539815	13173981	14279394	0	SRX2267720	SRS1758923	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.62581	0.40704	0.82002	0.59605	20	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	All anatomical structures
41472	41472	SRR4449262	SRX2267719	SRS1758924	SRP092030	PRJNA350377	Zebrafish Danio Rerio small RNA seq at approx. 50% epiboly	PRJNA350377	Transcriptome Analysis	Small RNAseq experiment of individual embryos from the 8 different spawns taken at gastrulation at approximately 50% epiboly			Danio rerio embryo at approx. 50% epiboly	Danio rerio embryo at approx. 50% epiboly	S12 RID0445	strain:ABTL\|dev stage:53% epiboly\|sex:not applicable\|tissue:whole embryo\|BioSampleModel:Model organism or animal									S12	S12 RID0445	S12 RID0445	Bar coded small RNA sequencing libraries were generated using the Ion Total RNA Seq Kit v2 and the Ion Xpress RNA Seq bar coding kit Thermo Fisher Scientific. Size distribution and yield of the resulting barcoded libraries were assessed using the 2200 TapeStation System with Agilent D1K ScreenTapes Agilent Technologies. Libraries were prepared for sequencing on the Ion Chef System Thermo Fisher Scientific. Sequencing was performed on an Ion Proton System using Ion PI v3 chips Thermo Fisher Scientific.			miRNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ION_TORRENT	Ion Torrent Proton		SRP092030		IonXpressRNA_012_rawlib.basecaller.bam	bam	51987914.0	1937451.0	IonXpressRNA 012 rawlib.basecaller.bam	0:26.83	A:14499922;C:11778716;G:11957347;T:13751929;N:0	26		14499922	11778716	11957347	13751929	0	SRX2267719	SRS1758924	SRA486759	UNIVERSITY OF AMSTERDAM, SILS\|RB&AB	UNIVERSITY OF AMSTERDAM, SILS	1	0.67286	0.44698	0.80919	0.58291	29	B	usable mapping rate	ion_torrent	ion_torrent	unknown	small_rna	unknown	bulk	unknown	unknown	Netherlands	2017-11-01	Gastrula	Embryo	Whole Organism	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
59623	59623	SRR11974583	SRX8518005	SRS6815486	SRP266770	PRJNA638603	small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish	GSE152189	Transcriptome Analysis	In order to investigate transcriptomic mechanisms underlying radiation exposure we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ? and control F1 C parents revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall 22 miRNAs 11 piRNA clusters 19 snRNAs and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data a total of 672 differentially expressed mRNAs could be linked to the DEmiRs of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor NFkB and PTEN signaling linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group 68.8% of which were U1 and U2 snRNAs. In addition 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR LINE and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs indicating expression of DEpiRNAs in response to activation of TEs. Finally 66.7% and 33.3% of lincRNAs in F1 ? were down and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent…		pubmed:33602989		F1 Gamma2 nmbu sncRNA 3	GSM4605882	tissue:Whole embryo\|develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from exposed parents	F1 Gamma2 nmbu sncRNA 3	Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped classified into genomic features and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5 using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values	Whole embryo		Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.		develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from exposed parents	GSM4605882	GSM4605882: F1 Gamma2 nmbu sncRNA 3; Danio rerio; miRNA Seq	GSM4605882		1	Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.	GEO Accession:GSM4605882	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP266770		nmbu_sncRNA_6_raw.fq.gz	fastq	566507200.0	11330144.0	GSM4605882 r1	0:50	A:167677443;C:125843251;G:148647392;T:124217714;N:121400	50		167677443	125843251	148647392	124217714	121400	SRX8518005	SRS6815486	SRA1085407	GEO	Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences	1	0.75254	0.48205	0.84346	0.59219	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Norway	2020-06-10	Gastrula	Embryo	Whole Organism	All anatomical structures
59624	59624	SRR11974582	SRX8518004	SRS6815485	SRP266770	PRJNA638603	small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish	GSE152189	Transcriptome Analysis	In order to investigate transcriptomic mechanisms underlying radiation exposure we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ? and control F1 C parents revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall 22 miRNAs 11 piRNA clusters 19 snRNAs and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data a total of 672 differentially expressed mRNAs could be linked to the DEmiRs of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor NFkB and PTEN signaling linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group 68.8% of which were U1 and U2 snRNAs. In addition 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR LINE and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs indicating expression of DEpiRNAs in response to activation of TEs. Finally 66.7% and 33.3% of lincRNAs in F1 ? were down and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent…		pubmed:33602989		F1 Gamma2 nmbu sncRNA 2	GSM4605881	tissue:Whole embryo\|develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from exposed parents	F1 Gamma2 nmbu sncRNA 2	Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped classified into genomic features and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5 using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values	Whole embryo		Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.		develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from exposed parents	GSM4605881	GSM4605881: F1 Gamma2 nmbu sncRNA 2; Danio rerio; miRNA Seq	GSM4605881		1	Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.	GEO Accession:GSM4605881	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP266770		nmbu_sncRNA_5_raw.fq.gz	fastq	579779650.0	11595593.0	GSM4605881 r1	0:50	A:173232869;C:126599907;G:152751070;T:127092652;N:103152	50		173232869	126599907	152751070	127092652	103152	SRX8518004	SRS6815485	SRA1085407	GEO	Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences	1	0.7644	0.48211	0.84583	0.59288	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Norway	2020-06-10	Gastrula	Embryo	Whole Organism	All anatomical structures
59625	59625	SRR11974581	SRX8518003	SRS6815484	SRP266770	PRJNA638603	small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish	GSE152189	Transcriptome Analysis	In order to investigate transcriptomic mechanisms underlying radiation exposure we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ? and control F1 C parents revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall 22 miRNAs 11 piRNA clusters 19 snRNAs and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data a total of 672 differentially expressed mRNAs could be linked to the DEmiRs of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor NFkB and PTEN signaling linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group 68.8% of which were U1 and U2 snRNAs. In addition 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR LINE and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs indicating expression of DEpiRNAs in response to activation of TEs. Finally 66.7% and 33.3% of lincRNAs in F1 ? were down and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent…		pubmed:33602989		F1 Gamma1 nmbu sncRNA 1	GSM4605880	tissue:Whole embryo\|develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from exposed parents	F1 Gamma1 nmbu sncRNA 1	Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped classified into genomic features and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5 using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values	Whole embryo		Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.		develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from exposed parents	GSM4605880	GSM4605880: F1 Gamma1 nmbu sncRNA 1; Danio rerio; miRNA Seq	GSM4605880		1	Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.	GEO Accession:GSM4605880	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP266770		nmbu_sncRNA_4_raw.fq.gz	fastq	649357050.0	12987141.0	GSM4605880 r1	0:50	A:191891965;C:145644319;G:171130267;T:140550711;N:139788	50		191891965	145644319	171130267	140550711	139788	SRX8518003	SRS6815484	SRA1085407	GEO	Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences	1	0.75002	0.44712	0.84818	0.57467	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Norway	2020-06-10	Gastrula	Embryo	Whole Organism	All anatomical structures
59626	59626	SRR11974580	SRX8518002	SRS6815483	SRP266770	PRJNA638603	small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish	GSE152189	Transcriptome Analysis	In order to investigate transcriptomic mechanisms underlying radiation exposure we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ? and control F1 C parents revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall 22 miRNAs 11 piRNA clusters 19 snRNAs and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data a total of 672 differentially expressed mRNAs could be linked to the DEmiRs of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor NFkB and PTEN signaling linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group 68.8% of which were U1 and U2 snRNAs. In addition 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR LINE and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs indicating expression of DEpiRNAs in response to activation of TEs. Finally 66.7% and 33.3% of lincRNAs in F1 ? were down and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent…		pubmed:33602989		F1 Control3 nmbu sncRNA 3	GSM4605879	tissue:Whole embryo\|develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from control parents	F1 Control3 nmbu sncRNA 3	Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped classified into genomic features and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5 using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values	Whole embryo		Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.		develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from control parents	GSM4605879	GSM4605879: F1 Control3 nmbu sncRNA 3; Danio rerio; miRNA Seq	GSM4605879		1	Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.	GEO Accession:GSM4605879	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP266770		nmbu_sncRNA_3_raw.fq.gz	fastq	641762600.0	12835252.0	GSM4605879 r1	0:50	A:187476040;C:147628502;G:173061052;T:133488938;N:108068	50		187476040	147628502	173061052	133488938	108068	SRX8518002	SRS6815483	SRA1085407	GEO	Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences	1	0.68333	0.36693	0.8493	0.57501	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Norway	2020-06-10	Gastrula	Embryo	Whole Organism	All anatomical structures
59627	59627	SRR11974579	SRX8518001	SRS6815482	SRP266770	PRJNA638603	small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish	GSE152189	Transcriptome Analysis	In order to investigate transcriptomic mechanisms underlying radiation exposure we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ? and control F1 C parents revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall 22 miRNAs 11 piRNA clusters 19 snRNAs and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data a total of 672 differentially expressed mRNAs could be linked to the DEmiRs of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor NFkB and PTEN signaling linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group 68.8% of which were U1 and U2 snRNAs. In addition 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR LINE and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs indicating expression of DEpiRNAs in response to activation of TEs. Finally 66.7% and 33.3% of lincRNAs in F1 ? were down and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent…		pubmed:33602989		F1 Control2 nmbu sncRNA 2	GSM4605878	tissue:Whole embryo\|develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from control parents	F1 Control2 nmbu sncRNA 2	Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped classified into genomic features and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5 using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values	Whole embryo		Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.		develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from control parents	GSM4605878	GSM4605878: F1 Control2 nmbu sncRNA 2; Danio rerio; miRNA Seq	GSM4605878		1	Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.	GEO Accession:GSM4605878	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP266770		nmbu_sncRNA_2_raw.fq.gz	fastq	531815250.0	10636305.0	GSM4605878 r1	0:50	A:155930702;C:122952623;G:141743533;T:111074299;N:114093	50		155930702	122952623	141743533	111074299	114093	SRX8518001	SRS6815482	SRA1085407	GEO	Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences	1	0.65896	0.35164	0.8453	0.57438	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Norway	2020-06-10	Gastrula	Embryo	Whole Organism	All anatomical structures
59628	59628	SRR11974578	SRX8518000	SRS6815481	SRP266770	PRJNA638603	small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish	GSE152189	Transcriptome Analysis	In order to investigate transcriptomic mechanisms underlying radiation exposure we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ? and control F1 C parents revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall 22 miRNAs 11 piRNA clusters 19 snRNAs and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data a total of 672 differentially expressed mRNAs could be linked to the DEmiRs of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor NFkB and PTEN signaling linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group 68.8% of which were U1 and U2 snRNAs. In addition 45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR LINE and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs indicating expression of DEpiRNAs in response to activation of TEs. Finally 66.7% and 33.3% of lincRNAs in F1 ? were down and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent…		pubmed:33602989		F1 Control1 nmbu sncRNA 1	GSM4605877	tissue:Whole embryo\|develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from control parents	F1 Control1 nmbu sncRNA 1	Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 – 36 nt Length filtered reads were mapped classified into genomic features and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5 using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values	Whole embryo		Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.		develomental stage:5.5 hpf 50 percent epiboly\|strain:AB\|genotype:wild type\|group:F1 from control parents	GSM4605877	GSM4605877: F1 Control1 nmbu sncRNA 1; Danio rerio; miRNA Seq	GSM4605877		1	Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics Germany and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific USA. sequencing libraries were prepared using the NEBnext® Small RNA Library Prep Set for Illumina® New England Biolabs® inc USA from each sample 1 μg of total RNA was used as input material.	GEO Accession:GSM4605877	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP266770		nmbu_sncRNA_1_raw.fq.gz	fastq	534855250.0	10697105.0	GSM4605877 r1	0:50	A:156249541;C:120087413;G:145230236;T:113171967;N:116093	50		156249541	120087413	145230236	113171967	116093	SRX8518000	SRS6815481	SRA1085407	GEO	Alestrøm ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences	1	0.74031	0.40182	0.83366	0.60438	50	B	usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	nebnext	bulk	unknown	unknown	Norway	2020-06-10	Gastrula	Embryo	Whole Organism	All anatomical structures
60445	60445	SRR12272862	SRX8777892	SRS7048444	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C2	C2 C2 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200712	C2C220200712	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500		SRP272672	loader:fastq load.py	C2_C2_2_4.fq	fastq	542610936.0	21965958.0	C2 C2 2 4.fq.gz	0:24.70	A:95221617;C:122628624;G:167025611;T:157730855;N:4229	24		95221617	122628624	167025611	157730855	4229	SRX8777892	SRS7048444	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.8119	0.10745	0.85717	0.51338	22	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60446	60446	SRR12272863	SRX8777891	SRS7048443	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C2	C2 C2 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C2\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:100ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C2C220200711	C2C220200711	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500		SRP272672	loader:fastq load.py	C2_C2_1_4.fq	fastq	542847476.0	22614181.0	C2 C2 1 4.fq.gz	0:24.00	A:99999101;C:125407906;G:162383758;T:155055099;N:1612	24		99999101	125407906	162383758	155055099	1612	SRX8777891	SRS7048443	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.84327	0.10491	0.83256	0.52046	19	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60447	60447	SRR12272864	SRX8777890	SRS7048442	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C1	C1 C1 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200712	C1C120200712	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500		SRP272672	loader:fastq load.py	C1_C1_2_4.fq	fastq	570918284.0	22577002.0	C1 C1 2 4.fq.gz	0:25.29	A:100121235;C:130480588;G:178656113;T:161652765;N:7583	25		100121235	130480588	178656113	161652765	7583	SRX8777890	SRS7048442	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.85096	0.12542	0.82873	0.51535	22	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60448	60448	SRR12272865	SRX8777889	SRS7048441	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C1	C1 C1 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C1\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:1ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C1C120200711	C1C120200711	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500		SRP272672	loader:fastq load.py	C1_C1_1_4.fq	fastq	545089417.0	22812164.0	C1 C1 1 4.fq.gz	0:23.89	A:99851844;C:125314095;G:166401335;T:153521167;N:976	23		99851844	125314095	166401335	153521167	976	SRX8777889	SRS7048441	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.84602	0.11725	0.83159	0.51353	19	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60449	60449	SRR12272866	SRX8777888	SRS7048440	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C0	C0 C0 2 4	replicate:biological replicate 2\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200712	C0C020200712	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500		SRP272672	loader:fastq load.py	C0_C0_2_4.fq	fastq	527443144.0	23174740.0	C0 C0 2 4.fq.gz	0:22.76	A:102368401;C:120843229;G:151690193;T:152540806;N:515	22		102368401	120843229	151690193	152540806	515	SRX8777888	SRS7048440	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.83063	0.08114	0.85169	0.50894	16	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
60450	60450	SRR12272867	SRX8777887	SRS7048439	SRP272672	PRJNA647444	mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA	PRJNA647444	Other	Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.				C0	C0 C0 1 4	replicate:biological replicate 1\|strain:AB\|isolate:C0\|breed:not applicable\|cultivar:not applicable\|ecotype:not applicable\|age:not applicable\|dev stage:not applicable\|sex:pooled male and female\|tissue:the whole\|collection date:2019 11 01\|geo loc name:China: Shenzhen Guangdong\|phenotype:0ug/L\|BioSampleModel:Model organism or animal									RNA seq of zebrafish	C0C020200711	C0C020200711	RNA seq of zebrafish in different conditions			miRNA-Seq	TRANSCRIPTOMIC	RANDOM PCR	SINGLE	BGISEQ	BGISEQ-500		SRP272672	loader:fastq load.py	C0_C0_1_4.fq	fastq	511759408.0	22673361.0	C0 C0 1 4.fq.gz	0:22.57	A:100879182;C:120237907;G:142799495;T:147842595;N:229	22		100879182	120237907	142799495	147842595	229	SRX8777887	SRS7048439	SRA1101037	Southern University of Science and Technology\|School of Environmental Science and Engineering	Southern University of Science and Technology	1	0.83904	0.0823	0.84741	0.49929	22	B	usable mapping rate	bgi	bgi	unknown	random_priming	unknown	bulk	unknown	unknown	China	2020-08-05	Undetermined	Embryo	Whole Organism	All anatomical structures
70542	70542	SRR19996277	SRX16037367	SRS13717223	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 3 [miRNA Seq]	GSM6294388	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 3 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294388	GSM6294388: High fat diet rep 3 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294388 r1	GSM6294388	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD6_AGAACGCA_L001_R1_001.fastq.gz	fastq	1216000000.0	16000000.0	GSM6294388 r1	0:76 1:0	A:356587691;C:315255282;G:298515494;T:245619001;N:22532	76	0	356587691	315255282	298515494	245619001	22532	SRX16037367	SRS13717223	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.54851	0.13461	0.86825	0.63082	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70543	70543	SRR19996278	SRX16037367	SRS13717223	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 3 [miRNA Seq]	GSM6294388	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 3 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294388	GSM6294388: High fat diet rep 3 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294388 r1	GSM6294388	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD6_AGAACGCA_L001_R1_002.fastq.gz	fastq	112508424.0	1480374.0	GSM6294388 r2	0:76 1:0	A:33065142;C:29043993;G:27540664;T:22855718;N:2907	76	0	33065142	29043993	27540664	22855718	2907	SRX16037367	SRS13717223	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.55607	0.14424	0.86856	0.65786	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70544	70544	SRR19996279	SRX16037367	SRS13717223	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 3 [miRNA Seq]	GSM6294388	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 3 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294388	GSM6294388: High fat diet rep 3 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294388 r1	GSM6294388	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD6_AGAACGCA_L002_R1_001.fastq.gz	fastq	1216000000.0	16000000.0	GSM6294388 r3	0:76 1:0	A:356672501;C:315052549;G:298481239;T:245763880;N:29831	76	0	356672501	315052549	298481239	245763880	29831	SRX16037367	SRS13717223	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.55045	0.13717	0.86624	0.63636	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70545	70545	SRR19996280	SRX16037367	SRS13717223	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 3 [miRNA Seq]	GSM6294388	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 3 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294388	GSM6294388: High fat diet rep 3 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294388 r1	GSM6294388	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD6_AGAACGCA_L002_R1_002.fastq.gz	fastq	102490788.0	1348563.0	GSM6294388 r4	0:76 1:0	A:30091848;C:26419434;G:25045256;T:20909065;N:25185	76	0	30091848	26419434	25045256	20909065	25185	SRX16037367	SRS13717223	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.55804	0.14662	0.87172	0.65108	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70546	70546	SRR19996281	SRX16037366	SRS13717222	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 2 [miRNA Seq]	GSM6294387	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 2 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294387	GSM6294387: High fat diet rep 2 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294387 r1	GSM6294387	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD5_TTACGGCA_L001_R1_001.fastq.gz	fastq	1216000000.0	16000000.0	GSM6294387 r1	0:76 1:0	A:356185568;C:317412171;G:296624759;T:245755522;N:21980	76	0	356185568	317412171	296624759	245755522	21980	SRX16037366	SRS13717222	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.03308	0.01021	0.98683	0.63053	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70547	70547	SRR19996282	SRX16037366	SRS13717222	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 2 [miRNA Seq]	GSM6294387	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 2 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294387	GSM6294387: High fat diet rep 2 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294387 r1	GSM6294387	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD5_TTACGGCA_L001_R1_002.fastq.gz	fastq	95272840.0	1253590.0	GSM6294387 r2	0:76 1:0	A:27984022;C:24743485;G:23171781;T:19371284;N:2268	76	0	27984022	24743485	23171781	19371284	2268	SRX16037366	SRS13717222	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.03532	0.01151	0.98689	0.62615	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70548	70548	SRR19996283	SRX16037366	SRS13717222	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 2 [miRNA Seq]	GSM6294387	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 2 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294387	GSM6294387: High fat diet rep 2 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294387 r1	GSM6294387	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD5_TTACGGCA_L002_R1_001.fastq.gz	fastq	1216000000.0	16000000.0	GSM6294387 r3	0:76 1:0	A:356307606;C:317122785;G:296627283;T:245913596;N:28730	76	0	356307606	317122785	296627283	245913596	28730	SRX16037366	SRS13717222	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.03317	0.01043	0.98695	0.61321	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70549	70549	SRR19996284	SRX16037366	SRS13717222	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 2 [miRNA Seq]	GSM6294387	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 2 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294387	GSM6294387: High fat diet rep 2 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294387 r1	GSM6294387	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD5_TTACGGCA_L002_R1_002.fastq.gz	fastq	81590028.0	1073553.0	GSM6294387 r4	0:76 1:0	A:23941275;C:21160767;G:19806367;T:16659459;N:22160	76	0	23941275	21160767	19806367	16659459	22160	SRX16037366	SRS13717222	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.03628	0.01168	0.98727	0.61077	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70550	70550	SRR19996285	SRX16037365	SRS13717221	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 1 [miRNA Seq]	GSM6294386	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 1 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294386	GSM6294386: High fat diet rep 1 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294386 r1	GSM6294386	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD4_GTTCGTTG_L001_R1_001.fastq.gz	fastq	1216000000.0	16000000.0	GSM6294386 r1	0:76 1:0	A:353927140;C:317362066;G:299615370;T:245072880;N:22544	76	0	353927140	317362066	299615370	245072880	22544	SRX16037365	SRS13717221	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.037	0.01164	0.98754	0.60746	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70551	70551	SRR19996286	SRX16037365	SRS13717221	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 1 [miRNA Seq]	GSM6294386	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 1 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294386	GSM6294386: High fat diet rep 1 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294386 r1	GSM6294386	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD4_GTTCGTTG_L001_R1_002.fastq.gz	fastq	99836868.0	1313643.0	GSM6294386 r2	0:76 1:0	A:29129510;C:25927485;G:24526547;T:20250631;N:2695	76	0	29129510	25927485	24526547	20250631	2695	SRX16037365	SRS13717221	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.04011	0.01334	0.98752	0.60265	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70552	70552	SRR19996287	SRX16037365	SRS13717221	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 1 [miRNA Seq]	GSM6294386	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 1 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294386	GSM6294386: High fat diet rep 1 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294386 r1	GSM6294386	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD4_GTTCGTTG_L002_R1_001.fastq.gz	fastq	1216000000.0	16000000.0	GSM6294386 r3	0:76 1:0	A:354019911;C:317095108;G:299593671;T:245261603;N:29707	76	0	354019911	317095108	299593671	245261603	29707	SRX16037365	SRS13717221	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.03873	0.01273	0.98831	0.61561	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70553	70553	SRR19996288	SRX16037365	SRS13717221	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		High fat diet rep 1 [miRNA Seq]	GSM6294386	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based\|geo loc name:missing\|collection date:missing	High fat diet rep 1 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:High fat diet egg yolk based	GSM6294386	GSM6294386: High fat diet rep 1 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294386 r1	GSM6294386	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		HFD4_GTTCGTTG_L002_R1_002.fastq.gz	fastq	89899564.0	1182889.0	GSM6294386 r4	0:76 1:0	A:26203037;C:23320851;G:22042236;T:18308620;N:24820	76	0	26203037	23320851	22042236	18308620	24820	SRX16037365	SRS13717221	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.04092	0.01402	0.98806	0.60312	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70554	70554	SRR19996289	SRX16037364	SRS13717220	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		Standard diet rep 3 [miRNA Seq]	GSM6294385	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:Standard diet\|geo loc name:missing\|collection date:missing	Standard diet rep 3 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:Standard diet	GSM6294385	GSM6294385: Standard diet rep 3 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294385 r1	GSM6294385	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		SD3_TTGGACCT_L001_R1_001.fastq.gz	fastq	1112575856.0	14639156.0	GSM6294385 r1	0:76 1:0	A:332460940;C:266146733;G:266385877;T:247560550;N:21756	76	0	332460940	266146733	266385877	247560550	21756	SRX16037364	SRS13717220	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.72337	0.15566	0.8888	0.58805	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	All anatomical structures
70555	70555	SRR19996290	SRX16037364	SRS13717220	SRP385069	PRJNA856147	Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq]	GSE207549	Transcriptome Analysis	Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen.	parent bioproject:PRJNA856140	pubmed:37443828		Standard diet rep 3 [miRNA Seq]	GSM6294385	source name:whole larvae 30\|tissue:whole larvae 30\|strain:AB strain\|treatment:Standard diet\|geo loc name:missing\|collection date:missing	Standard diet rep 3 [miRNA Seq]	Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model.	whole larvae 30	anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD].	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs	Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.	tissue:whole larvae 30\|strain:AB strain\|treatment:Standard diet	GSM6294385	GSM6294385: Standard diet rep 3 [miRNA Seq]; Danio rerio; miRNA Seq	GSM6294385 r1	GSM6294385	1	Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs		miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP385069		SD3_TTGGACCT_L002_R1_001.fastq.gz	fastq	1111477200.0	14624700.0	GSM6294385 r2	0:76 1:0	A:332129850;C:265653100;G:266119260;T:247526586;N:48404	76	0	332129850	265653100	266119260	247526586	48404	SRX16037364	SRS13717220	SRA1449581	MIGALGalilee Research Institute	MIGALGalilee Research Institute	1	0.72447	0.15572	0.88982	0.58556	76	B	usable mapping rate	illumina	hiseq_era	3prime	size_fractionation	unknown	bulk	unknown	unknown	Israel	2022-07-06	Multi-stage	Multi-stage	Whole Organism	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");;