{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_strategy = \"miRNA-Seq\" and tissue_curation = \"Embryo Imprecise\"", "rows": [[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.", null, "pubmed:26574018", null, "Embryo Replicate 3 sRNAseq", "GSM1376619", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "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, null, null, null, 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, null, 0.01776, null, 0.97782, null, 0.77023, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:26574018", null, "Embryo Replicate 2 sRNAseq", "GSM1376618", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "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, null, null, null, 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, null, 0.00234, null, 0.99515, null, 0.73854, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:26574018", null, "Embryo Replicate 1 sRNAseq", "GSM1376617", null, "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 Friedl\u00e4nder 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 m r 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\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560 Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the mirVana\u2122 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 1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 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", null, "SRP041544", null, null, "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, null, null, null, 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, null, 0.00461, null, 0.99379, null, 0.8448, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "RPL5 MO [miRNA]", "GSM1408095", null, "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\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "Zebrafish embryos were kept in a 28.5\u2103 incubator to 48hpf", "genotype/variation:RPL5 morpholino knockdown|developmental stage:48hpf", "GSM1408095", "GSM1408095: RPL5 MO [miRNA]; Danio rerio; miRNA Seq", "GSM1408095", null, "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\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "GEO Accession:GSM1408095", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP043064", null, null, "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, null, null, null, 263908052, 257987133, 278889068, 292410262, 40210, "SRX585640", "SRS631986", "SRA169796", "GEO", "Beijing Institute of Genomics", 1, 3e-05, null, 0.0, null, 0.99991, null, 0.5, null, 81, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2014-06-10", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "morpholino control [miRNA]", "GSM1408094", null, "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\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "Zebrafish embryos were kept in a 28.5\u2103 incubator to 48hpf", "genotype/variation:control morpholino|developmental stage:48hpf", "GSM1408094", "GSM1408094: morpholino control [miRNA]; Danio rerio; miRNA Seq", "GSM1408094", null, "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\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "GEO Accession:GSM1408094", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP043064", null, null, null, null, 308681847.0, 3810887.0, "GSM1408094 r1", "0:81", "A:63686404;C:75263287;G:80056961;T:89650625;N:24570", 81, null, null, null, 63686404, 75263287, 80056961, 89650625, 24570, "SRX585639", "SRS631982", "SRA169796", "GEO", "Beijing Institute of Genomics", 1, 8e-05, null, 2e-05, null, 0.99991, null, 0.42857, null, 81, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2014-06-10", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "pubmed:25454948", null, "Zeb fish Emb t 24h", "GSM1517418", null, "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\u2032 adaptor sequences starting with \u201cTGGAATTC\u201d 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 \u201818nt long seed length\u2019 and \u2018no 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\u2019 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", null, "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s 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\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA the 5\u2019 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.", null, "genotype/variation:WT|developmental stage:embryo 24h", "GSM1517418", "GSM1517418: Zeb fish Emb t 24h; Danio rerio; miRNA Seq", "GSM1517418", null, "1", "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s 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\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA the 5\u2019 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", null, "SRP048545", null, null, "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, null, null, null, 675086979, 579211488, 812576920, 680856005, 67212, "SRX718003", "SRS713863", "SRA188351", "GEO", "Narry Kim Lab, School of Biological Sciences, Seoul National University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2014-09-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "pubmed:25454948", null, "Zeb fish Emb t 30m", "GSM1517417", null, "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\u2032 adaptor sequences starting with \u201cTGGAATTC\u201d 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 \u201818nt long seed length\u2019 and \u2018no 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\u2019 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", null, "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s 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\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA the 5\u2019 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.", null, "genotype/variation:WT|developmental stage:embryo 30m", "GSM1517417", "GSM1517417: Zeb fish Emb t 30m; Danio rerio; miRNA Seq", "GSM1517417", null, "1", "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s 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\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA the 5\u2019 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", null, "SRP048545", null, null, "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, null, null, null, 854040134, 726173965, 952338238, 848081062, 82192, "SRX718002", "SRS713862", "SRA188351", "GEO", "Narry Kim Lab, School of Biological Sciences, Seoul National University", 1, 1e-05, null, 0.0, null, 0.99997, null, 1.0, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2014-09-30", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "pubmed:25454948", null, "Zeb fish Emb t 10m", "GSM1517416", null, "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\u2032 adaptor sequences starting with \u201cTGGAATTC\u201d 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 \u201818nt long seed length\u2019 and \u2018no 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\u2019 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", null, "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s 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\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA the 5\u2019 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.", null, "genotype/variation:WT|developmental stage:embryo 10m", "GSM1517416", "GSM1517416: Zeb fish Emb t 10m; Danio rerio; miRNA Seq", "GSM1517416", null, "1", "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s 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\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA the 5\u2019 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", null, "SRP048545", null, null, "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, null, null, null, 847877403, 714050198, 934084609, 843302102, 81385, "SRX718001", "SRS713861", "SRA188351", "GEO", "Narry Kim Lab, School of Biological Sciences, Seoul National University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2014-09-30", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "pubmed:25454948", null, "Zeb fish Emb t 0m", "GSM1517415", null, "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\u2032 adaptor sequences starting with \u201cTGGAATTC\u201d 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 \u201818nt long seed length\u2019 and \u2018no 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\u2019 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", null, "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s 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\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA the 5\u2019 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.", null, "genotype/variation:WT|developmental stage:embryo 0m", "GSM1517415", "GSM1517415: Zeb fish Emb t 0m; Danio rerio; miRNA Seq", "GSM1517415", null, "1", "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s 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\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA the 5\u2019 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", null, "SRP048545", null, null, "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, null, null, null, 800912828, 671516191, 883139862, 779944407, 76005, "SRX718000", "SRS713860", "SRA188351", "GEO", "Narry Kim Lab, School of Biological Sciences, Seoul National University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2014-09-30", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "Emb MO Ct 48hpf", "GSM1571860", null, "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 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 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", null, "1", "For each library 1 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571860", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "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, null, null, 72708202, 91561004, 102921744, 71122135, 9632, "SRX822003", "SRS801698", "SRA221043", "GEO", "IIT, CNR", 1, 0.86712, null, 0.22408, null, 0.92725, null, 0.50365, null, 23, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "Emb MO Tbx5a 48hpf", "GSM1571859", null, "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 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 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", null, "1", "For each library 1 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571859", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "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, null, null, 60415193, 62111082, 75168882, 64515539, 8436, "SRX822002", "SRS801697", "SRA221043", "GEO", "IIT, CNR", 1, 0.52287, null, 0.13984, null, 0.8788, null, 0.6354, null, 30, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "Emb MO Ct 24hpf rep2", "GSM1571858", null, "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 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 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", null, "1", "For each library 1 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571858", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "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, null, null, 66055828, 65184020, 81768559, 68892445, 9099, "SRX822001", "SRS801696", "SRA221043", "GEO", "IIT, CNR", 1, 0.56084, null, 0.23499, null, 0.86819, null, 0.64638, null, 22, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "Emb MO Ct 24hpf rep1", "GSM1571857", null, "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 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 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", null, "1", "For each library 1 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571857", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "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, null, null, 126881333, 133281439, 163930613, 117435553, 17186, "SRX822000", "SRS801695", "SRA221043", "GEO", "IIT, CNR", 1, 0.53436, null, 0.20796, null, 0.9009, null, 0.55394, null, 34, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "Emb MO Tbx5a 24hpf rep2", "GSM1571856", null, "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 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 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", null, "1", "For each library 1 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571856", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "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, null, null, 82709386, 83987865, 107681867, 88122760, 11582, "SRX821999", "SRS801694", "SRA221043", "GEO", "IIT, CNR", 1, 0.58925, null, 0.2498, null, 0.86821, null, 0.65549, null, 30, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "Emb MO Tbx5a 24hpf rep1", "GSM1571855", null, "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 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 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", null, "1", "For each library 1 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571855", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "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, null, null, 88725326, 102855219, 121123717, 86418155, 12162, "SRX821998", "SRS801693", "SRA221043", "GEO", "IIT, CNR", 1, 0.66472, null, 0.25948, null, 0.89623, null, 0.54913, null, 34, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "Emb MO Ct 48hpf [miRNA seq]", "GSM1707594", null, "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 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 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", null, "1", "For each library 1 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1707594", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP059278", null, null, "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, null, null, null, 417902194, 195580811, 153264728, 266159736, 160971, "SRX1054376", "SRS957216", "SRA272222", "GEO", "IIT, CNR", 1, 0.05412, null, 0.01319, null, 0.97693, null, 0.22489, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2015-06-09", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, "Emb MO Tbx5a 48hpf [miRNA seq]", "GSM1707593", null, "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 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 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", null, "1", "For each library 1 \u03bcg 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 \u00b5l elution buffer Illumina for at least 2 hours at room temperature to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1707593", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP059278", null, null, "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, null, null, null, 430923990, 193052690, 149627446, 265119627, 132087, "SRX1054375", "SRS957217", "SRA272222", "GEO", "IIT, CNR", 1, 0.01858, null, 0.00322, null, 0.98699, null, 0.23156, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2015-06-09", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:30090366", null, "6 48 0.5\u00b5M OTA [miRNA seq]", "GSM1832841", null, "tissue:embryo control|strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:0.5 \u00b5M ochratoxin A from 6 hpf to 48 hpf", "6 48 0.5\u00b5M 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\u2032 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\u00ae 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\u2032 and 5\u2032 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.\u00a0 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 \u00b5M ochratoxin A from 6 hpf to 48 hpf", "GSM1832841", "GSM1832841: 6 48 0.5\u00b5M OTA [miRNA seq]; Danio rerio; miRNA Seq", "GSM1832841", null, "1", "Total RNA was extracted by Trizol\u00ae 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\u2032 and 5\u2032 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.\u00a0 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", null, "SRP061587", null, null, "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, null, null, 74462826, 72958352, 87201353, 75455198, 0, "SRX1118699", "SRS1011434", "SRA280185", "GEO", "ntu", 1, 0.00671, null, 0.00134, null, 0.99594, null, 0.39026, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2015-07-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, "pubmed:30090366", null, "6 48 control [miRNA seq]", "GSM1832840", null, "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\u2032 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\u00ae 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\u2032 and 5\u2032 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.\u00a0 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", null, "1", "Total RNA was extracted by Trizol\u00ae 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\u2032 and 5\u2032 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.\u00a0 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", null, "SRP061587", null, null, "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, null, null, 75126425, 71798677, 85490341, 76532368, 0, "SRX1118698", "SRS1011435", "SRA280185", "GEO", "ntu", 1, 0.00833, null, 0.00166, null, 0.99476, null, 0.42762, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2015-07-25", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41406, "SRR4423130", "SRX2245314", "SRS1745863", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 10 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: prim 16 stage31 hpf", "348 10", "348 10", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S10small.fastq", "fastq", 427409571.0, 5026564.0, "S10small.fastq", "0:85.03", "A:98026046;C:116630773;G:114413502;T:98339250;N:0", 85, null, null, null, 98026046, 116630773, 114413502, 98339250, 0, "SRX2245314", "SRS1745863", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.81583, null, 0.17938, null, 0.9094, null, 0.63072, null, 126, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41407, "SRR4423129", "SRX2245313", "SRS1745862", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 9 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: prim 5 stage24 hpf", "348 9", "348 9", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S09small.fastq", "fastq", 516614705.0, 6246071.0, "S09small.fastq", "0:82.71", "A:117786535;C:140799134;G:139362428;T:118666608;N:0", 82, null, null, null, 117786535, 140799134, 139362428, 118666608, 0, "SRX2245313", "SRS1745862", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.81132, null, 0.18952, null, 0.88925, null, 0.69719, null, 17, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41408, "SRR4423128", "SRX2245312", "SRS1745850", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 12 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: protruding mouth stage72 hpf", "348 12", "348 12", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S12small.fastq", "fastq", 186817590.0, 3062463.0, "S12small.fastq", "0:61.00", "A:42863072;C:49941244;G:49513828;T:44499446;N:0", 61, null, null, null, 42863072, 49941244, 49513828, 44499446, 0, "SRX2245312", "SRS1745850", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.77668, null, 0.17381, null, 0.8915, null, 0.54189, null, 36, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [41409, "SRR4423127", "SRX2245311", "SRS1745851", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 11 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: long pec stage48 hpf", "348 11", "348 11", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S11small.fastq", "fastq", 405003101.0, 5197273.0, "S11small.fastq", "0:77.93", "A:93494059;C:109265919;G:106696649;T:95546474;N:0", 77, null, null, null, 93494059, 109265919, 106696649, 95546474, 0, "SRX2245311", "SRS1745851", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.78244, null, 0.17047, null, 0.93379, null, 0.6272, null, 30, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41428, "SRR4423108", "SRX2245292", "SRS1745857", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 5 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 90% epiboly stage 9 hpf", "348 5", "348 5", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S05small.fastq", "fastq", 412237561.0, 3386443.0, "S05small.fastq", "0:121.73", "A:91644321;C:118905395;G:115070912;T:86616933;N:0", 121, null, null, null, 91644321, 118905395, 115070912, 86616933, 0, "SRX2245292", "SRS1745857", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.81233, null, 0.06309, null, 0.93385, null, 0.93973, null, 163, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41429, "SRR4423107", "SRX2245291", "SRS1745856", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 6 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 4 somite stage11.3 hpf", "348 6", "348 6", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S06small.fastq", "fastq", 535288776.0, 4443685.0, "S06small.fastq", "0:120.46", "A:119322177;C:152704452;G:149509408;T:113752739;N:0", 120, null, null, null, 119322177, 152704452, 149509408, 113752739, 0, "SRX2245291", "SRS1745856", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.82872, null, 0.09035, null, 0.93194, null, 0.81296, null, 159, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41430, "SRR4423106", "SRX2245290", "SRS1745854", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 3 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: zfs:0000015 stage 4.7 hpf", "348 3", "348 3", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S03small.fastq", "fastq", 1025732824.0, 7452991.0, "S03small.fastq", "0:137.63", "A:225573059;C:298586545;G:288470386;T:213102834;N:0", 137, null, null, null, 225573059, 298586545, 288470386, 213102834, 0, "SRX2245290", "SRS1745854", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.8983, null, 0.04271, null, 0.95546, null, 0.91281, null, 159, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41431, "SRR4423105", "SRX2245289", "SRS1745855", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 4 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 70% epiboly stage7 hpf", "348 4", "348 4", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S04small.fastq", "fastq", 193259658.0, 1840126.0, "S04small.fastq", "0:105.03", "A:43516548;C:54669405;G:53501927;T:41571778;N:0", 105, null, null, null, 43516548, 54669405, 53501927, 41571778, 0, "SRX2245289", "SRS1745855", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.81053, null, 0.16265, null, 0.90698, null, 0.92112, null, 159, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41432, "SRR4423104", "SRX2245288", "SRS1745853", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 1 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 64 cells2 hpf", "348 1", "348 1", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S01small.fastq", "fastq", 91910627.0, 1396009.0, "S01small.fastq", "0:65.84", "A:21663404;C:25661192;G:25069267;T:19516764;N:0", 65, null, null, null, 21663404, 25661192, 25069267, 19516764, 0, "SRX2245288", "SRS1745853", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.56828, null, 0.1715, null, 0.92435, null, 0.90047, null, 34, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41433, "SRR4423103", "SRX2245287", "SRS1745852", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 2 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: high stage3.3 hpf", "348 2", "348 2", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S02small.fastq", "fastq", 304535574.0, 3376105.0, "S02small.fastq", "0:90.20", "A:69193719;C:84372087;G:86707481;T:64262287;N:0", 90, null, null, null, 69193719, 84372087, 86707481, 64262287, 0, "SRX2245287", "SRS1745852", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.56812, null, 0.09695, null, 0.93474, null, 0.93654, null, 51, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41436, "SRR4423100", "SRX2245284", "SRS1745849", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 7 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 12 somite stage15 hpf", "348 7", "348 7", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S07small.fastq", "fastq", 279201769.0, 2713759.0, "S07small.fastq", "0:102.88", "A:61655863;C:78667355;G:77702440;T:61176111;N:0", 102, null, null, null, 61655863, 78667355, 77702440, 61176111, 0, "SRX2245284", "SRS1745849", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.79087, null, 0.10046, null, 0.89221, null, 0.77892, null, 158, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41437, "SRR4423099", "SRX2245283", "SRS1745848", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 8 Dr", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: 22 somite stage20 hpf", "348 8", "348 8", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 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 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S08small.fastq", "fastq", 520785540.0, 4495080.0, "S08small.fastq", "0:115.86", "A:115224831;C:149325753;G:144978190;T:111256766;N:0", 115, null, null, null, 115224831, 149325753, 144978190, 111256766, 0, "SRX2245283", "SRS1745848", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.83781, null, 0.08976, null, 0.92904, null, 0.80492, null, 183, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "G56 miRNA", "GSM3349122", null, "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\u2019 and 5\u2019 adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98\u2103 30 s 11 \u00d7 98\u2103 10 s 60\u2103 30 s 72 \u2103 15 s for 72 \u2103 10 min 4\u2103. 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\u2122 dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/\u00b5l 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", null, "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\u2103 30 s 11 \u00d7 98\u2103 10 s 60\u2103 30 s 72 \u2103 15 s for 72 \u2103 10 min 4\u2103. 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\u2122 dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/\u00b5l and the size of cDNA was 140 160 bp.", "GEO Accession:GSM3349122", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP158508", null, null, null, null, 655037050.0, 13100741.0, "GSM3349122 r1", "0:50 1:0", "A:161448247;C:135821164;G:200213833;T:156824030;N:729776", 50, 0, null, null, 161448247, 135821164, 200213833, 156824030, 729776, "SRX4582847", "SRS3697100", "SRA761361", "GEO", "Nanjing University", 1, 0.00066, null, 6e-05, null, 0.99896, null, 0.64583, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "miseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-08-21", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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.", null, null, null, "WT miRNA", "GSM3349121", null, "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\u2019 and 5\u2019 adaptors were added to the miRNA sequentially. cDNA was then reverse transcribed from the miRNA and amplified using a PCR reaction 98\u2103 30 s 11 \u00d7 98\u2103 10 s 60\u2103 30 s 72 \u2103 15 s for 72 \u2103 10 min 4\u2103. 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\u2122 dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/\u00b5l 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", null, "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\u2103 30 s 11 \u00d7 98\u2103 10 s 60\u2103 30 s 72 \u2103 15 s for 72 \u2103 10 min 4\u2103. 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\u2122 dsDNA HS Aglient 2100. The concentration of the library was no lower than 0.5 ng/\u00b5l and the size of cDNA was 140 160 bp.", "GEO Accession:GSM3349121", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP158508", null, null, null, null, 627151350.0, 12543027.0, "GSM3349121 r1", "0:50 1:0", "A:153340174;C:128104541;G:192611227;T:152395340;N:700068", 50, 0, null, null, 153340174, 128104541, 192611227, 152395340, 700068, "SRX4582846", "SRS3697099", "SRA761361", "GEO", "Nanjing University", 1, 0.0006, null, 0.00012, null, 0.99904, null, 0.60759, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "miseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-08-21", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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\u00b0C 30 days and cold acclimation 18\u00b0C 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 \u00b0C as control and at 18 \u00b0C for 30 days seperately. Each condition has three biological replica.", null, "pubmed:31923196", null, "ZF4 18 30d cold3", "GSM3946004", null, "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\u02daC 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\u00b0C 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", null, "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", null, "SRP215029", null, null, "6.fq.gz", "fastq", 888718150.0, 17774363.0, "GSM3946004 r1", "0:50", "A:200112040;C:206776226;G:254640770;T:227172753;N:16361", 50, null, null, null, 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, null, 0.00027, null, 0.99799, null, 0.4985, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-17", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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\u00b0C 30 days and cold acclimation 18\u00b0C 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 \u00b0C as control and at 18 \u00b0C for 30 days seperately. Each condition has three biological replica.", null, "pubmed:31923196", null, "ZF4 18 30d cold2", "GSM3946003", null, "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\u02daC 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\u00b0C 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", null, "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", null, "SRP215029", null, null, "5.fq.gz", "fastq", 853031700.0, 17060634.0, "GSM3946003 r1", "0:50", "A:192338096;C:205750986;G:242627478;T:212299265;N:15875", 50, null, null, null, 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, null, 0.00045, null, 0.99738, null, 0.47457, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-17", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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\u00b0C 30 days and cold acclimation 18\u00b0C 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 \u00b0C as control and at 18 \u00b0C for 30 days seperately. Each condition has three biological replica.", null, "pubmed:31923196", null, "ZF4 18 30d cold1", "GSM3946002", null, "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\u02daC 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\u00b0C 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", null, "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", null, "SRP215029", null, null, "4.fq.gz", "fastq", 878731000.0, 17574620.0, "GSM3946002 r1", "0:50", "A:196907854;C:209105082;G:251308531;T:221393524;N:16009", 50, null, null, null, 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, null, 0.00089, null, 0.99691, null, 0.52247, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-17", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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\u00b0C 30 days and cold acclimation 18\u00b0C 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 \u00b0C as control and at 18 \u00b0C for 30 days seperately. Each condition has three biological replica.", null, "pubmed:31923196", null, "ZF4 28 con3", "GSM3946001", null, "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\u02daC 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\u00b0C 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", null, "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", null, "SRP215029", null, null, "3.fq.gz", "fastq", 908953950.0, 18179079.0, "GSM3946001 r1", "0:50", "A:206519605;C:210829105;G:259204569;T:232383846;N:16825", 50, null, null, null, 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, null, 0.00042, null, 0.99756, null, 0.48, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-17", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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\u00b0C 30 days and cold acclimation 18\u00b0C 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 \u00b0C as control and at 18 \u00b0C for 30 days seperately. Each condition has three biological replica.", null, "pubmed:31923196", null, "ZF4 28 con2", "GSM3946000", null, "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\u02daC 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\u00b0C 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", null, "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", null, "SRP215029", null, null, "2.fq.gz", "fastq", 876929500.0, 17538590.0, "GSM3946000 r1", "0:50", "A:198651931;C:204780756;G:249251465;T:224229047;N:16301", 50, null, null, null, 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, null, 0.00237, null, 0.99559, null, 0.5232, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-17", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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\u00b0C 30 days and cold acclimation 18\u00b0C 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 \u00b0C as control and at 18 \u00b0C for 30 days seperately. Each condition has three biological replica.", null, "pubmed:31923196", null, "ZF4 28 con1", "GSM3945999", null, "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\u02daC 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\u00b0C 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", null, "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", null, "SRP215029", null, null, "1.fq.gz", "fastq", 957098100.0, 19141962.0, "GSM3945999 r1", "0:50", "A:217645979;C:223129215;G:273039214;T:243266316;N:17376", 50, null, null, null, 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, null, 0.0007, null, 0.99701, null, 0.51905, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2019-07-17", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, null, "miRNA of MZdgcr8 3", "GSM4396432", null, "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 \u226412 2 number of base pairs in the stem region of the predicted hairpin \u226516 3 cutoff of free energy kCal/mol \u2264 15 4 length of hairpin up and down stems + terminal loop \u226550 5 length of hairpin loop \u2264200. 6 number of nucleotides in one bulge in mature region \u22644 7 number of biased errors in one bulge in mature region \u22642 8 number of biased bulges in mature region \u22642 9 number of errors in mature region \u22644 10 number of base pairs in the mature region of the predicted hairpin \u226512 11 percent of mature in stem \u226580. Supplementary files format and content: excel expression profiles", "Embryo", null, "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", null, "strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8", "GSM4396432", "GSM4396432: miRNA of MZdgcr8 3; Danio rerio; miRNA Seq", "GSM4396432", null, "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", null, "SRP251978", null, null, "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, null, null, 146678206, 139956283, 181049484, 135139840, 31937, "SRX7870077", "SRS6278494", "SRA1052219", "GEO", "The Chinese University of Hong Kong", 1, 0.00091, null, 0.0001, null, 0.9987, null, 0.73076, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, null, "miRNA of MZdgcr8 2", "GSM4396431", null, "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 \u226412 2 number of base pairs in the stem region of the predicted hairpin \u226516 3 cutoff of free energy kCal/mol \u2264 15 4 length of hairpin up and down stems + terminal loop \u226550 5 length of hairpin loop \u2264200. 6 number of nucleotides in one bulge in mature region \u22644 7 number of biased errors in one bulge in mature region \u22642 8 number of biased bulges in mature region \u22642 9 number of errors in mature region \u22644 10 number of base pairs in the mature region of the predicted hairpin \u226512 11 percent of mature in stem \u226580. Supplementary files format and content: excel expression profiles", "Embryo", null, "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", null, "strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8", "GSM4396431", "GSM4396431: miRNA of MZdgcr8 2; Danio rerio; miRNA Seq", "GSM4396431", null, "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", null, "SRP251978", null, null, "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, null, null, 124901241, 134604417, 148078897, 124932015, 89384, "SRX7870076", "SRS6278493", "SRA1052219", "GEO", "The Chinese University of Hong Kong", 1, 0.0002, null, 2e-05, null, 0.99935, null, 0.51428, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, null, "miRNA of MZdgcr8 1", "GSM4396430", null, "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 \u226412 2 number of base pairs in the stem region of the predicted hairpin \u226516 3 cutoff of free energy kCal/mol \u2264 15 4 length of hairpin up and down stems + terminal loop \u226550 5 length of hairpin loop \u2264200. 6 number of nucleotides in one bulge in mature region \u22644 7 number of biased errors in one bulge in mature region \u22642 8 number of biased bulges in mature region \u22642 9 number of errors in mature region \u22644 10 number of base pairs in the mature region of the predicted hairpin \u226512 11 percent of mature in stem \u226580. Supplementary files format and content: excel expression profiles", "Embryo", null, "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", null, "strain:AB|tissue:embryo|age:4.5hpf|genotype:MZdgcr8", "GSM4396430", "GSM4396430: miRNA of MZdgcr8 1; Danio rerio; miRNA Seq", "GSM4396430", null, "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", null, "SRP251978", null, null, "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, null, null, 137533072, 149724383, 163915952, 137198731, 2010, "SRX7870075", "SRS6278492", "SRA1052219", "GEO", "The Chinese University of Hong Kong", 1, 0.0014, null, 0.00031, null, 0.99795, null, 0.62441, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, null, "miRNA of Wild type 3", "GSM4396429", null, "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 \u226412 2 number of base pairs in the stem region of the predicted hairpin \u226516 3 cutoff of free energy kCal/mol \u2264 15 4 length of hairpin up and down stems + terminal loop \u226550 5 length of hairpin loop \u2264200. 6 number of nucleotides in one bulge in mature region \u22644 7 number of biased errors in one bulge in mature region \u22642 8 number of biased bulges in mature region \u22642 9 number of errors in mature region \u22644 10 number of base pairs in the mature region of the predicted hairpin \u226512 11 percent of mature in stem \u226580. Supplementary files format and content: excel expression profiles", "Embryo", null, "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", null, "strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type", "GSM4396429", "GSM4396429: miRNA of Wild type 3; Danio rerio; miRNA Seq", "GSM4396429", null, "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", null, "SRP251978", null, null, "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, null, null, 171239999, 140558088, 209452609, 167641448, 37306, "SRX7870074", "SRS6278490", "SRA1052219", "GEO", "The Chinese University of Hong Kong", 1, 0.00247, null, 0.00016, null, 0.99797, null, 0.60356, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, null, "miRNA of Wild type 2", "GSM4396428", null, "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 \u226412 2 number of base pairs in the stem region of the predicted hairpin \u226516 3 cutoff of free energy kCal/mol \u2264 15 4 length of hairpin up and down stems + terminal loop \u226550 5 length of hairpin loop \u2264200. 6 number of nucleotides in one bulge in mature region \u22644 7 number of biased errors in one bulge in mature region \u22642 8 number of biased bulges in mature region \u22642 9 number of errors in mature region \u22644 10 number of base pairs in the mature region of the predicted hairpin \u226512 11 percent of mature in stem \u226580. Supplementary files format and content: excel expression profiles", "Embryo", null, "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", null, "strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type", "GSM4396428", "GSM4396428: miRNA of Wild type 2; Danio rerio; miRNA Seq", "GSM4396428", null, "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", null, "SRP251978", null, null, "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, null, null, 161673690, 168811670, 190321246, 159208682, 2647, "SRX7870073", "SRS6278491", "SRA1052219", "GEO", "The Chinese University of Hong Kong", 1, 0.03809, null, 0.00119, null, 0.99318, null, 0.59584, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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", null, null, "miRNA of Wild type 1", "GSM4396427", null, "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 \u226412 2 number of base pairs in the stem region of the predicted hairpin \u226516 3 cutoff of free energy kCal/mol \u2264 15 4 length of hairpin up and down stems + terminal loop \u226550 5 length of hairpin loop \u2264200. 6 number of nucleotides in one bulge in mature region \u22644 7 number of biased errors in one bulge in mature region \u22642 8 number of biased bulges in mature region \u22642 9 number of errors in mature region \u22644 10 number of base pairs in the mature region of the predicted hairpin \u226512 11 percent of mature in stem \u226580. Supplementary files format and content: excel expression profiles", "Embryo", null, "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", null, "strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type", "GSM4396427", "GSM4396427: miRNA of Wild type 1; Danio rerio; miRNA Seq", "GSM4396427", null, "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", null, "SRP251978", null, null, "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, null, null, 144656910, 150045615, 169161904, 143018153, 2271, "SRX7870072", "SRS6278489", "SRA1052219", "GEO", "The Chinese University of Hong Kong", 1, 0.0559, null, 0.00242, null, 0.99064, null, 0.54228, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-08", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 45, "expanded_columns": [], "expandable_columns": [], "columns": ["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.centername", "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.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", 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prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"experiment.library_layout\" = :p0 and \"experiment.library_strategy\" = :p1 and \"tissue_curation\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "miRNA-Seq", "p2": "Embryo Imprecise"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_strategy=miRNA-Seq&tissue_curation=Embryo+Imprecise", "results": [{"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 45, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Embryo+Imprecise", "selected": true}], "truncated": false}, "experiment.library_source": {"name": 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