{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_strategy = \"miRNA-Seq\", experiment.platform = \"ILLUMINA\" and tissue_curation_coarse = \"All anatomical structures\"", "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 <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Embryo", "N/A", "Total RNA were extracted using mirVana\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 <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Embryo", "N/A", "Total RNA were extracted using mirVana\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 <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Embryo", "N/A", "Total RNA were extracted using mirVana\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"], [39671, "SRR2043046", "SRX1041307", "SRS947739", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 200nM  sample3", "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3", "HBCD 200nM 3", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3", "Sample  HBCD 200nM 3", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, "Sample_HBCD_200nM-3.fastq.tar.gz", "fastq", 549695784.0, 16657448.0, "Sample  HBCD 200nM 3", "0:33", "A:120885057;C:120386921;G:146939259;T:161323403;N:161144", 33, null, null, null, 120885057, 120386921, 146939259, 161323403, 161144, "SRX1041307", "SRS947739", "SRA269780", "MG", "Xiamen University", 1, 0.13819, null, 0.03714, null, 0.94968, null, 0.52004, null, 33, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-09-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39672, "SRR2043044", "SRX1041306", "SRS947738", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 200nM  sample2", "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep2", "HBCD 200nM 2", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2", "Sample  HBCD 200nM 2", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, "Sample_HBCD_200nM-2.fastq.tar.gz", "fastq", 566585217.0, 17169249.0, "Sample  HBCD 200nM 2", "0:33", "A:119904892;C:129504656;G:159539041;T:157545273;N:91355", 33, null, null, null, 119904892, 129504656, 159539041, 157545273, 91355, "SRX1041306", "SRS947738", "SRA269780", "MG", "Xiamen University", 1, 0.07072, null, 0.01837, null, 0.96246, null, 0.52439, null, 33, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39673, "SRR2043035", "SRX1041305", "SRS947737", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 200nM  sample1", "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep1", "HBCD 200nM 1", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 200nM 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep1", "Sample  HBCD 200nM 1", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, "Sample_HBCD_200nM-1.fastq.tar.gz", "fastq", 636936228.0, 17692673.0, "Sample  HBCD 200nM 1", "0:36", "A:138321201;C:126054708;G:184822056;T:187709777;N:28486", 36, null, null, null, 138321201, 126054708, 184822056, 187709777, 28486, "SRX1041305", "SRS947737", "SRA269780", "MG", "Xiamen University", 1, 0.04374, null, 0.0115, null, 0.97839, null, 0.29573, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-09-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39674, "SRR2043030", "SRX1041276", "SRS947712", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 2nM  sample3", "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep3", "HBCD 2nM 3", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 200 nM HBCD rep3", "Sample HBCD 2nM 3", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, "Sample_HBCD_2nM-3.fastq.tar.gz", "fastq", 636936228.0, 17692673.0, "Sample HBCD 2nM 3", "0:36", "A:138321201;C:126054708;G:184822056;T:187709777;N:28486", 36, null, null, null, 138321201, 126054708, 184822056, 187709777, 28486, "SRX1041276", "SRS947712", "SRA269780", "MG", "Xiamen University", 1, 0.04377, null, 0.01174, null, 0.97812, null, 0.30675, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39675, "SRR2042999", "SRX1041271", "SRS947707", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 2nM  sample2", "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2", "HBCD 2nM 2", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep2", "Sample HBCD 2nM 2", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, "Sample_HBCD_2nM-2.fastq.tar.gz", "fastq", 482176476.0, 13393791.0, "Sample HBCD 2nM 2", "0:36", "A:104565872;C:92998014;G:137403437;T:147164823;N:44330", 36, null, null, null, 104565872, 92998014, 137403437, 147164823, 44330, "SRX1041271", "SRS947707", "SRA269780", "MG", "Xiamen University", 1, 0.0759, null, 0.02077, null, 0.97025, null, 0.33489, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-09-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39676, "SRR2040574", "SRX1038901", "SRS945650", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 2nM  sample1", "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep1", "HBCD 2nM 1", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:HBCD 2nM 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the 2 nM HBCD rep1", "Sample HBCD 2nM 1", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, "Sample_HBCD_2nM-1.fastq.tar.gz", "fastq", 327925620.0, 9109045.0, "Sample HBCD 2nM 1", "0:36", "A:71167117;C:63917852;G:94874537;T:97936051;N:30063", 36, null, null, null, 71167117, 63917852, 94874537, 97936051, 30063, "SRX1038901", "SRS945650", "SRA269780", "MG", "Xiamen University", 1, 0.06484, null, 0.01622, null, 0.97459, null, 0.35746, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39677, "SRR2040573", "SRX1038898", "SRS945648", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 0nM  sample3", "zebrafish at normal developmental age of 72hpf in the control rep3", "control 3", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:control 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the control  rep3", "Sample control 3", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, "Sample_control-3.fastq.tar.gz", "fastq", 456812301.0, 13842797.0, "Sample control 3", "0:33", "A:99424011;C:100923631;G:121758068;T:134398048;N:308543", 33, null, null, null, 99424011, 100923631, 121758068, 134398048, 308543, "SRX1038898", "SRS945648", "SRA269780", "MG", "Xiamen University", 1, 0.14866, null, 0.03878, null, 0.95079, null, 0.53781, null, 33, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-09-18", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39678, "SRR2040572", "SRX1038893", "SRS945643", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "HBCD 0nM  sample2", "zebrafish at normal developmental age of 72hpf in the control rep2", "control 2", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:control 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the control  rep2", "Sample control 2", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, null, null, 451846230.0, 13692310.0, "Sample control 2", "0:33", "A:100056403;C:97812076;G:121442936;T:132449348;N:85467", 33, null, null, null, 100056403, 97812076, 121442936, 132449348, 85467, "SRX1038893", "SRS945643", "SRA269780", "MG", "Xiamen University", 1, 0.06007, null, 0.01901, null, 0.96794, null, 0.4743, null, 33, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [39679, "SRR2040562", "SRX1038887", "SRS945623", "SRP058729", "PRJNA284830", "MicroRNA expression changes during zebrafish Danio\u00a0rerio development induced by hexabromocyclododecane", "PRJNA284830", "Whole Genome Sequencing", "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0  2  20 and 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", null, null, "Hexabromocyclododecane HBCD  one of the most widely used brominated flame retardants  has been found to cause toxic effects on animals. Although microRNAs miRNAs play an important role in many biological and metabolic processes  whether and how they are involved in the process of HBCD induced toxicity is largely unknown. In the present study  zebrafish embryos were exposed to HBCD at low concentrations of 0 2 20 200 nM. Subsequently  RNA was isolated from the embryo pool and the miRNAs expression profiles were analyzed using deep sequencing.", "zebrafish at normal developmental age of 72hpf in the control rep1", "control 1", null, "breed:zebrafish|strain:Wild type TU strain|age:72 hpf\u00a3\u00a8hpf stage:embryo|sex:pooled male and female|tissue:whole zebrafish|treatment:control 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "zebrafish at normal developmental age of 72hpf in the control  rep1", "Sample control 1", "1", "1", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>33</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP058729", null, null, "Sample_control-1.fastq.tar.gz", "fastq", 398024253.0, 12061341.0, "Sample control 1", "0:33", "A:90133666;C:86672655;G:103932053;T:117192591;N:93288", 33, null, null, null, 90133666, 86672655, 103932053, 117192591, 93288, "SRX1038887", "SRS945623", "SRA269780", "MG", "Xiamen University", 1, 0.08082, null, 0.02367, null, 0.96106, null, 0.52033, null, 33, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-05-27", "Larval", "Larval", "Whole Organism", "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"], [41244, "SRR3953261", "SRX1977497", "SRS1585138", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "500 \u03bcg/l BDE47 treatment miRNA", "GSM2252184", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "500 \u03bcg/l BDE47 treatment miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252184", "GSM2252184: 500 \u03bcg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq", "GSM2252184", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252184", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_500_1_filtered.fastq.gz", "fastq", 427211416.0, 18037304.0, "GSM2252184 r1", "0:23.68 1:0", "A:104654735;C:95575450;G:107353019;T:119612667;N:15545", 23, 0, null, null, 104654735, 95575450, 107353019, 119612667, 15545, "SRX1977497", "SRS1585138", "SRA444471", "GEO", "Tongji University", 1, 0.85356, null, 0.06282, null, 0.88609, null, 0.63407, null, 21, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41245, "SRR3953260", "SRX1977496", "SRS1585141", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "5 \u03bcg/l BDE47 treatment miRNA", "GSM2252183", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "5 \u03bcg/l BDE47 treatment miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252183", "GSM2252183: 5 \u03bcg/l BDE47 treatment miRNA; Danio rerio; miRNA Seq", "GSM2252183", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252183", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_5_1_filtered.fastq.gz", "fastq", 450698842.0, 19202408.0, "GSM2252183 r1", "0:23.47 1:0", "A:112159775;C:101086362;G:111723361;T:125713845;N:15499", 23, 0, null, null, 112159775, 101086362, 111723361, 125713845, 15499, "SRX1977496", "SRS1585141", "SRA444471", "GEO", "Tongji University", 1, 0.84838, null, 0.06014, null, 0.88637, null, 0.6441, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41246, "SRR3953259", "SRX1977495", "SRS1585136", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "s DMSO vehicle miRNA", "GSM2252182", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "s DMSO vehicle miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252182", "GSM2252182: s DMSO vehicle miRNA; Danio rerio; miRNA Seq", "GSM2252182", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252182", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_s_1_filtered.fq.gz", "fastq", 383701320.0, 16988819.0, "GSM2252182 r1", "0:22.59 1:0", "A:97700155;C:85144858;G:93319367;T:107531046;N:5894", 22, 0, null, null, 97700155, 85144858, 93319367, 107531046, 5894, "SRX1977495", "SRS1585136", "SRA444471", "GEO", "Tongji University", 1, 0.86023, null, 0.05501, null, 0.89534, null, 0.59715, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [41247, "SRR3953258", "SRX1977494", "SRS1585137", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "c Wildtype miRNA", "GSM2252181", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "c Wildtype miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252181", "GSM2252181: c Wildtype miRNA; Danio rerio; miRNA Seq", "GSM2252181", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252181", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_c_1_filtered.fastq.gz", "fastq", 413922462.0, 17365113.0, "GSM2252181 r1", "0:23.84 1:0", "A:102173642;C:93233248;G:103684592;T:114815345;N:15635", 23, 0, null, null, 102173642, 93233248, 103684592, 114815345, 15635, "SRX1977494", "SRS1585137", "SRA444471", "GEO", "Tongji University", 1, 0.85083, null, 0.06831, null, 0.88152, null, 0.63274, null, 27, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "Larval", "Larval", "Whole Organism", "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"], [53033, "SRR9674344", "SRX6434730", "SRS5089289", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "rnpc3 WT 1 [miRNA seq]", "GSM3938561", null, "source name:Wildtype siblings of rnpc3 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of rnpc3 mutants|Stage:7 dpf|tissue:whole fish embryos", "rnpc3 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Wildtype siblings of rnpc3 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of rnpc3 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938561", "GSM3938561: rnpc3 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938561", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938561", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Rpc3_1Ctrl.fastq.gz", "fastq", 1129597674.0, 22148974.0, "GSM3938561 r1", "0:51", "A:255811479;C:280511308;G:313965625;T:279284342;N:24920", 51, null, null, null, 255811479, 280511308, 313965625, 279284342, 24920, "SRX6434730", "SRS5089289", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00979, null, 0.00166, null, 0.99588, null, 0.63728, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53034, "SRR9674343", "SRX6434729", "SRS5089288", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 WT 1 [miRNA seq]", "GSM3938560", null, "source name:Wildtype siblings of smn1 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Wildtype siblings of smn1 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938560", "GSM3938560: smn1 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938560", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938560", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_1Ctrl.fastq.gz", "fastq", 1381751976.0, 27093176.0, "GSM3938560 r1", "0:51", "A:323091185;C:348663819;G:380517013;T:329446099;N:33860", 51, null, null, null, 323091185, 348663819, 380517013, 329446099, 33860, "SRX6434729", "SRS5089288", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00712, null, 0.00142, null, 0.99642, null, 0.66315, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53035, "SRR9674342", "SRX6434728", "SRS5089287", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 WT 1 [miRNA seq]", "GSM3938559", null, "source name:Wildtype siblings of germin5 mutants  repeat 1|strain background:TAB 5|genotype/variation:Wildtype siblings of germin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 WT 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Wildtype siblings of germin5 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Wildtype siblings of germin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938559", "GSM3938559: gemin5 WT 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938559", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938559", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_1Ctrl.fastq.gz", "fastq", 1347630171.0, 26424121.0, "GSM3938559 r1", "0:51", "A:307019777;C:335315873;G:378259746;T:327002846;N:31929", 51, null, null, null, 307019777, 335315873, 378259746, 327002846, 31929, "SRX6434728", "SRS5089287", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00723, null, 0.00127, null, 0.99582, null, 0.63934, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53036, "SRR9674341", "SRX6434727", "SRS5089286", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 3 [miRNA seq]", "GSM3938558", null, "source name:Homozygous smn1 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous smn1 mutants  repeat 3", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938558", "GSM3938558: smn1 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938558", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938558", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_3hom.fastq.gz", "fastq", 1269172638.0, 24885738.0, "GSM3938558 r1", "0:51", "A:290351922;C:320656517;G:354834895;T:303300306;N:28998", 51, null, null, null, 290351922, 320656517, 354834895, 303300306, 28998, "SRX6434727", "SRS5089286", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.0061, null, 0.00111, null, 0.9962, null, 0.5917, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53037, "SRR9674340", "SRX6434726", "SRS5089285", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 2 [miRNA seq]", "GSM3938557", null, "source name:Homozygous smn1 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous smn1 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938557", "GSM3938557: smn1 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938557", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938557", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_2hom.fastq.gz", "fastq", 1625802786.0, 31878486.0, "GSM3938557 r1", "0:51", "A:376836190;C:399950981;G:453572869;T:395403783;N:38963", 51, null, null, null, 376836190, 399950981, 453572869, 395403783, 38963, "SRX6434726", "SRS5089285", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00609, null, 0.00111, null, 0.99638, null, 0.63347, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53038, "SRR9674339", "SRX6434725", "SRS5089284", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "smn1 hom 1 [miRNA seq]", "GSM3938556", null, "source name:Homozygous smn1 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "smn1 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous smn1 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous smn1 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938556", "GSM3938556: smn1 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938556", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938556", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Smn1_1hom.fastq.gz", "fastq", 1553527320.0, 30461320.0, "GSM3938556 r1", "0:51", "A:360279409;C:388795394;G:432335873;T:372080058;N:36586", 51, null, null, null, 360279409, 388795394, 432335873, 372080058, 36586, "SRX6434725", "SRS5089284", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00691, null, 0.00137, null, 0.99638, null, 0.61909, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53039, "SRR9674338", "SRX6434724", "SRS5089283", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 3 [miRNA seq]", "GSM3938555", null, "source name:Homozygous gemin5 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin5 mutants  repeat 3", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938555", "GSM3938555: gemin5 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938555", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938555", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_3hom.fastq.gz", "fastq", 1162857936.0, 22801136.0, "GSM3938555 r1", "0:51", "A:267576310;C:282684680;G:327841913;T:284728561;N:26472", 51, null, null, null, 267576310, 282684680, 327841913, 284728561, 26472, "SRX6434724", "SRS5089283", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00597, null, 0.00114, null, 0.99618, null, 0.62386, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53040, "SRR9674337", "SRX6434723", "SRS5089282", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 2 [miRNA seq]", "GSM3938554", null, "source name:Homozygous gemin5 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin5 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938554", "GSM3938554: gemin5 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938554", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938554", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_2hom.fastq.gz", "fastq", 1612392846.0, 31615546.0, "GSM3938554 r1", "0:51", "A:360634123;C:389619637;G:457463377;T:404638471;N:37238", 51, null, null, null, 360634123, 389619637, 457463377, 404638471, 37238, "SRX6434723", "SRS5089282", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00538, null, 0.00085, null, 0.99677, null, 0.62726, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53041, "SRR9674336", "SRX6434722", "SRS5089281", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin5 hom 1 [miRNA seq]", "GSM3938553", null, "source name:Homozygous gemin5 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin5 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin5 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin5 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938553", "GSM3938553: gemin5 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938553", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938553", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_Gmn5_1hom.fastq.gz", "fastq", 1734523362.0, 34010262.0, "GSM3938553 r1", "0:51", "A:400823854;C:428868747;G:484830308;T:419961177;N:39276", 51, null, null, null, 400823854, 428868747, 484830308, 419961177, 39276, "SRX6434722", "SRS5089281", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.00485, null, 0.00098, null, 0.99636, null, 0.65384, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53042, "SRR9674335", "SRX6434721", "SRS5089280", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 3 [miRNA seq]", "GSM3938552", null, "source name:Homozygous gemin6 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin6 mutants  repeat 3", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938552", "GSM3938552: gemin6 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938552", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938552", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_3.fastq.gz", "fastq", 3450343851.0, 67653801.0, "GSM3938552 r1", "0:51", "A:777873635;C:888116741;G:969513398;T:814785464;N:54613", 51, null, null, null, 777873635, 888116741, 969513398, 814785464, 54613, "SRX6434721", "SRS5089280", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01435, null, 0.00222, null, 0.99486, null, 0.71333, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53043, "SRR9674334", "SRX6434720", "SRS5089279", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 2 [miRNA seq]", "GSM3938551", null, "source name:Homozygous gemin6 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin6 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938551", "GSM3938551: gemin6 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938551", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938551", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_2.fastq.gz", "fastq", 1586876781.0, 31115231.0, "GSM3938551 r1", "0:51", "A:373921059;C:393906222;G:435371208;T:383652895;N:25397", 51, null, null, null, 373921059, 393906222, 435371208, 383652895, 25397, "SRX6434720", "SRS5089279", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01456, null, 0.00199, null, 0.99488, null, 0.65884, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53044, "SRR9674333", "SRX6434719", "SRS5089278", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin6 hom 1 [miRNA seq]", "GSM3938550", null, "source name:Homozygous gemin6 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin6 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin6 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin6 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938550", "GSM3938550: gemin6 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938550", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938550", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G6_1.fastq.gz", "fastq", 1632291159.0, 32005709.0, "GSM3938550 r1", "0:51", "A:387703621;C:405051941;G:452019824;T:387489473;N:26300", 51, null, null, null, 387703621, 405051941, 452019824, 387489473, 26300, "SRX6434719", "SRS5089278", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01378, null, 0.00168, null, 0.99482, null, 0.66266, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53045, "SRR9674332", "SRX6434718", "SRS5089277", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 3 [miRNA seq]", "GSM3938549", null, "source name:Homozygous gemin4 mutants  repeat 3|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 3 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin4 mutants  repeat 3", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938549", "GSM3938549: gemin4 hom 3 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938549", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938549", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_3.fastq.gz", "fastq", 1079490837.0, 21166487.0, "GSM3938549 r1", "0:51", "A:247548301;C:266526237;G:295997407;T:269401582;N:17310", 51, null, null, null, 247548301, 266526237, 295997407, 269401582, 17310, "SRX6434718", "SRS5089277", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01616, null, 0.00211, null, 0.99486, null, 0.65494, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53046, "SRR9674331", "SRX6434717", "SRS5089276", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 2 [miRNA seq]", "GSM3938548", null, "source name:Homozygous gemin4 mutants  repeat 2|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 2 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin4 mutants  repeat 2", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938548", "GSM3938548: gemin4 hom 2 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938548", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938548", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_2.fastq.gz", "fastq", 6427925862.0, 126037762.0, "GSM3938548 r1", "0:51", "A:1491339645;C:1560095279;G:1804953332;T:1571434430;N:103176", 51, null, null, null, 1491339645, 1560095279, 1804953332, 1571434430, 103176, "SRX6434717", "SRS5089276", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01032, null, 0.00157, null, 0.99504, null, 0.70577, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [53047, "SRR9674330", "SRX6434716", "SRS5089275", "SRP214428", "PRJNA554249", "the role of SMN complex in tissue regeneration", "GSE134187", "Transcriptome Analysis", "we conducted RNA Seq and MiRNA Seq to screen the molecular targets and pathways involved in tissue regeneration of SMN complex members Overall design: we compared the 3 regeneration gene mutants to the 4 non regeneration gene mutants.", null, null, null, "gemin4 hom 1 [miRNA seq]", "GSM3938547", null, "source name:Homozygous gemin4 mutants  repeat 1|strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "gemin4 hom 1 [miRNA seq]", "Reads are trimmed using Trimmomatic v0.36 Trimmed reads are aligned using STAR 2.5.4a mRNA or \"hisat2 2.2.1.0   no softclip   no spliced alignment    rna strandness R   new summary\" miRNA abundance is measured by RSEM \"rsem calculate expression   paired end   forward prob 0.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output\" for mRNA Seq  \"rsem calculate expression   forward prob 1.0   alignments  p 16   seed 987347   calc ci   calc pme   estimate rspd   time   no bam output   fragment length mean 22   fragment length sd 10   seed length 15\" for miRNA Seq Genome build: danRer10/Ensembl release 91 for mRNA Seq  miRBase mature miRNA for microRNA Seq Supplementary files format and content: RSEM output  gene abundance", "Homozygous gemin4 mutants  repeat 1", null, "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain background:TAB 5|genotype/variation:Homozygous gemin4 mutants|Stage:7 dpf|tissue:whole fish embryos", "GSM3938547", "GSM3938547: gemin4 hom 1 [miRNA seq]; Danio rerio; miRNA Seq", "GSM3938547", null, "1", "Embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. Prepare one paired end index library from each total RNA sample  pool all libraries  load  pool on HiSeq 2500  run as indexed 50 base single end reads. embryos were placed in Qiazol  and RNA was extracted by using Qiagen miRNeasy Mini Kit. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3938547", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214428", null, null, "mir_G4_1.fastq.gz", "fastq", 3063591624.0, 60070424.0, "GSM3938547 r1", "0:51", "A:710248035;C:750319193;G:848095316;T:754879685;N:49395", 51, null, null, null, 710248035, 750319193, 848095316, 754879685, 49395, "SRX6434716", "SRS5089275", "SRA920248", "GEO", "Burgess, NHGRI, NIH", 1, 0.01137, null, 0.00151, null, 0.99527, null, 0.69096, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "bulk", "bulk", null, "United States", "2019-07-12", "Larval", "Larval", "Whole Organism", "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"], [59623, "SRR11974583", "SRX8518005", "SRS6815486", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Gamma2 nmbu sncRNA 3", "GSM4605882", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "F1 Gamma2 nmbu sncRNA 3", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "GSM4605882", "GSM4605882: F1 Gamma2 nmbu sncRNA 3; Danio rerio; miRNA Seq", "GSM4605882", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605882", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_6_raw.fq.gz", "fastq", 566507200.0, 11330144.0, "GSM4605882 r1", "0:50", "A:167677443;C:125843251;G:148647392;T:124217714;N:121400", 50, null, null, null, 167677443, 125843251, 148647392, 124217714, 121400, "SRX8518005", "SRS6815486", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.75254, null, 0.48205, null, 0.84346, null, 0.59219, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59624, "SRR11974582", "SRX8518004", "SRS6815485", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Gamma2 nmbu sncRNA 2", "GSM4605881", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "F1 Gamma2 nmbu sncRNA 2", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "GSM4605881", "GSM4605881: F1 Gamma2 nmbu sncRNA 2; Danio rerio; miRNA Seq", "GSM4605881", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605881", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_5_raw.fq.gz", "fastq", 579779650.0, 11595593.0, "GSM4605881 r1", "0:50", "A:173232869;C:126599907;G:152751070;T:127092652;N:103152", 50, null, null, null, 173232869, 126599907, 152751070, 127092652, 103152, "SRX8518004", "SRS6815485", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.7644, null, 0.48211, null, 0.84583, null, 0.59288, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59625, "SRR11974581", "SRX8518003", "SRS6815484", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Gamma1 nmbu sncRNA 1", "GSM4605880", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "F1 Gamma1 nmbu sncRNA 1", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from exposed parents", "GSM4605880", "GSM4605880: F1 Gamma1 nmbu sncRNA 1; Danio rerio; miRNA Seq", "GSM4605880", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605880", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_4_raw.fq.gz", "fastq", 649357050.0, 12987141.0, "GSM4605880 r1", "0:50", "A:191891965;C:145644319;G:171130267;T:140550711;N:139788", 50, null, null, null, 191891965, 145644319, 171130267, 140550711, 139788, "SRX8518003", "SRS6815484", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.75002, null, 0.44712, null, 0.84818, null, 0.57467, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59626, "SRR11974580", "SRX8518002", "SRS6815483", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Control3 nmbu sncRNA 3", "GSM4605879", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "F1 Control3 nmbu sncRNA 3", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "GSM4605879", "GSM4605879: F1 Control3 nmbu sncRNA 3; Danio rerio; miRNA Seq", "GSM4605879", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605879", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_3_raw.fq.gz", "fastq", 641762600.0, 12835252.0, "GSM4605879 r1", "0:50", "A:187476040;C:147628502;G:173061052;T:133488938;N:108068", 50, null, null, null, 187476040, 147628502, 173061052, 133488938, 108068, "SRX8518002", "SRS6815483", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.68333, null, 0.36693, null, 0.8493, null, 0.57501, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59627, "SRR11974579", "SRX8518001", "SRS6815482", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Control2 nmbu sncRNA 2", "GSM4605878", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "F1 Control2 nmbu sncRNA 2", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "GSM4605878", "GSM4605878: F1 Control2 nmbu sncRNA 2; Danio rerio; miRNA Seq", "GSM4605878", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605878", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_2_raw.fq.gz", "fastq", 531815250.0, 10636305.0, "GSM4605878 r1", "0:50", "A:155930702;C:122952623;G:141743533;T:111074299;N:114093", 50, null, null, null, 155930702, 122952623, 141743533, 111074299, 114093, "SRX8518001", "SRS6815482", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.65896, null, 0.35164, null, 0.8453, null, 0.57438, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [59628, "SRR11974578", "SRX8518000", "SRS6815481", "SRP266770", "PRJNA638603", "small non coding RNA expression profile in F1 progeny from irradiated adults zebrafish", "GSE152189", "Transcriptome Analysis", "In order to investigate transcriptomic mechanisms underlying radiation exposure  we exposed zebrafish 6 mpf ttwo xxx.7 mGy/h of g radiation 5.2 Gy total dose during gametogenesis for 27 days. F1 offspring from exposed parents were sampled at xxx.5 hpf late blastula/early gastrula one year post parental exposure  for small RNA sequence analysis to determine changes in the sncRNA expression profile. Pairwise comparison between F1 generation from exposed F1 ?  and control F1 C parents  revealed several classes of sncRNAs and one class of lncRNA differentially expressed. Overall  22 miRNAs  11 piRNA clusters  19 snRNAs  and 21 lincRNA were found differentially expressed. When linking the DEmiRs to our previously published mRNA data  a total of 672 differentially expressed mRNAs could be linked to the DEmiRs  of which 380 followed the canonical inverse relation in miRNA mRNA interaction. Pathway analysis revealed these 380 mRNAs involved in insulin receptor  NFkB and PTEN signaling  linking to apoptosis and cancers. The 84.2% of differentially expressed snRNAs were down regulated in the F1 ? group  68.8% of which were U1 and U2 snRNAs. In addition  45% of differentially expressed DEpiRNA clusters were found associated to 9 TEs LTR  LINE  and TIR p=0.0024. DEpiRNA clusters were expressed from the opposite strand of the associated TEs  indicating expression of DEpiRNAs in response to activation of TEs. Finally  66.7% and 33.3% of lincRNAs in F1 ? were down  and up regulated respectively. The cancer and development related lincRNAs malat 1 was found among the most down regulated genes  denoting a link between lincRNAs expression and altered phenotypes reported previously in our parallel studies. Overall design: One year post parental exposure during gametogenesis to 60Co source at 8.7 mGy/h 5.2 Gy total dose  three biological replicates of F1 embryos were collected in pools of 100 individuals from both exposed and control groups. Total RNA corresponding to sampled embryos in each experimental group was extracted and sent for small RNA sequencing under platform Illumina 4000. The 6 small RNA libraries obtained from 3 biological replicates in each experimental group were analyzed for small non coding RNA profiling and differential expression.", null, "pubmed:33602989", null, "F1 Control1 nmbu sncRNA 1", "GSM4605877", null, "tissue:Whole embryo|develomental stage:5.5 hpf 50 percent epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "F1 Control1 nmbu sncRNA 1", "Raw reads were trimmed from adapter sequences and quality assessed using Trim Galore! v0.3.7 Raw reads were filtered by length using on terminal commands to retain reads within the range 18 \u2013 36 nt Length filtered reads were mapped  classified into genomic features  and counted using Unitas v1.5.2 under default settings miRNAs were quantified with miRDeep2 v0.0.5  using the built in script quantifier.pl piRNA clusters were predicted using proTRAC v4.2.4 under default values Genome build: GRCz10 Supplementary files format and content: matrix of raw read counts abundances as comma separated values", "Whole embryo", null, "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", null, "develomental stage:5.5 hpf 50 percent  epiboly|strain:AB|genotype:wild type|group:F1 from control parents", "GSM4605877", "GSM4605877: F1 Control1 nmbu sncRNA 1; Danio rerio; miRNA Seq", "GSM4605877", null, "1", "Batches of 100 embryos in triplicates were homogenized using Magnalyser Beads Roche Diagnostics  Germany  and total RNA was isolated using Trizol following the instructions of manufacturer Thermo Fisher Scientific  USA. sequencing libraries were prepared using the NEBnext\u00ae Small RNA Library Prep Set for Illumina\u00ae  New England Biolabs\u00ae inc  USA from each sample 1 \u03bcg of total RNA was used as input material.", "GEO Accession:GSM4605877", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP266770", null, null, "nmbu_sncRNA_1_raw.fq.gz", "fastq", 534855250.0, 10697105.0, "GSM4605877 r1", "0:50", "A:156249541;C:120087413;G:145230236;T:113171967;N:116093", 50, null, null, null, 156249541, 120087413, 145230236, 113171967, 116093, "SRX8518000", "SRS6815481", "SRA1085407", "GEO", "Alestr\u00f8m ZFlab, Basic Sicences and Aquatic medicine, Norwegian University of Life Sciences", 1, 0.74031, null, 0.40182, null, 0.83366, null, 0.60438, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Norway", "2020-06-10", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [63643, "SRR13979112", "SRX10356673", "SRS8474629", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TiBP rep4", "GSM5174052", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TiBP rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174052", "GSM5174052: miRNA TiBP rep4; Danio rerio; miRNA Seq", "GSM5174052", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174052", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s028-indexRPI28-CAAAAG-52_S28_L001_R1_001.fastq.gz", "fastq", 910334614.0, 9013214.0, "GSM5174052 r1", "0:101 1:0", "A:290447743;C:219962173;G:188092578;T:211816048;N:16072", 101, 0, null, null, 290447743, 219962173, 188092578, 211816048, 16072, "SRX10356673", "SRS8474629", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00011, null, 0.0, null, 0.99967, null, 0.75, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63644, "SRR13979111", "SRX10356672", "SRS8474628", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TiBP rep3", "GSM5174051", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TiBP rep3", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174051", "GSM5174051: miRNA TiBP rep3; Danio rerio; miRNA Seq", "GSM5174051", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174051", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s027-indexRPI27-ATTCCT-51_S27_L001_R1_001.fastq.gz", "fastq", 1206610034.0, 11946634.0, "GSM5174051 r1", "0:101 1:0", "A:350061820;C:302802434;G:235521116;T:318199102;N:25562", 101, 0, null, null, 350061820, 302802434, 235521116, 318199102, 25562, "SRX10356672", "SRS8474628", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00013, null, 0.0, null, 0.99965, null, 0.79166, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63645, "SRR13979110", "SRX10356671", "SRS8474626", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TiBP rep2", "GSM5174050", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TiBP rep2", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174050", "GSM5174050: miRNA TiBP rep2; Danio rerio; miRNA Seq", "GSM5174050", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174050", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s026-indexRPI26-ATGAGC-50_S26_L001_R1_001.fastq.gz", "fastq", 464537279.0, 4599379.0, "GSM5174050 r1", "0:101 1:0", "A:139497834;C:112216637;G:99887123;T:112926329;N:9356", 101, 0, null, null, 139497834, 112216637, 99887123, 112926329, 9356, "SRX10356671", "SRS8474626", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00022, null, 1e-05, null, 0.99955, null, 0.61538, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63646, "SRR13979109", "SRX10356670", "SRS8474627", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TiBP rep1", "GSM5174049", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TiBP rep1", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174049", "GSM5174049: miRNA TiBP rep1; Danio rerio; miRNA Seq", "GSM5174049", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174049", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s025-indexRPI25-ACTGAT-49_S25_L001_R1_001.fastq.gz", "fastq", 1146926508.0, 11355708.0, "GSM5174049 r1", "0:101 1:0", "A:344954395;C:275566512;G:235491109;T:290891698;N:22794", 101, 0, null, null, 344954395, 275566512, 235491109, 290891698, 22794, "SRX10356670", "SRS8474627", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00019, null, 1e-05, null, 0.99965, null, 0.71875, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63647, "SRR13979108", "SRX10356669", "SRS8474625", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TPP rep4", "GSM5174048", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TPP rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174048", "GSM5174048: miRNA TPP rep4; Danio rerio; miRNA Seq", "GSM5174048", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174048", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s036-indexRPI36-CCAACA-60_S36_L001_R1_001.fastq.gz", "fastq", 927517340.0, 9183340.0, "GSM5174048 r1", "0:101 1:0", "A:288988916;C:242744912;G:181427113;T:214337769;N:18630", 101, 0, null, null, 288988916, 242744912, 181427113, 214337769, 18630, "SRX10356669", "SRS8474625", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00023, null, 1e-05, null, 0.99955, null, 0.70731, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63648, "SRR13979107", "SRX10356668", "SRS8474624", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TPP rep3", "GSM5174047", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TPP rep3", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174047", "GSM5174047: miRNA TPP rep3; Danio rerio; miRNA Seq", "GSM5174047", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174047", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s035-indexRPI35-CATTTT-59_S35_L001_R1_001.fastq.gz", "fastq", 1013252907.0, 10032207.0, "GSM5174047 r1", "0:101 1:0", "A:295518831;C:243561888;G:197719671;T:276430583;N:21934", 101, 0, null, null, 295518831, 243561888, 197719671, 276430583, 21934, "SRX10356668", "SRS8474624", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00013, null, 0.0, null, 0.99973, null, 0.48, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63649, "SRR13979106", "SRX10356667", "SRS8474623", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TPP rep2", "GSM5174046", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TPP rep2", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174046", "GSM5174046: miRNA TPP rep2; Danio rerio; miRNA Seq", "GSM5174046", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174046", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s034-indexRPI34-CATGGC-58_S34_L001_R1_001.fastq.gz", "fastq", 907210381.0, 8982281.0, "GSM5174046 r1", "0:101 1:0", "A:265012714;C:227793861;G:194928689;T:219454152;N:20965", 101, 0, null, null, 265012714, 227793861, 194928689, 219454152, 20965, "SRX10356667", "SRS8474623", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00013, null, 0.0, null, 0.99965, null, 0.875, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63650, "SRR13979105", "SRX10356666", "SRS8474622", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TPP rep1", "GSM5174045", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TPP rep1", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174045", "GSM5174045: miRNA TPP rep1; Danio rerio; miRNA Seq", "GSM5174045", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174045", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s033-indexRPI33-CAGGCG-57_S33_L001_R1_001.fastq.gz", "fastq", 980681013.0, 9709713.0, "GSM5174045 r1", "0:101 1:0", "A:286952877;C:245397809;G:220787030;T:227522023;N:21274", 101, 0, null, null, 286952877, 245397809, 220787030, 227522023, 21274, "SRX10356666", "SRS8474622", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00021, null, 1e-05, null, 0.99961, null, 0.72222, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63651, "SRR13979104", "SRX10356665", "SRS8474621", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBPH rep4", "GSM5174044", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TBPH rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174044", "GSM5174044: miRNA TBPH rep4; Danio rerio; miRNA Seq", "GSM5174044", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174044", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s012-indexRPI12-CTTGTA-24_S12_L001_R1_001.fastq.gz", "fastq", 879997850.0, 8712850.0, "GSM5174044 r1", "0:101 1:0", "A:257202916;C:211754629;G:179803383;T:231218549;N:18373", 101, 0, null, null, 257202916, 211754629, 179803383, 231218549, 18373, "SRX10356665", "SRS8474621", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00022, null, 0.0, null, 0.99961, null, 0.55, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63652, "SRR13979103", "SRX10356664", "SRS8474620", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBPH rep3", "GSM5174043", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TBPH rep3", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174043", "GSM5174043: miRNA TBPH rep3; Danio rerio; miRNA Seq", "GSM5174043", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174043", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s011-indexRPI11-GGCTAC-23_S11_L001_R1_001.fastq.gz", "fastq", 883707883.0, 8749583.0, "GSM5174043 r1", "0:101 1:0", "A:256575313;C:222504855;G:189827000;T:214781797;N:18918", 101, 0, null, null, 256575313, 222504855, 189827000, 214781797, 18918, "SRX10356664", "SRS8474620", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00021, null, 0.0, null, 0.99961, null, 0.725, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63653, "SRR13979102", "SRX10356663", "SRS8474619", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBPH rep2", "GSM5174042", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TBPH rep2", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174042", "GSM5174042: miRNA TBPH rep2; Danio rerio; miRNA Seq", "GSM5174042", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174042", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s010-indexRPI10-TAGCTT-22_S10_L001_R1_001.fastq.gz", "fastq", 727499667.0, 7202967.0, "GSM5174042 r1", "0:101 1:0", "A:212029291;C:175832603;G:148851978;T:190770471;N:15324", 101, 0, null, null, 212029291, 175832603, 148851978, 190770471, 15324, "SRX10356663", "SRS8474619", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00025, null, 1e-05, null, 0.99951, null, 0.68181, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63654, "SRR13979101", "SRX10356662", "SRS8474618", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBPH rep1", "GSM5174041", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TBPH rep1", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174041", "GSM5174041: miRNA TBPH rep1; Danio rerio; miRNA Seq", "GSM5174041", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174041", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s009-indexRPI9-GATCAG-21_S9_L001_R1_001.fastq.gz", "fastq", 351322743.0, 3478443.0, "GSM5174041 r1", "0:101 1:0", "A:105338110;C:85172820;G:75749691;T:85054964;N:7158", 101, 0, null, null, 105338110, 85172820, 75749691, 85054964, 7158, "SRX10356662", "SRS8474618", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00036, null, 1e-05, null, 0.99953, null, 0.52238, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63655, "SRR13979100", "SRX10356661", "SRS8474616", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TCEP rep4", "GSM5174040", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TCEP rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174040", "GSM5174040: miRNA TCEP rep4; Danio rerio; miRNA Seq", "GSM5174040", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174040", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s044-indexRPI44-TATAAT-72_S44_L001_R1_001.fastq.gz", "fastq", 904258656.0, 8953056.0, "GSM5174040 r1", "0:101 1:0", "A:282578101;C:207780974;G:175938229;T:237943510;N:17842", 101, 0, null, null, 282578101, 207780974, 175938229, 237943510, 17842, "SRX10356661", "SRS8474616", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.0002, null, 0.0, null, 0.99951, null, 0.72972, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63656, "SRR13979099", "SRX10356660", "SRS8474615", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TCEP rep3", "GSM5174039", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TCEP rep3", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174039", "GSM5174039: miRNA TCEP rep3; Danio rerio; miRNA Seq", "GSM5174039", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174039", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s043-indexRPI43-TACAGC-71_S43_L001_R1_001.fastq.gz", "fastq", 908098777.0, 8991077.0, "GSM5174039 r1", "0:101 1:0", "A:274350569;C:227463819;G:185316266;T:220948697;N:19426", 101, 0, null, null, 274350569, 227463819, 185316266, 220948697, 19426, "SRX10356660", "SRS8474615", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00015, null, 0.0, null, 0.99965, null, 0.57142, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63657, "SRR13979098", "SRX10356659", "SRS8474617", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TCEP rep2", "GSM5174038", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TCEP rep2", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174038", "GSM5174038: miRNA TCEP rep2; Danio rerio; miRNA Seq", "GSM5174038", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174038", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s042-indexRPI42-TAATCG-70_S42_L001_R1_001.fastq.gz", "fastq", 738320403.0, 7310103.0, "GSM5174038 r1", "0:101 1:0", "A:221107544;C:178181142;G:152128298;T:186889068;N:14351", 101, 0, null, null, 221107544, 178181142, 152128298, 186889068, 14351, "SRX10356659", "SRS8474617", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00017, null, 0.0, null, 0.99965, null, 0.59375, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63658, "SRR13979097", "SRX10356658", "SRS8474612", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TCEP rep1", "GSM5174037", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TCEP rep1", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174037", "GSM5174037: miRNA TCEP rep1; Danio rerio; miRNA Seq", "GSM5174037", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174037", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s041-indexRPI41-GACGAC-69_S41_L001_R1_001.fastq.gz", "fastq", 470221761.0, 4655661.0, "GSM5174037 r1", "0:101 1:0", "A:142688200;C:117856681;G:100380615;T:109286679;N:9586", 101, 0, null, null, 142688200, 117856681, 100380615, 109286679, 9586, "SRX10356658", "SRS8474612", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00028, null, 1e-05, null, 0.99951, null, 0.66666, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63659, "SRR13979096", "SRX10356657", "SRS8474613", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TDBPP rep4", "GSM5174036", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TDBPP rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174036", "GSM5174036: miRNA TDBPP rep4; Danio rerio; miRNA Seq", "GSM5174036", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174036", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s024-indexRPI24-GGTAGC-48_S24_L001_R1_001.fastq.gz", "fastq", 889897668.0, 8810868.0, "GSM5174036 r1", "0:101 1:0", "A:253810688;C:216798740;G:203615337;T:215653771;N:19132", 101, 0, null, null, 253810688, 216798740, 203615337, 215653771, 19132, "SRX10356657", "SRS8474613", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00019, null, 0.0, null, 0.99963, null, 0.41176, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63660, "SRR13979095", "SRX10356656", "SRS8474614", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TDBPP rep3", "GSM5174035", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TDBPP rep3", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174035", "GSM5174035: miRNA TDBPP rep3; Danio rerio; miRNA Seq", "GSM5174035", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174035", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s023-indexRPI23-GAGTGG-47_S23_L001_R1_001.fastq.gz", "fastq", 528666623.0, 5234323.0, "GSM5174035 r1", "0:101 1:0", "A:145917522;C:125201606;G:128827845;T:128709318;N:10332", 101, 0, null, null, 145917522, 125201606, 128827845, 128709318, 10332, "SRX10356656", "SRS8474614", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00024, null, 0.0, null, 0.99961, null, 0.56818, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63661, "SRR13979094", "SRX10356655", "SRS8474609", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TDBPP rep2", "GSM5174034", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TDBPP rep2", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174034", "GSM5174034: miRNA TDBPP rep2; Danio rerio; miRNA Seq", "GSM5174034", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174034", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s022-indexRPI22-CGTACG-46_S22_L001_R1_001.fastq.gz", "fastq", 906963537.0, 8979837.0, "GSM5174034 r1", "0:101 1:0", "A:246251307;C:236436405;G:206539134;T:217717657;N:19034", 101, 0, null, null, 246251307, 236436405, 206539134, 217717657, 19034, "SRX10356655", "SRS8474609", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00015, null, 0.0, null, 0.99967, null, 0.65384, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63662, "SRR13979093", "SRX10356654", "SRS8474611", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TDBPP rep1", "GSM5174033", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TDBPP rep1", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174033", "GSM5174033: miRNA TDBPP rep1; Danio rerio; miRNA Seq", "GSM5174033", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174033", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s021-indexRPI21-GTTTCG-45_S21_L001_R1_001.fastq.gz", "fastq", 556898547.0, 5513847.0, "GSM5174033 r1", "0:101 1:0", "A:149304325;C:137357612;G:124103413;T:146121425;N:11772", 101, 0, null, null, 149304325, 137357612, 124103413, 146121425, 11772, "SRX10356654", "SRS8474611", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00021, null, 0.0, null, 0.99957, null, 0.7027, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63663, "SRR13979092", "SRX10356653", "SRS8474610", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TCPP rep4", "GSM5174032", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TCPP rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174032", "GSM5174032: miRNA TCPP rep4; Danio rerio; miRNA Seq", "GSM5174032", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174032", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s016-indexRPI16-CCGTCC-28_S16_L001_R1_001.fastq.gz", "fastq", 885697179.0, 8769279.0, "GSM5174032 r1", "0:101 1:0", "A:247836719;C:241737695;G:181087463;T:215012979;N:22323", 101, 0, null, null, 247836719, 241737695, 181087463, 215012979, 22323, "SRX10356653", "SRS8474610", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00019, null, 0.0, null, 0.99967, null, 0.68571, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63664, "SRR13979091", "SRX10356652", "SRS8474608", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TCPP rep3", "GSM5174031", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TCPP rep3", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174031", "GSM5174031: miRNA TCPP rep3; Danio rerio; miRNA Seq", "GSM5174031", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174031", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s015-indexRPI15-ATGTCA-27_S15_L001_R1_001.fastq.gz", "fastq", 566510010.0, 5609010.0, "GSM5174031 r1", "0:101 1:0", "A:170383116;C:137048514;G:115945259;T:143122249;N:10872", 101, 0, null, null, 170383116, 137048514, 115945259, 143122249, 10872, "SRX10356652", "SRS8474608", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00025, null, 0.0, null, 0.99967, null, 0.54347, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63665, "SRR13979090", "SRX10356651", "SRS8474607", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TCPP rep2", "GSM5174030", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TCPP rep2", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174030", "GSM5174030: miRNA TCPP rep2; Danio rerio; miRNA Seq", "GSM5174030", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174030", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s014-indexRPI14-AGTTCC-26_S14_L001_R1_001.fastq.gz", "fastq", 892405902.0, 8835702.0, "GSM5174030 r1", "0:101 1:0", "A:259754435;C:224608997;G:182748088;T:225275385;N:18997", 101, 0, null, null, 259754435, 224608997, 182748088, 225275385, 18997, "SRX10356651", "SRS8474607", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00022, null, 0.0, null, 0.99951, null, 0.64285, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63666, "SRR13979089", "SRX10356650", "SRS8474606", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TCPP rep1", "GSM5174029", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TCPP rep1", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174029", "GSM5174029: miRNA TCPP rep1; Danio rerio; miRNA Seq", "GSM5174029", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174029", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s013-indexRPI13-AGTCAA-25_S13_L001_R1_001.fastq.gz", "fastq", 1059166295.0, 10486795.0, "GSM5174029 r1", "0:101 1:0", "A:329962449;C:255719926;G:216763563;T:256700660;N:19697", 101, 0, null, null, 329962449, 255719926, 216763563, 256700660, 19697, "SRX10356650", "SRS8474606", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00013, null, 1e-05, null, 0.99969, null, 0.63636, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63667, "SRR13979088", "SRX10356649", "SRS8474605", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBBPA rep4", "GSM5174028", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TBBPA rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174028", "GSM5174028: miRNA TBBPA rep4; Danio rerio; miRNA Seq", "GSM5174028", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174028", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s008-indexRPI8-ACTTGA-20_S8_L001_R1_001.fastq.gz", "fastq", 868526270.0, 8599270.0, "GSM5174028 r1", "0:101 1:0", "A:259616680;C:210636450;G:178110756;T:220145615;N:16769", 101, 0, null, null, 259616680, 210636450, 178110756, 220145615, 16769, "SRX10356649", "SRS8474605", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00023, null, 0.0, null, 0.99961, null, 0.67441, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63668, "SRR13979087", "SRX10356648", "SRS8474604", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBBPA rep3", "GSM5174027", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TBBPA rep3", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174027", "GSM5174027: miRNA TBBPA rep3; Danio rerio; miRNA Seq", "GSM5174027", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174027", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s007-indexRPI7-CAGATC-19_S7_L001_R1_001.fastq.gz", "fastq", 493578011.0, 4886911.0, "GSM5174027 r1", "0:101 1:0", "A:147046152;C:124953541;G:102431606;T:119137120;N:9592", 101, 0, null, null, 147046152, 124953541, 102431606, 119137120, 9592, "SRX10356648", "SRS8474604", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00024, null, 1e-05, null, 0.99947, null, 0.76744, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63669, "SRR13979086", "SRX10356647", "SRS8474603", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBBPA rep2", "GSM5174026", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TBBPA rep2", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174026", "GSM5174026: miRNA TBBPA rep2; Danio rerio; miRNA Seq", "GSM5174026", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174026", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s006-indexRPI6-GCCAAT-18_S6_L001_R1_001.fastq.gz", "fastq", 910368853.0, 9013553.0, "GSM5174026 r1", "0:101 1:0", "A:270122236;C:230334670;G:190520709;T:219373774;N:17464", 101, 0, null, null, 270122236, 230334670, 190520709, 219373774, 17464, "SRX10356647", "SRS8474603", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00023, null, 0.0, null, 0.99949, null, 0.72727, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63670, "SRR13979085", "SRX10356646", "SRS8474602", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBBPA rep1", "GSM5174025", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA TBBPA rep1", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174025", "GSM5174025: miRNA TBBPA rep1; Danio rerio; miRNA Seq", "GSM5174025", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174025", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s005-indexRPI5-ACAGTG-17_S5_L001_R1_001.fastq.gz", "fastq", 894131992.0, 8852792.0, "GSM5174025 r1", "0:101 1:0", "A:261443048;C:220215927;G:200185007;T:212270956;N:17054", 101, 0, null, null, 261443048, 220215927, 200185007, 212270956, 17054, "SRX10356646", "SRS8474602", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00021, null, 1e-05, null, 0.99953, null, 0.7027, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63671, "SRR13979084", "SRX10356645", "SRS8474601", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBBPA DBPE rep4", "GSM5174024", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE", "miRNA TBBPA DBPE rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf DBPE", "GSM5174024", "GSM5174024: miRNA TBBPA DBPE rep4; Danio rerio; miRNA Seq", "GSM5174024", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174024", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s040-indexRPI40-CTCAGA-68_S40_L001_R1_001.fastq.gz", "fastq", 567614950.0, 5619950.0, "GSM5174024 r1", "0:101 1:0", "A:171789620;C:142600627;G:115292068;T:137921194;N:11441", 101, 0, null, null, 171789620, 142600627, 115292068, 137921194, 11441, "SRX10356645", "SRS8474601", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00014, null, 0.0, null, 0.99965, null, 0.55555, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63672, "SRR13979083", "SRX10356644", "SRS8474600", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBBPA DBPE rep3", "GSM5174023", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE", "miRNA TBBPA DBPE rep3", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf DBPE", "GSM5174023", "GSM5174023: miRNA TBBPA DBPE rep3; Danio rerio; miRNA Seq", "GSM5174023", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174023", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s039-indexRPI39-CTATAC-67_S39_L001_R1_001.fastq.gz", "fastq", 883651020.0, 8749020.0, "GSM5174023 r1", "0:101 1:0", "A:267266527;C:221471697;G:172032269;T:222861646;N:18881", 101, 0, null, null, 267266527, 221471697, 172032269, 222861646, 18881, "SRX10356644", "SRS8474600", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00024, null, 1e-05, null, 0.99959, null, 0.65116, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63673, "SRR13979082", "SRX10356643", "SRS8474599", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBBPA DBPE rep2", "GSM5174022", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE", "miRNA TBBPA DBPE rep2", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf DBPE", "GSM5174022", "GSM5174022: miRNA TBBPA DBPE rep2; Danio rerio; miRNA Seq", "GSM5174022", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174022", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s038-indexRPI38-CTAGCT-66_S38_L001_R1_001.fastq.gz", "fastq", 311086666.0, 3080066.0, "GSM5174022 r1", "0:101 1:0", "A:90852851;C:77957592;G:63570096;T:78699630;N:6497", 101, 0, null, null, 90852851, 77957592, 63570096, 78699630, 6497, "SRX10356643", "SRS8474599", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00036, null, 1e-05, null, 0.99947, null, 0.6875, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63674, "SRR13979081", "SRX10356642", "SRS8474598", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA TBBPA DBPE rep1", "GSM5174021", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf DBPE", "miRNA TBBPA DBPE rep1", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf DBPE", "GSM5174021", "GSM5174021: miRNA TBBPA DBPE rep1; Danio rerio; miRNA Seq", "GSM5174021", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174021", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s037-indexRPI37-CGGAAT-65_S37_L001_R1_001.fastq.gz", "fastq", 1002314506.0, 9923906.0, "GSM5174021 r1", "0:101 1:0", "A:303735625;C:240217618;G:214324562;T:244016797;N:19904", 101, 0, null, null, 303735625, 240217618, 214324562, 244016797, 19904, "SRX10356642", "SRS8474598", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00024, null, 1e-05, null, 0.99953, null, 0.66666, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2021-03-16", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63675, "SRR13979080", "SRX10356641", "SRS8474597", "SRP310924", "PRJNA714931", "Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks", "GSE169013", "Transcriptome Analysis", "Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals FRCs  an ubiquitous group of chemicals in the environment Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 \u00b5L of RNAzol Molecular Research Center  Inc. and the tubes were immediately placed into a bullet blender Next Advance  using settings recommended by the manufacturer. The RNA was purified using the Direct zol MiniPrep kit Zymo Research  including an optional DNase 1 digestion treatment for 15 minutes. RNA integrity RIN was assessed using an Agilent Bioanalyzer Santa Clara  CA  and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing  mRNA was poly A selected  libraries were prepared with the PrepX\u2122 mRNA and Illumina sequencing workflow Wafergen Biosystems. For miRNA seq  the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing  an Illumina HiSeq 3000 sequencer Illumina  San Diego was used for mRNA and small RNA single end sequencing at 100 and 50 base pairs  respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2 .  RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 Kim et al.  2013 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome. For miR identification and quantification  a combination of miRDeep2 v2.0.0.8  miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package  edgeR; mRNAs with a log2 fold change =1.5 and Benjamini Hochberg BH adjusted p = 0.05 were considered differentially expressed while an adjusted p = 0.05 was applied to miRs without xxx fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package. Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs eg: osbpl2a and miRs eg  mir 125b 5p  showed differential expression common to multiple FRCs 10 and 7 respectively. These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions  including apoptosis  neurodevelopment  lipid regulation and inflammation. Commonly disrupted transcription factors TFs such as RXR  RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA TF and mRNA miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE 47. Conclusions: Our study is the first to establish a mRNA miR TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals. Overall design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from xxx ttwo xxx hpf", null, "pubmed:33898466", null, "miRNA IPP rep4", "GSM5174020", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA IPP rep4", "For mRNA seq  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For mRNA seq  the Bioconductor package  edgeR v3.26.0  was used to normalize gene counts and determine differential expression For miRNA  reads were evaluated by FastQC v0.11.3 to detect major sequencing problems  and then trimmed for quality control with Skewer v0.2.2  to remove ends of reads with low mean Phred quality score. RNA seq alignment and quantification proceeded with Bowtie2 v2.2.3 being used to build HISAT2 genome index files from the Genome Reference Consortium Zebrafish Build 10 GRCz10 genome For miRNA  the Bioconductor package  edgeR v3.26.0  was used to normalize miRNA gene counts and determine expression Genome build: GRz10 for mRNA Supplementary files format and content: DGE rlog TMM normalized counts FRC mRNA.tab is a tab delimited text files include TMM normalized values for each Sample Supplementary files format and content: Combined HTSeq count table FRC mRNA.tab is a tab delimited text files contain raw gene counts for every gene and every sample Supplementary files format and content: DGE rlog transformed counts FRC miRNA.tab is a tab delimited text file with transformed miRNA counts for each sample Supplementary files format and content: Count matrix FRC miRNA.tab is a tab delimited text file with miRNA counts for each sample", "zebrafish whole embryos", "Embryos were treated with EC80 or limit concentrations of FRCs from 6 hpf to 48 hpf.", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", null, "strain:5D|developmental stage:48 hpf", "GSM5174020", "GSM5174020: miRNA IPP rep4; Danio rerio; miRNA Seq", "GSM5174020", null, "1", "FRC exposed embryos were homogenzied in RNAzol 4 replicates per treatment and total RNA was extracted using the Direct zol MiniPrep kit. Total RNA was then processed for library preparation mRNA and small RNA libraries were prepared using the PrepX\u2122 mRNA and Illumina TruSeq Small RNA library kit respectively. Illumina HiSeq 3000  single end  100 bp for mRNA and 50 bp for small RNA", "GEO Accession:GSM5174020", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s032-indexRPI32-CACTCA-56_S32_L001_R1_001.fastq.gz", "fastq", 1129258881.0, 11180781.0, "GSM5174020 r1", "0:101 1:0", "A:335239774;C:296599595;G:223965990;T:273431685;N:21837", 101, 0, null, null, 335239774, 296599595, 223965990, 273431685, 21837, "SRX10356641", "SRS8474597", "SRA1207022", "GEO", "Robert L. 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