{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Hatching\" and experiment.library_strategy = \"miRNA-Seq\"", "rows": [[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"], [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"], [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"], [40975, "SRR3498291", "SRX1756837", "SRS1433368", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 48hpf E2", "GSM2150816", null, "source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP", "NoEndo 48hpf E2", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:48hpf|tissue:Endothelial|stain:GFP", "GSM2150816", "GSM2150816: NoEndo 48hpf E2; Danio rerio; miRNA Seq", "GSM2150816", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150816", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "NoEndo_48hpf_E2.fastq.gz", "fastq", 553364740.0, 7281115.0, "GSM2150816 r1", "0:76", "A:129173344;C:134804122;G:141026546;T:148331467;N:29261", 76, null, null, null, 129173344, 134804122, 141026546, 148331467, 29261, "SRX1756837", "SRS1433368", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [40976, "SRR3498290", "SRX1756836", "SRS1433367", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 48hpf E1", "GSM2150815", null, "source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP", "NoEndo 48hpf E1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:48hpf|tissue:Endothelial|stain:GFP", "GSM2150815", "GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq", "GSM2150815", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150815", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "NoEndo_48hpf_E1.fastq.gz", "fastq", 1204752152.0, 15852002.0, "GSM2150815 r1", "0:76", "A:297517299;C:293969730;G:317491224;T:295696492;N:77407", 76, null, null, null, 297517299, 293969730, 317491224, 295696492, 77407, "SRX1756836", "SRS1433367", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [40981, "SRR3498285", "SRX1756831", "SRS1433362", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 48hpf E2", "GSM2150810", null, "source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP", "Endo 48hpf E2", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:48hpf|tissue:Endothelial|stain:GFP", "GSM2150810", "GSM2150810: Endo 48hpf E2; Danio rerio; miRNA Seq", "GSM2150810", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150810", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "Endo_48hpf_E2.fastq.gz", "fastq", 1254556624.0, 16507324.0, "GSM2150810 r1", "0:76", "A:316229540;C:323340793;G:307552357;T:307354555;N:79379", 76, null, null, null, 316229540, 323340793, 307552357, 307354555, 79379, "SRX1756831", "SRS1433362", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [40982, "SRR3498284", "SRX1756830", "SRS1433361", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 48hpf E1", "GSM2150809", null, "source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP", "Endo 48hpf E1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:48hpf|tissue:Endothelial|stain:GFP", "GSM2150809", "GSM2150809: Endo 48hpf E1; Danio rerio; miRNA Seq", "GSM2150809", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150809", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "Endo_48hpf_E1.fastq.gz", "fastq", 1449497080.0, 19072330.0, "GSM2150809 r1", "0:76", "A:362564557;C:370330864;G:364749441;T:351760774;N:91444", 76, null, null, null, 362564557, 370330864, 364749441, 351760774, 91444, "SRX1756830", "SRS1433361", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [41409, "SRR4423127", "SRX2245311", "SRS1745851", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 11 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:long pec stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: long pec stage48 hpf", "348 11", "348 11", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S11small.fastq", "fastq", 405003101.0, 5197273.0, "S11small.fastq", "0:77.93", "A:93494059;C:109265919;G:106696649;T:95546474;N:0", 77, null, null, null, 93494059, 109265919, 106696649, 95546474, 0, "SRX2245311", "SRS1745851", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.78244, null, 0.17047, null, 0.93379, null, 0.6272, null, 30, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [55539, "SRR10532695", "SRX7216660", "SRS5719128", "SRP233258", "PRJNA591815", "Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis", "PRJNA591815", "Other", "MicroRNAs are sequentially processed by two RNAse III enzymes  Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation  where it becomes the most abundant miRNA. However  the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.", null, null, null, null, "miR 144 mutant", null, "isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:miR 144 / |phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA from peripheral blood from 2 dpf zebrafish embryos  miR 451 mutant", "sRNA Mut miR 144", "sRNA Mut miR 144", "Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 /  embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/N*NCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/N*NAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "sRNA-miR-144.fastq.gz", "fastq", 284208421.0, 7813754.0, "sRNA miR 144.fastq.gz", "0:36.37", "A:63063755;C:66933795;G:92235682;T:61966771;N:8418", 36, null, null, null, 63063755, 66933795, 92235682, 61966771, 8418, "SRX7216660", "SRS5719128", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.02041, null, 0.00444, null, 0.98512, null, 0.44771, null, 28, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [55540, "SRR10532696", "SRX7216659", "SRS5719127", "SRP233258", "PRJNA591815", "Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis", "PRJNA591815", "Other", "MicroRNAs are sequentially processed by two RNAse III enzymes  Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation  where it becomes the most abundant miRNA. However  the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.", null, null, null, null, "wild type", null, "isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:wild type|phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Small RNA from peripheral blood from 2 dpf zebrafish embryos  wild type", "sRNA WT", "sRNA WT", "Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 /  embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/N*NCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/N*NAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP233258", null, null, "sRNA-WT.fastq.gz", "fastq", 294275059.0, 8550051.0, "sRNA WT.fastq.gz", "0:34.42", "A:65237071;C:85092331;G:80441993;T:63494506;N:9158", 34, null, null, null, 65237071, 85092331, 80441993, 63494506, 9158, "SRX7216659", "SRS5719127", "SRA1002853", "University of East Anglia|Biological Sciences", "University of East Anglia", 1, 0.00854, null, 0.00213, null, 0.99184, null, 0.55467, null, 31, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-11-26", "Hatching", "Embryo", "Blood", "Hematopoietic System"], [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. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00013, null, 0.0, null, 0.99959, 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"], [63676, "SRR13979079", "SRX10356640", "SRS8474596", "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 rep3", "GSM5174019", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA IPP 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", "GSM5174019", "GSM5174019: miRNA IPP rep3; Danio rerio; miRNA Seq", "GSM5174019", 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:GSM5174019", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s031-indexRPI31-CACGAT-55_S31_L001_R1_001.fastq.gz", "fastq", 1364695941.0, 13511841.0, "GSM5174019 r1", "0:101 1:0", "A:408343873;C:341704999;G:281119661;T:333499060;N:28348", 101, 0, null, null, 408343873, 341704999, 281119661, 333499060, 28348, "SRX10356640", "SRS8474596", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00016, null, 0.0, null, 0.99961, null, 0.68965, 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"], [63677, "SRR13979078", "SRX10356639", "SRS8474595", "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 rep2", "GSM5174018", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA IPP 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", "GSM5174018", "GSM5174018: miRNA IPP rep2; Danio rerio; miRNA Seq", "GSM5174018", 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:GSM5174018", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s030-indexRPI30-CACCGG-54_S30_L001_R1_001.fastq.gz", "fastq", 1118435923.0, 11073623.0, "GSM5174018 r1", "0:101 1:0", "A:322914077;C:292720303;G:241919484;T:260855307;N:26752", 101, 0, null, null, 322914077, 292720303, 241919484, 260855307, 26752, "SRX10356639", "SRS8474595", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.0002, null, 1e-05, null, 0.99959, null, 0.74285, 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"], [63678, "SRR13979077", "SRX10356638", "SRS8474594", "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 rep1", "GSM5174017", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA IPP 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", "GSM5174017", "GSM5174017: miRNA IPP rep1; Danio rerio; miRNA Seq", "GSM5174017", 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:GSM5174017", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s029-indexRPI29-CAACTA-53_S29_L001_R1_001.fastq.gz", "fastq", 965915217.0, 9563517.0, "GSM5174017 r1", "0:101 1:0", "A:298517953;C:241792467;G:190277966;T:235308237;N:18594", 101, 0, null, null, 298517953, 241792467, 190277966, 235308237, 18594, "SRX10356638", "SRS8474594", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00011, null, 0.0, null, 0.99973, 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"], [63679, "SRR13979076", "SRX10356637", "SRS8474593", "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 BDE 47 rep4", "GSM5174016", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA BDE 47 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", "GSM5174016", "GSM5174016: miRNA BDE 47 rep4; Danio rerio; miRNA Seq", "GSM5174016", 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:GSM5174016", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s020-indexRPI20-GTGGCC-44_S20_L001_R1_001.fastq.gz", "fastq", 990919989.0, 9811089.0, "GSM5174016 r1", "0:101 1:0", "A:281268229;C:247800394;G:221010761;T:240816791;N:23814", 101, 0, null, null, 281268229, 247800394, 221010761, 240816791, 23814, "SRX10356637", "SRS8474593", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00016, null, 0.0, null, 0.99965, null, 0.7, 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"], [63680, "SRR13979075", "SRX10356636", "SRS8474592", "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 BDE 47 rep3", "GSM5174015", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA BDE 47 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", "GSM5174015", "GSM5174015: miRNA BDE 47 rep3; Danio rerio; miRNA Seq", "GSM5174015", 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:GSM5174015", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s019-indexRPI19-GTGAAA-43_S19_L001_R1_001.fastq.gz", "fastq", 936520278.0, 9272478.0, "GSM5174015 r1", "0:101 1:0", "A:292610982;C:215924738;G:200657250;T:227310895;N:16413", 101, 0, null, null, 292610982, 215924738, 200657250, 227310895, 16413, "SRX10356636", "SRS8474592", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00017, null, 0.0, null, 0.99961, null, 0.6, 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"], [63681, "SRR13979074", "SRX10356635", "SRS8474591", "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 BDE 47 rep2", "GSM5174014", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA BDE 47 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", "GSM5174014", "GSM5174014: miRNA BDE 47 rep2; Danio rerio; miRNA Seq", "GSM5174014", 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:GSM5174014", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s018-indexRPI18-GTCCGC-42_S18_L001_R1_001.fastq.gz", "fastq", 923871038.0, 9147238.0, "GSM5174014 r1", "0:101 1:0", "A:261826604;C:240583077;G:197471686;T:223966265;N:23406", 101, 0, null, null, 261826604, 240583077, 197471686, 223966265, 23406, "SRX10356635", "SRS8474591", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00019, null, 0.0, null, 0.99963, null, 0.70588, 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"], [63682, "SRR13979073", "SRX10356634", "SRS8474588", "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 BDE 47 rep1", "GSM5174013", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA BDE 47 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", "GSM5174013", "GSM5174013: miRNA BDE 47 rep1; Danio rerio; miRNA Seq", "GSM5174013", 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:GSM5174013", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s017-indexRPI17-GTAGAG-41_S17_L001_R1_001.fastq.gz", "fastq", 963214780.0, 9536780.0, "GSM5174013 r1", "0:101 1:0", "A:290268878;C:222146596;G:216903245;T:233878186;N:17875", 101, 0, null, null, 290268878, 222146596, 216903245, 233878186, 17875, "SRX10356634", "SRS8474588", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00013, null, 0.0, null, 0.99971, null, 0.58333, 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"], [63683, "SRR13979072", "SRX10356633", "SRS8474589", "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 Control rep4", "GSM5174012", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA Control 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", "GSM5174012", "GSM5174012: miRNA Control rep4; Danio rerio; miRNA Seq", "GSM5174012", 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:GSM5174012", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s004-indexRPI4-TGACCA-4_S4_L001_R1_001.fastq.gz", "fastq", 776677274.0, 7689874.0, "GSM5174012 r1", "0:101 1:0", "A:233505881;C:196049592;G:158864473;T:188241779;N:15549", 101, 0, null, null, 233505881, 196049592, 158864473, 188241779, 15549, "SRX10356633", "SRS8474589", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00024, null, 0.0, null, 0.99949, null, 0.76086, 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"], [63684, "SRR13979071", "SRX10356632", "SRS8474590", "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 Control rep3", "GSM5174011", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA Control 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", "GSM5174011", "GSM5174011: miRNA Control rep3; Danio rerio; miRNA Seq", "GSM5174011", 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:GSM5174011", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s003-indexRPI3-TTAGGC-3_S3_L001_R1_001.fastq.gz", "fastq", 489457615.0, 4846115.0, "GSM5174011 r1", "0:101 1:0", "A:141598763;C:118796680;G:105152559;T:123899061;N:10552", 101, 0, null, null, 141598763, 118796680, 105152559, 123899061, 10552, "SRX10356632", "SRS8474590", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00037, null, 0.0, null, 0.99947, 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"], [63685, "SRR13979070", "SRX10356631", "SRS8474586", "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 Control rep2", "GSM5174010", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA Control 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", "GSM5174010", "GSM5174010: miRNA Control rep2; Danio rerio; miRNA Seq", "GSM5174010", 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:GSM5174010", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s002-indexRPI2-CGATGT-2_S2_L001_R1_001.fastq.gz", "fastq", 777242066.0, 7695466.0, "GSM5174010 r1", "0:101 1:0", "A:226389551;C:187485077;G:166405949;T:196945091;N:16398", 101, 0, null, null, 226389551, 187485077, 166405949, 196945091, 16398, "SRX10356631", "SRS8474586", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00026, null, 0.0, null, 0.99957, null, 0.62, 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"], [63686, "SRR13979069", "SRX10356630", "SRS8474585", "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 Control rep1", "GSM5174009", null, "tissue:zebrafish whole embryos|strain:5D|developmental stage:48 hpf", "miRNA Control 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", "GSM5174009", "GSM5174009: miRNA Control rep1; Danio rerio; miRNA Seq", "GSM5174009", 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:GSM5174009", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP310924", null, null, "miRNA_lane1-s001-indexRPI1-ATCACG-1_S1_L001_R1_001.fastq.gz", "fastq", 370858163.0, 3671863.0, "GSM5174009 r1", "0:101 1:0", "A:112058381;C:93306905;G:75506546;T:89979021;N:7310", 101, 0, null, null, 112058381, 93306905, 75506546, 89979021, 7310, "SRX10356630", "SRS8474585", "SRA1207022", "GEO", "Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University", 1, 0.00033, null, 1e-05, null, 0.99949, null, 0.64516, 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"], [63802, "SRR14066779", "SRX10441277", "SRS8573405", "SRP312051", "PRJNA716861", "Zebrafish Bdnf CRISPR/CAS9 knock out", "PRJNA716861", "Other", "RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish", null, null, null, null, "SD 16", null, "strain:AB|isolate:MUT48 small4|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio Bdnf mutant", "Bdnf Libr16", "Bdnf Libr16", "Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312051", null, null, "MUT48_small4_R1_001.fastq.gz", "fastq", 1346335212.0, 17714937.0, "MUT48 small4 R1 001.fastq.gz", "0:76 1:0", "A:416374120;C:317460666;G:293419951;T:319049435;N:31040", 76, 0, null, null, 416374120, 317460666, 293419951, 319049435, 31040, "SRX10441277", "SRS8573405", "SRA1209895", "Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms", "Stazione Zoologica Anton Dohrn", 1, 0.00179, null, 0.00093, null, 0.99935, null, 0.5625, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Italy", "2021-03-25", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63803, "SRR14066776", "SRX10441276", "SRS8573404", "SRP312051", "PRJNA716861", "Zebrafish Bdnf CRISPR/CAS9 knock out", "PRJNA716861", "Other", "RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish", null, null, null, null, "SD 15", null, "strain:AB|isolate:MUT48 small3|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio Bdnf mutant", "Bdnf Libr15", "Bdnf Libr15", "Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312051", null, null, "MUT48_small3_R1_001.fastq.gz", "fastq", 1304806760.0, 17168510.0, "MUT48 small3 R1 001.fastq.gz", "0:76 1:0", "A:387991384;C:335175146;G:279195316;T:302418185;N:26729", 76, 0, null, null, 387991384, 335175146, 279195316, 302418185, 26729, "SRX10441276", "SRS8573404", "SRA1209895", "Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms", "Stazione Zoologica Anton Dohrn", 1, 0.00621, null, 0.00334, null, 0.99926, null, 0.64343, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Italy", "2021-03-25", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63804, "SRR14066777", "SRX10441275", "SRS8573403", "SRP312051", "PRJNA716861", "Zebrafish Bdnf CRISPR/CAS9 knock out", "PRJNA716861", "Other", "RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish", null, null, null, null, "SD 14", null, "strain:AB|isolate:WT48 small4|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio Bdnf mutant", "Bdnf Libr14", "Bdnf Libr14", "Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312051", null, null, "WT48_small4_R1_001.fastq.gz", "fastq", 1339796780.0, 17628905.0, "WT48 small4 R1 001.fastq.gz", "0:76 1:0", "A:416769744;C:315222509;G:273799428;T:333973227;N:31872", 76, 0, null, null, 416769744, 315222509, 273799428, 333973227, 31872, "SRX10441275", "SRS8573403", "SRA1209895", "Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms", "Stazione Zoologica Anton Dohrn", 1, 0.00503, null, 0.00127, null, 0.99888, null, 0.67632, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Italy", "2021-03-25", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [63805, "SRR14066778", "SRX10441274", "SRS8573402", "SRP312051", "PRJNA716861", "Zebrafish Bdnf CRISPR/CAS9 knock out", "PRJNA716861", "Other", "RNA seq of WT and Bdnf CRISPR/CAS9 KO of 24 hpf and 48 hpf zebrafish", null, null, null, null, "SD 13", null, "strain:AB|isolate:WT48 small3|age:48 hpf stage:Long pec|sex:pooled male and female|tissue:pool of 50 individuals|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNAseq of Danio rerio Bdnf mutant", "Bdnf Libr13", "Bdnf Libr13", "Indexed libraries were prepared from 1 g/ea purified RNA with TruSeq SmallRNA Sample Prep Kit Illumina and TruSeq Stranded Total RNA Library Prep Kit Illumina. Libraries were quantified using the Agilent 2100 Bioanalyzer and pooled such that each index tagged sample was present in equimolar amounts  with final concentration of the pooled samples of 2 nM. The pooled samples were subject to cluster generation and sequencing using an Illumina HiSeq 2500 System Illumina in a 1x50 single read SmallRNA and 2x100 paired end RNA Seq format at a final concentration of 10 pmol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP312051", null, null, "WT48_small3_R1_001.fastq.gz", "fastq", 1212286260.0, 15951135.0, "WT48 small3 R1 001.fastq.gz", "0:76 1:0", "A:374600889;C:299473187;G:252454435;T:285727773;N:29976", 76, 0, null, null, 374600889, 299473187, 252454435, 285727773, 29976, "SRX10441274", "SRS8573402", "SRA1209895", "Stazione Zoologica Anton Dohrn|Biology and Evolution of Marine Organisms", "Stazione Zoologica Anton Dohrn", 1, 0.01297, null, 0.00494, null, 0.99849, null, 0.661, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "bulk", "bulk", null, "Italy", "2021-03-25", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [72366, "SRR22805212", "SRX18764981", "SRS16199877", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "44", "BHbisPhenolF 10uM for ribosome profiling replicate 2", null, "strain:AB|isolate:44|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "BHbisPhenolF 10uM for ribosome profiling replicate 2", "44", "44", "44", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "BHPF_10uM_for_ribosome_profiling_replicate_2_R1.fastq.gz BHPF_10uM_for_ribosome_profiling_replicate_2_R2.fastq.gz", "fastq fastq", 14888679600.0, 49628932.0, "BHbisPhenolF 10uM for ribosome profiling replicate 2 R1.fastq.gz", "0:150 1:150", "A:2177600650;C:2419699560;G:8025893657;T:2265187698;N:298035", 150, 150, null, null, 2177600650, 2419699560, 8025893657, 2265187698, 298035, "SRX18764981", "SRS16199877", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.0, 0.64018, 0.0, 0.06137, 1.0, 0.83913, null, 0.80601, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [72367, "SRR22805213", "SRX18764980", "SRS16199875", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "43", "BHbisPhenolF 10uM for ribosome profiling replicate 1", null, "strain:AB|isolate:43|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "BHbisPhenolF 10uM for ribosome profiling replicate 1", "43", "43", "43", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "BHPF_10uM_for_ribosome_profiling_replicate_1_R1.fastq.gz BHPF_10uM_for_ribosome_profiling_replicate_1_R2.fastq.gz", "fastq fastq", 15098951400.0, 50329838.0, "BHbisPhenolF 10uM for ribosome profiling replicate 1 R1.fastq.gz", "0:150 1:150", "A:2096550012;C:2382609157;G:8321980233;T:2297312503;N:499495", 150, 150, null, null, 2096550012, 2382609157, 8321980233, 2297312503, 499495, "SRX18764980", "SRS16199875", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 4e-05, 0.62435, 0.0, 0.06076, 0.99993, 0.84279, 0.75, 0.77804, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [72368, "SRR22805214", "SRX18764979", "SRS16199876", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "42", "DMSO control for ribosome profiling replicate 2", null, "strain:AB|isolate:42|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMSO control for ribosome profiling replicate 2", "42", "42", "42", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "DMSO_control_for_ribosome_profiling_replicate_2_R1.fastq.gz DMSO_control_for_ribosome_profiling_replicate_2_R2.fastq.gz", "fastq fastq", 13980558600.0, 46601862.0, "DMSO control for ribosome profiling replicate 2 R1.fastq.gz", "0:150 1:150", "A:2002344572;C:2128464587;G:7737629750;T:2111846347;N:273344", 150, 150, null, null, 2002344572, 2128464587, 7737629750, 2111846347, 273344, "SRX18764979", "SRS16199876", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.0, 0.5747, 0.0, 0.04778, 1.0, 0.85411, null, 0.72362, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [72369, "SRR22805215", "SRX18764978", "SRS16199874", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "41", "DMSO control for ribosome profiling replicate 1", null, "strain:AB|isolate:41|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "DMSO control for ribosome profiling replicate 1", "41", "41", "41", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "DMSO_control_for_ribosome_profiling_replicate_1_R1.fastq.gz DMSO_control_for_ribosome_profiling_replicate_1_R2.fastq.gz", "fastq fastq", 15802088100.0, 52673627.0, "DMSO control for ribosome profiling replicate 1 R1.fastq.gz", "0:150 1:150", "A:2301580863;C:2488100262;G:8575515119;T:2436818717;N:73139", 150, 150, null, null, 2301580863, 2488100262, 8575515119, 2436818717, 73139, "SRX18764978", "SRS16199874", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.0, 0.59521, 0.0, 0.05092, 1.0, 0.84471, null, 0.75944, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [72375, "SRR22805221", "SRX18764972", "SRS16199868", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "36", "36.ythdf2 MO for ribosome profiling replicate 2", null, "strain:AB|isolate:36|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "36.ythdf2 MO for ribosome profiling replicate 2", "36", "36", "36", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "ythdf2_MO_for_ribosome_profiling_replicate_2_R1.fastq.gz ythdf2_MO_for_ribosome_profiling_replicate_2_R2.fastq.gz", "fastq fastq", 17815545600.0, 59385152.0, "ythdf2 MO for ribosome profiling replicate 2 R1.fastq.gz", "0:150 1:150", "A:2527267522;C:2803112888;G:9669305830;T:2815502488;N:356872", 150, 150, null, null, 2527267522, 2803112888, 9669305830, 2815502488, 356872, "SRX18764972", "SRS16199868", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.0, 0.6595, 0.0, 0.05763, 1.0, 0.82359, null, 0.76446, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [72376, "SRR22805222", "SRX18764971", "SRS16199867", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "35", "35.ythdf2 MO for ribosome profiling replicate 1", null, "strain:AB|isolate:35|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "35.ythdf2 MO for ribosome profiling replicate 1", "35", "35", "35", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "ythdf2_MO_for_ribosome_profiling_replicate_1_R1.fastq.gz ythdf2_MO_for_ribosome_profiling_replicate_1_R2.fastq.gz", "fastq fastq", 14133373800.0, 47111246.0, "ythdf2 MO for ribosome profiling replicate 1 R1.fastq.gz", "0:150 1:150", "A:2066299382;C:2279837250;G:7718113208;T:2069058663;N:65297", 150, 150, null, null, 2066299382, 2279837250, 7718113208, 2069058663, 65297, "SRX18764971", "SRS16199867", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.0, 0.68906, 0.0, 0.06024, 1.0, 0.81633, null, 0.76663, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [72377, "SRR22805223", "SRX18764970", "SRS16199866", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "34", "34.Control knockdown for ribosome profiling replicate 2", null, "strain:AB|isolate:34|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "34.Control knockdown for ribosome profiling replicate 2", "34", "34", "34", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "Control_knockdown_for_ribosome_profiling_replicate_2_R1.fastq.gz Control_knockdown_for_ribosome_profiling_replicate_2_R2.fastq.gz", "fastq fastq", 15570048000.0, 51900160.0, "Control knockdown for ribosome profiling replicate 2 R1.fastq.gz", "0:150 1:150", "A:2253659984;C:2507376043;G:8463755127;T:2344938646;N:318200", 150, 150, null, null, 2253659984, 2507376043, 8463755127, 2344938646, 318200, "SRX18764970", "SRS16199866", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.0, 0.57539, 0.0, 0.06254, 1.0, 0.86989, null, 0.80447, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [72378, "SRR22805224", "SRX18764969", "SRS16199865", "SRP413700", "PRJNA906294", "Danio rerio Raw sequence reads", "PRJNA906294", "Other", "Investigating BPA substitute BHbisPhenolF for zebrafish cardiac and vascular toxicity", null, null, null, "33", "33.Control knockdown for ribosome profiling replicate 1", null, "strain:AB|isolate:33|dev stage:48hpf|sex:not determined|tissue:whole embryos|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "33.Control knockdown for ribosome profiling replicate 1", "33", "33", "33", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP413700", null, null, "Control_knockdown_for_ribosome_profiling_replicate_1_R1.fastq.gz Control_knockdown_for_ribosome_profiling_replicate_1_R2.fastq.gz", "fastq fastq", 21657503400.0, 72191678.0, "Control knockdown for ribosome profiling replicate 1 R1.fastq.gz", "0:150 1:150", "A:3052615137;C:3123462026;G:12407511554;T:3073813355;N:101328", 150, 150, null, null, 3052615137, 3123462026, 12407511554, 3073813355, 101328, "SRX18764969", "SRS16199865", "SRA1560952", "Zhejiang University|Institute of Genetics", "Zhejiang University", 2, 0.0, 0.51073, 0.0, 0.05546, 1.0, 0.88162, null, 0.79972, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-12-19", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 69, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.library_strategy\" = :p1 order by rowid limit 101", "params": {"p0": "Hatching", "p1": "miRNA-Seq"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching", "selected": true}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "size fractionation", "label": "size fractionation", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&experiment.library_selection=size+fractionation", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "cDNA", "label": "cDNA", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 61, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 68, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&experiment.platform=ILLUMINA", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&experiment.platform=ION_TORRENT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Embryo", "label": "Embryo", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Hatching", "label": "Hatching", "count": 69, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=miRNA-Seq", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 63, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&tissue_curation_coarse=Cardiovascular+System", "selected": false}, {"value": "Hematopoietic System", "label": "Hematopoietic System", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&tissue_curation_coarse=Hematopoietic+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 56, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&tissue_curation=Whole+Organism", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Endothelium", "label": "Endothelium", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&tissue_curation=Endothelium", "selected": false}, {"value": "Blood", "label": "Blood", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&tissue_curation=Blood", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq", "results": [{"value": "bulk", "label": "bulk", "count": 48, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&technology=bulk", "selected": false}, {"value": "unknown", "label": "unknown", "count": 21, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&experiment.library_strategy=miRNA-Seq&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 131.6238599974895}