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Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. 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A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. 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The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 48h silver bulk", "GSM935122", null, "source name:Dre 48h silver bulk|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver bulk 0.6 1.6\u00b5m; 5 \u00b5g/L|barcode:GCGC", "Dre 48h silver bulk", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. 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The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 48h silver NP", "GSM935121", null, "source name:Dre 48h silver NP|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:silver nanoparticles 10nm; 5\u00b5g/L|barcode:GCTG", "Dre 48h silver NP", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 48h silver NP", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. 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The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 48h control", "GSM935120", null, "source name:Dre 48h control|strain:wild type WIK strain|tissue:whole embryos|developmental stage:48 hpf|treatment:control|barcode:GCTT", "Dre 48h control", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 48h control", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. 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Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. 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The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 24h silver ions", "GSM935119", null, "source name:Dre 24h silver ions|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver ions 0.25 \u00b5g/L of silver nitrate|barcode:GCTA", "Dre 24h silver ions", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 24h silver ions", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. 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Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. 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The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 24h silver bulk", "GSM935118", null, "source name:Dre 24h silver bulk|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver bulk 0.6 1.6\u00b5m; 5 \u00b5g/L|barcode:GCTC", "Dre 24h silver bulk", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 24h silver bulk", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver bulk 0.6 1.6\u00b5m; 5 \u00b5g/L|barcode:GCTC", "GSM935118", "GSM935118: Dre 24h silver bulk; Danio rerio; OTHER", "GSM935118 1", "GSM935118: Dre 24h silver bulk", "1", null, "GEO Accession:GSM935118", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_24h_bulk.gz", "fastq", 53296632.0, 1480462.0, "GSM935118 r1", "0:36", "A:8986044;C:17367907;G:13631579;T:13181001;N:130101", 36, null, null, null, 8986044, 17367907, 13631579, 13181001, 130101, "SRX148956", "SRS334485", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.078, null, 0.00708, null, 0.96877, null, 0.4609, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36379, "SRR499865", "SRX148955", "SRS334484", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 24h silver NP", "GSM935117", null, "source name:Dre 24h silver NP|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver nanoparticles 10nm; 5\u00b5g/L|barcode:GCAG", "Dre 24h silver NP", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 24h silver NP", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:silver nanoparticles 10nm; 5\u00b5g/L|barcode:GCAG", "GSM935117", "GSM935117: Dre 24h silver NP; Danio rerio; OTHER", "GSM935117 1", "GSM935117: Dre 24h silver NP", "1", null, "GEO Accession:GSM935117", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_24h_NP.gz", "fastq", 103827096.0, 2884086.0, "GSM935117 r1", "0:36", "A:22437552;C:29017806;G:28385826;T:23907583;N:78329", 36, null, null, null, 22437552, 29017806, 28385826, 23907583, 78329, "SRX148955", "SRS334484", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.16321, null, 0.01606, null, 0.94631, null, 0.45783, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36380, "SRR499864", "SRX148954", "SRS334483", "SRP013309", "PRJNA167302", "Transcriptomic profiles of zebrafish embryos exposed to silver nanoparticles  bulk and ions using HT SuperSAGE in a Illumina GA2 platform", "GSE38125", "Other", "Silver nanoparticles cause toxicity in exposed organisms and are an environmental health concern. The mechanisms of silver nanoparticle toxicity  however  remain unclear. We examined the effects of exposure to silver in nano   bulk  and ionic forms on zebrafish embryos Danio rerio using a Next Generation Sequencing approach in an Illumina platform High Throughput SuperSAGE. Significant alterations in gene expression were found for all treatments and many of the gene pathways affected  most notably those associated with oxidative phosphorylation and protein synthesis  overlapped strongly between the three treatments indicating similar mechanisms of toxicity for the three forms of silver studied. Changes in oxidative phosphorylation indicated a down regulation of this pathway at 24h of exposure  but with a recovery at 48h. This finding was consistent with a dose dependent decrease in oxygen consumption at 24h  but not at 48h  following exposure to silver ions. Overall  our data provide support for the hypothesis that the toxicity caused by silver nanoparticles is principally associated with bioavailable silver ions in exposed zebrafish embryos. These findings are important in the evaluation of the risk that silver particles may pose to exposed vertebrate organisms. Overall design: mRNA profiles of whole zebrafish embryos at 24 hpf and 48 hpf exposed to silver in nano  bulk and ionic forms were generated by deep sequencing using HT SuperSAGE Illumina GA2.", null, "pubmed:23758687", null, "Dre 24h control", "GSM935116", null, "source name:Dre 24h control|strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:control|barcode:GCAT", "Dre 24h control", "FASTQ/A Barcode splitter from the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/download.html was used to separate the samples from each lane using the 4 base barcode. FASTQ to FASTA from the FASTX Toolkit was used to convert the fastq files to fasta files. FASTQ/A trimmer from the FASTX Toolkit was used to remove the barcodes the first 4 bases from the sequence. A Perl script was used to remove all bases post the last occurence of CATG NlaIII restriction site  used for sequence tag preparation in each of the sequences FASTX collapser was used to collapse the sequences and calculate the frequency of unique sequence tags unitags in each library Supplementary files format and content: tabulated text files include frequency of all unitags in the treatment library", "Dre 24h control", "Stock solutions for Ag NP  Ag Bulk and silver nitrate were made up in ultrapure water  and sonicated for 1 h to ensure dispersal of the particles. Exposures were conducted in glass chambers  at 28+/  1\u00b0C with a 12h light: dark photoperiod. Immediately prior to the start of the exposures  glass chambers received 400 mL of ISO water  prepared according to OECD guidelines for zebrafish embryo experiments http://www.oecd.org/  containing 5 \u00b5g/L of 10nm Ag NP  5  \u00b5g/L of Ag Bulk or 0.25  \u00b5g/L of silver nitrate. A control chamber was set up containing water alone.  Solutions were replaced every 12h during the exposure period  and dead embryos were removed at the times of replacement of the exposure water. At 24h and 48h  3 pools of 50 embryos were removed from each exposure tank  immediately frozen in liquid nitrogen and stored at  80\u00b0C for analysis of gene expression. The experiment was terminated at 48 hpf.", "High throughput HT SuperSAGE libraries were prepared as described in Matsumura et al 2010  PLoS ONE 58:e12010. Samples were multiplexed on each lane of the Illumina flow cell.", "Adult WIK zebrafish were kept in the aquarium facilites at the University of Exeter according to the protocols described in Paull et al.  2008 Aquat Toxicol. 872:115 26. Fish were allowed to breed naturally and eggs were collected in glass egg chambers  approximately 1 hpf. Eggs were then cleaned and unfertilised embryos were removed prior to the exposures.", "strain:wild type WIK strain|tissue:whole embryos|developmental stage:24 hpf|treatment:control|barcode:GCAT", "GSM935116", "GSM935116: Dre 24h control; Danio rerio; OTHER", "GSM935116 1", "GSM935116: Dre 24h control", "1", null, "GEO Accession:GSM935116", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013309", null, null, "Dre_24h_control.gz", "fastq", 85032468.0, 2362013.0, "GSM935116 r1", "0:36", "A:16524315;C:24822030;G:21632275;T:21837611;N:216237", 36, null, null, null, 16524315, 24822030, 21632275, 21837611, 216237, "SRX148954", "SRS334483", "SRA053074", "GEO", "van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter", 1, 0.13983, null, 0.01175, null, 0.95966, null, 0.52467, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "other", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2012-05-22", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [68502, "SRR18074848", "SRX14226378", "SRS12047703", "SRP358067", "PRJNA803151", "mRNA aging shapes the Cap2 methylome in mammalian mRNA", "GSE196043", "Other", "The mRNA cap structure is a major site of dynamic mRNA methylation.  mRNA caps exist in either the Cap1 or Cap2 form  depending on the presence of 2' O methylation on the first  or both the first and second transcribed nucleotide  respectively.  However  the identity of Cap2 containing mRNAs and the function of Cap2 are unclear.  Here we describe CLAM Cap Seq  a method for transcriptome wide mapping and quantification of Cap2.  We find that unlike other epitranscriptomic modifications  Cap2 can occur on all mRNAs.  Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol.  As a result  Cap2 is enriched on long lived mRNAs.  We find that large increases in the abundance of Cap1 leads to activation of RIG I  especially in conditions where RIG I expression is increased.  The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG I.  We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs.  Overall  these results reveal an immunostimulatory role for Cap1  and that Cap2 functions to reduce activation of the innate immune response. Overall design: We developed next generation sequencing methods for quantification of Cap2 methylation in bulk mRNA CapTag seq  as well as in individual mRNAs in a transcriptome wide manner CLAM Cap seq. Furthermore  we developed tools for measuring translation and stability of transcript start nucleotide TSN mRNA isoforms by combining polysome profiling and actinomycin D treatment with TSS seq transcription start site sequencing.", null, "pubmed:36725932", null, "Zebrafish CapQuant seq 2", "GSM5907184", null, "source name:48 hpf embryo|cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "Zebrafish CapQuant seq 2", "Removal of low quality reads and three prime end adapter trimming was performed with flexbar v2.5. Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2. Read trimming was performed using seqtk package v1.3. Read alignement to fly  mouse or human genome was conducted using Bowtie v1.2.3. five prime end read coverage was calculated per each genomic position using BEDTools v2.28.0. Genome build: Drosohila melanogaster; dm6  Mus musculus; mm10  Homo sapiens; hg38.", "48 hpf embryo", null, "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", "Zebrafish AB line embryos were maintained in E3 medium at 28 degrees and staged as previously described Kimmel et al.  Developmental Dynamics  1995.", "cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "GSM5907184", "GSM5907184: Zebrafish CapQuant seq 2; Danio rerio; OTHER", "GSM5907184 r1", "GSM5907184", "1", "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP358067", null, null, "Zebrafish_CQS2_R1.fastq.gz", "fastq", 658260009.0, 12907059.0, "GSM5907184 r1", "0:51 1:0", "A:158463141;C:142984303;G:213148834;T:143656235;N:7496", 51, 0, null, null, 158463141, 142984303, 213148834, 143656235, 7496, "SRX14226378", "SRS12047703", "SRA1545466", "Pharmacology, Weill Cornell Medicine", "Pharmacology, Weill Cornell Medicine", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-18", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [68503, "SRR18074849", "SRX14226377", "SRS12047702", "SRP358067", "PRJNA803151", "mRNA aging shapes the Cap2 methylome in mammalian mRNA", "GSE196043", "Other", "The mRNA cap structure is a major site of dynamic mRNA methylation.  mRNA caps exist in either the Cap1 or Cap2 form  depending on the presence of 2' O methylation on the first  or both the first and second transcribed nucleotide  respectively.  However  the identity of Cap2 containing mRNAs and the function of Cap2 are unclear.  Here we describe CLAM Cap Seq  a method for transcriptome wide mapping and quantification of Cap2.  We find that unlike other epitranscriptomic modifications  Cap2 can occur on all mRNAs.  Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol.  As a result  Cap2 is enriched on long lived mRNAs.  We find that large increases in the abundance of Cap1 leads to activation of RIG I  especially in conditions where RIG I expression is increased.  The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG I.  We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs.  Overall  these results reveal an immunostimulatory role for Cap1  and that Cap2 functions to reduce activation of the innate immune response. Overall design: We developed next generation sequencing methods for quantification of Cap2 methylation in bulk mRNA CapTag seq  as well as in individual mRNAs in a transcriptome wide manner CLAM Cap seq. Furthermore  we developed tools for measuring translation and stability of transcript start nucleotide TSN mRNA isoforms by combining polysome profiling and actinomycin D treatment with TSS seq transcription start site sequencing.", null, "pubmed:36725932", null, "Zebrafish CapQuant seq 1", "GSM5907183", null, "source name:48 hpf embryo|cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "Zebrafish CapQuant seq 1", "Removal of low quality reads and three prime end adapter trimming was performed with flexbar v2.5. Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2. Read trimming was performed using seqtk package v1.3. Read alignement to fly  mouse or human genome was conducted using Bowtie v1.2.3. five prime end read coverage was calculated per each genomic position using BEDTools v2.28.0. Genome build: Drosohila melanogaster; dm6  Mus musculus; mm10  Homo sapiens; hg38.", "48 hpf embryo", null, "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", "Zebrafish AB line embryos were maintained and staged as previously described Kimmel et al.  Developmental Dynamics  1995.", "cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "GSM5907183", "GSM5907183: Zebrafish CapQuant seq 1; Danio rerio; OTHER", "GSM5907183 r1", "GSM5907183", "1", "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP358067", null, null, "Zebrafish_CQS1_R1.fastq.gz", "fastq", 1636691694.0, 32091994.0, "GSM5907183 r1", "0:51 1:0", "A:394187895;C:355520591;G:529426272;T:357424863;N:132073", 51, 0, null, null, 394187895, 355520591, 529426272, 357424863, 132073, "SRX14226377", "SRS12047702", "SRA1545466", "Pharmacology, Weill Cornell Medicine", "Pharmacology, Weill Cornell Medicine", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-18", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 10, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", 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"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 \"experiment.library_layout\" = :p0 and \"experiment.library_selection\" = :p1 and \"technology\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "other", "p2": "bulk"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "OTHER", "label": "OTHER", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&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?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "other", "label": "other", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&technology=bulk", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&technology=bulk", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "Embryo", "label": "Embryo", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "Hatching", "label": "Hatching", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&devstage_curation=Hatching", "selected": false}, {"value": "Pharyngula", "label": "Pharyngula", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&devstage_curation=Pharyngula", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&tissue_curation_coarse=All+anatomical+structures", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&tissue_curation=Whole+Organism", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk&tissue_curation=Embryo+Imprecise", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other&technology=bulk", "results": [{"value": "bulk", "label": "bulk", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&experiment.library_selection=other", "selected": true}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 73.93364899326116}