metadata: run_metadata: 10 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and technology = "bulk"

10 rows where experiment.library_layout = "SINGLE", experiment.library_selection = "other" and technology = "bulk"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
36373	36373	SRR499871	SRX148961	SRS334490	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.	pubmed:23758687	Dre 48h silver ions	GSM935123	source name:Dre 48h silver ions\|strain:wild type WIK strain\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:silver ions 0.25 µg/L of silver nitrate\|barcode:GCGA	Dre 48h 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 48h 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°C 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 µg/L of 10nm Ag NP 5 µg/L of Ag Bulk or 0.25 µg/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°C 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:48 hpf\|treatment:silver ions 0.25 µg/L of silver nitrate\|barcode:GCGA	GSM935123	GSM935123: Dre 48h silver ions; Danio rerio; OTHER	GSM935123 1	GSM935123: Dre 48h silver ions	1		GEO Accession:GSM935123	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	Dre_48h_ag.gz	fastq	85514364.0	2375399.0	GSM935123 r1	0:36	A:18075876;C:24481350;G:23393114;T:19494907;N:69117	36		18075876	24481350	23393114	19494907	69117	SRX148961	SRS334490	SRA053074	GEO	van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter	1	0.11101	0.00946	0.96224	0.6991	36	B	usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	bulk	bulk	United Kingdom	2012-05-22	Hatching	Embryo	Whole Organism	All anatomical structures
36374	36374	SRR499870	SRX148960	SRS334489	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.	pubmed:23758687	Dre 48h silver bulk	GSM935122	source name:Dre 48h silver bulk\|strain:wild type WIK strain\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:silver bulk 0.6 1.6µm; 5 µg/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. 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 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°C 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 µg/L of 10nm Ag NP 5 µg/L of Ag Bulk or 0.25 µg/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°C 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:48 hpf\|treatment:silver bulk 0.6 1.6µm; 5 µg/L\|barcode:GCGC	GSM935122	GSM935122: Dre 48h silver bulk; Danio rerio; OTHER	GSM935122 1	GSM935122: Dre 48h silver bulk	1		GEO Accession:GSM935122	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	Dre_48h_bulk.gz	fastq	95750712.0	2659742.0	GSM935122 r1	0:36	A:17624901;C:29735122;G:26376026;T:21938121;N:76542	36		17624901	29735122	26376026	21938121	76542	SRX148960	SRS334489	SRA053074	GEO	van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter	1	0.18319	0.01693	0.94391	0.57004	36	B	usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	bulk	bulk	United Kingdom	2012-05-22	Hatching	Embryo	Whole Organism	All anatomical structures
36375	36375	SRR499869	SRX148959	SRS334488	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.	pubmed:23758687	Dre 48h silver NP	GSM935121	source name:Dre 48h silver NP\|strain:wild type WIK strain\|tissue:whole embryos\|developmental stage:48 hpf\|treatment:silver nanoparticles 10nm; 5µg/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°C 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 µg/L of 10nm Ag NP 5 µg/L of Ag Bulk or 0.25 µg/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°C 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:48 hpf\|treatment:silver nanoparticles 10nm; 5µg/L\|barcode:GCTG	GSM935121	GSM935121: Dre 48h silver NP; Danio rerio; OTHER	GSM935121 1	GSM935121: Dre 48h silver NP	1		GEO Accession:GSM935121	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	Dre_48h_NP.gz	fastq	52931304.0	1470314.0	GSM935121 r1	0:36	A:10003539;C:15279729;G:14487570;T:13116768;N:43698	36		10003539	15279729	14487570	13116768	43698	SRX148959	SRS334488	SRA053074	GEO	van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter	1	0.14206	0.01226	0.95477	0.58652	36	B	usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	bulk	bulk	United Kingdom	2012-05-22	Hatching	Embryo	Whole Organism	All anatomical structures
36376	36376	SRR499868	SRX148958	SRS334487	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.	pubmed:23758687	Dre 48h control	GSM935120	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°C 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 µg/L of 10nm Ag NP 5 µg/L of Ag Bulk or 0.25 µg/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°C 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:48 hpf\|treatment:control\|barcode:GCTT	GSM935120	GSM935120: Dre 48h control; Danio rerio; OTHER	GSM935120 1	GSM935120: Dre 48h control	1		GEO Accession:GSM935120	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	Dre_48h_control.gz	fastq	75389652.0	2094157.0	GSM935120 r1	0:36	A:13252992;C:21927091;G:18790968;T:21232585;N:186016	36		13252992	21927091	18790968	21232585	186016	SRX148958	SRS334487	SRA053074	GEO	van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter	1	0.12359	0.01182	0.95929	0.56028	36	B	usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	bulk	bulk	United Kingdom	2012-05-22	Hatching	Embryo	Whole Organism	All anatomical structures
36377	36377	SRR499867	SRX148957	SRS334486	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.	pubmed:23758687	Dre 24h silver ions	GSM935119	source name:Dre 24h silver ions\|strain:wild type WIK strain\|tissue:whole embryos\|developmental stage:24 hpf\|treatment:silver ions 0.25 µg/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°C 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 µg/L of 10nm Ag NP 5 µg/L of Ag Bulk or 0.25 µg/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°C 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 ions 0.25 µg/L of silver nitrate\|barcode:GCTA	GSM935119	GSM935119: Dre 24h silver ions; Danio rerio; OTHER	GSM935119 1	GSM935119: Dre 24h silver ions	1		GEO Accession:GSM935119	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	Dre_24h_ag.gz	fastq	57745404.0	1604039.0	GSM935119 r1	0:36	A:11280863;C:17795869;G:15444087;T:13175334;N:49251	36		11280863	17795869	15444087	13175334	49251	SRX148957	SRS334486	SRA053074	GEO	van Aerle Lab, Biosciences, College of Life and Environmental Sciences, University of Exeter	1	0.10143	0.00773	0.96435	0.60432	36	B	usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	bulk	bulk	United Kingdom	2012-05-22	Pharyngula	Embryo	Whole Organism	All anatomical structures
36378	36378	SRR499866	SRX148956	SRS334485	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.	pubmed:23758687	Dre 24h silver bulk	GSM935118	source name:Dre 24h silver bulk\|strain:wild type WIK strain\|tissue:whole embryos\|developmental stage:24 hpf\|treatment:silver bulk 0.6 1.6µm; 5 µg/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°C 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 µg/L of 10nm Ag NP 5 µg/L of Ag Bulk or 0.25 µg/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°C 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 1.6µm; 5 µg/L\|barcode:GCTC	GSM935118	GSM935118: Dre 24h silver bulk; Danio rerio; OTHER	GSM935118 1	GSM935118: Dre 24h silver bulk	1		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	Dre_24h_bulk.gz	fastq	53296632.0	1480462.0	GSM935118 r1	0:36	A:8986044;C:17367907;G:13631579;T:13181001;N:130101	36		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	0.00708	0.96877	0.4609	36	B	usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	bulk	bulk	United Kingdom	2012-05-22	Pharyngula	Embryo	Whole Organism	All anatomical structures
36379	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.	pubmed:23758687	Dre 24h silver NP	GSM935117	source name:Dre 24h silver NP\|strain:wild type WIK strain\|tissue:whole embryos\|developmental stage:24 hpf\|treatment:silver nanoparticles 10nm; 5µg/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°C 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 µg/L of 10nm Ag NP 5 µg/L of Ag Bulk or 0.25 µg/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°C 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; 5µg/L\|barcode:GCAG	GSM935117	GSM935117: Dre 24h silver NP; Danio rerio; OTHER	GSM935117 1	GSM935117: Dre 24h silver NP	1		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	Dre_24h_NP.gz	fastq	103827096.0	2884086.0	GSM935117 r1	0:36	A:22437552;C:29017806;G:28385826;T:23907583;N:78329	36		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	0.01606	0.94631	0.45783	36	B	usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	bulk	bulk	United Kingdom	2012-05-22	Pharyngula	Embryo	Whole Organism	All anatomical structures
36380	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.	pubmed:23758687	Dre 24h control	GSM935116	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°C 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 µg/L of 10nm Ag NP 5 µg/L of Ag Bulk or 0.25 µg/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°C 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		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	Dre_24h_control.gz	fastq	85032468.0	2362013.0	GSM935116 r1	0:36	A:16524315;C:24822030;G:21632275;T:21837611;N:216237	36		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	0.01175	0.95966	0.52467	36	B	usable mapping rate	illumina	early_illumina	unknown	other	unknown	bulk	bulk	bulk	United Kingdom	2012-05-22	Pharyngula	Embryo	Whole Organism	All anatomical structures
68502	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.	pubmed:36725932	Zebrafish CapQuant seq 2	GSM5907184	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		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.		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP358067	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	158463141	142984303	213148834	143656235	7496	SRX14226378	SRS12047703	SRA1545466	Pharmacology, Weill Cornell Medicine	Pharmacology, Weill Cornell Medicine	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	poly_a	unknown	bulk	bulk	bulk	United States	2022-02-18	Hatching	Embryo	Embryo Imprecise	All anatomical structures
68503	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.	pubmed:36725932	Zebrafish CapQuant seq 1	GSM5907183	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		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.		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP358067	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	394187895	355520591	529426272	357424863	132073	SRX14226377	SRS12047702	SRA1545466	Pharmacology, Weill Cornell Medicine	Pharmacology, Weill Cornell Medicine	1	0.0	0.0	1.0		51	T	under 1.2% mapping rate	illumina	hiseq_era	5prime	poly_a	unknown	bulk	bulk	bulk	United States	2022-02-18	Hatching	Embryo	Embryo Imprecise	All anatomical structures

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;