metadata: run_metadata: 12 rows where experiment.library_selection = "other", technology = "bulk" and tissue

12 rows where experiment.library_selection = "other", technology = "bulk" and tissue_curation = "Whole Organism"

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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
32033	32033	SRR28976522	SRX24505963	SRS21254128	SRP506702	PRJNA1109723	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267086	Other	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.		Zebrafish RIP seq Rbm24a Knock in IP	GSM8259538	source name:whole embryo\|tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:Rbm24a Knock in\|antibody:GFP\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq Rbm24a Knock in IP	Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample	whole embryo		Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:Rbm24a Knock in\|antibody:GFP	GSM8259538	GSM8259538: Zebrafish RIP seq Rbm24a Knock in IP; Danio rerio; RIP Seq	GSM8259538 r1	GSM8259538	1	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP506702	RIP_KI_IP_R2.fq.gz RIP_KI_IP_R1.fq.gz	fastq fastq	6457893104.0	21383752.0	GSM8259538 r1	0:151 1:151	A:975588225;C:2019180290;G:2469634919;T:992947702;N:541968	151	151	975588225	2019180290	2469634919	992947702	541968	SRX24505963	SRS21254128	SRA1863578	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university	2	0.90304	0.86018	0.20083	0.20471	0.96382	0.96743	0.96102	0.98876	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	China	2024-05-09	Cleavage	Embryo	Whole Organism	All anatomical structures
32034	32034	SRR28976523	SRX24505962	SRS21254127	SRP506702	PRJNA1109723	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267086	Other	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.		Zebrafish RIP seq wild type IP	GSM8259537	source name:whole embryo\|tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:wild type\|antibody:GFP\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq wild type IP	Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample	whole embryo		Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:wild type\|antibody:GFP	GSM8259537	GSM8259537: Zebrafish RIP seq wild type IP; Danio rerio; RIP Seq	GSM8259537 r1	GSM8259537	1	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP506702	RIP_WT_IP_R2.fq.gz RIP_WT_IP_R1.fq.gz	fastq fastq	4501412680.0	14905340.0	GSM8259537 r1	0:151 1:151	A:651609366;C:1285679784;G:1901211768;T:662533141;N:378621	151	151	651609366	1285679784	1901211768	662533141	378621	SRX24505962	SRS21254127	SRA1863578	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university	2	0.96426	0.81361	0.26579	0.2253	0.97784	0.97806	0.8699	0.93379	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	China	2024-05-09	Cleavage	Embryo	Whole Organism	All anatomical structures
32035	32035	SRR28976524	SRX24505961	SRS21254126	SRP506702	PRJNA1109723	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267086	Other	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.		Zebrafish RIP seq Rbm24a Knock in input	GSM8259536	source name:whole embryo\|tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:Rbm24a Knock in\|antibody:input\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq Rbm24a Knock in input	Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample	whole embryo		Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:Rbm24a Knock in\|antibody:input	GSM8259536	GSM8259536: Zebrafish RIP seq Rbm24a Knock in input; Danio rerio; RIP Seq	GSM8259536 r1	GSM8259536	1	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP506702	RIP_KI_Input_R2.fq.gz RIP_KI_Input_R1.fq.gz	fastq fastq	9539398726.0	31587413.0	GSM8259536 r1	0:151 1:151	A:2233069830;C:2078359171;G:3009942870;T:2217201959;N:824896	151	151	2233069830	2078359171	3009942870	2217201959	824896	SRX24505961	SRS21254126	SRA1863578	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university	2	0.90112	0.81448	0.02415	0.01993	0.79287	0.79807	0.47884	0.48186	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	China	2024-05-09	Cleavage	Embryo	Whole Organism	All anatomical structures
32036	32036	SRR28976525	SRX24505960	SRS21254125	SRP506702	PRJNA1109723	rbm24a is an organizer component of germ plasm to determine germ cell fate	GSE267086	Other	The formation of germ cells is a critical issue for the continuation of species. A large group of animals follow a preformation strategy to generate their primordial germ cells PGCs. They produce a set of localized maternal mRNAs and proteins to form phase separated germ plasm that functions as the PGC determinants but the mechanisms underlying the assembly of germ plasm is poorly understood. This study identifies Rbm24a as an enssential localized germ plasm protein component that controls the formation of large and functional germ plasm granules. Rbm24a is complexed with Buc and interacts with germ plasm mRNAs which determines the specific grasp of germ plasm mRNAs into the phase separated aggregates. Rbm24a absent granules fail to undergo kinesin dependent transport towards the cleavage furrows where small particles fuse into large ones. The loss of maternal rbm24a causes the complete degradation of germ plasm components and the disappearance of PGCs resulting in totally sterile animals. Our work establishes that Rbm24 is a critical nucleating organizer component of germ plasm highlighting an emerging common mechanism to read and recruit RNA component into phase separated condensates. Overall design: To elucidate the comprehensive RNA binding landscape of Rbm24a in zebrafish we employed RIP seq analysis on both rbm24a GFP knock in and wild type zebrafish.		Zebrafish RIP seq wild type input	GSM8259535	source name:whole embryo\|tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:wild type\|antibody:input\|geo loc name:missing\|collection date:missing	Zebrafish RIP seq wild type input	Each library was amplified by a 15 cycle PCR and 150 bp paired end sequencing was subjected to Illumina Nova seq 6000 to obtain the raw data. Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes raw counts for each Sample Supplementary files format and content: Bigwig file for each Sample	whole embryo		Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer’s instructions.	Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C	tissue:whole embryo\|developmental stage:4 cell stage\|cell type:embryonic cell\|genotype:wild type\|antibody:input	GSM8259535	GSM8259535: Zebrafish RIP seq wild type input; Danio rerio; RIP Seq	GSM8259535 r1	GSM8259535	1	Total RNAs were extracted from WT and Mrbm24a embryos at 4 cell sphere 24 hpf stage using TRIzol reagent Invitrogen and were precipitated by cold isopropanol 50% v/v in the presence of carrier glycogen 20 µg/each sample. 1 μg total RNA was used for following library preparation. The polyA mRNA isolation was performed using OligodT beads. The mRNA and RIP IP RNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second strand cDNA were synthesized. The purified double stranded cDNA was then treated to repair both ends and add a dA tailing in one reaction followed by a T A ligation to add adaptors to both ends. Size selection of Adaptor ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Nova seq 6000 instrument for sequencing using a 2x150 paired end PE configuration according to manufacturer's instructions.		RIP-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP506702	RIP_WT_Input_R2.fq.gz RIP_WT_Input_R1.fq.gz	fastq fastq	14180410302.0	46955001.0	GSM8259535 r1	0:151 1:151	A:3380011534;C:2883841476;G:4593876270;T:3321465622;N:1215400	151	151	3380011534	2883841476	4593876270	3321465622	1215400	SRX24505960	SRS21254125	SRA1863578	Ang Li, College of Life Sciences, shandong university	Ang Li, College of Life Sciences, shandong university	2	0.86497	0.64685	0.04432	0.02854	0.79324	0.8031	0.52927	0.53304	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	unknown	poly_a	unknown	bulk	bulk	bulk	China	2024-05-09	Cleavage	Embryo	Whole Organism	All anatomical structures
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

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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");;