run_metadata: 36374
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
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| 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 |