run_metadata: 36371
This data as json
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| 36371 | SRR498195 | SRX148642 | SRS334220 | SRP013245 | PRJNA167126 | The zebrafish embryo as an alternative model for the evaluation of liver toxicity using histopathology and expression profiling | GSE38042 | Transcriptome Analysis | The zebrafish is as a powerful vertebrate model system for modeling human disease including liver pathology. In ZFE hepatic responses can be expected post exposure to hepatotoxicants because hepatocytes are present from 36 hpf and at 72 hpf the liver is fully functioning. These characteristics make the whole ZFE an attractive alternative model for compound induced hepatotoxicity screening. Therefore the main objective of this study is to further strengthen the applicability of whole ZFE as an alternative model for hepatotoxicity testing with a special focus on the ability to identify gene expression responses in whole ZFE that are suggestive of hepatotoxicity. Deep sequence technology is applied to assess whether hepatotoxicity specific transcripts that are identified in livers of hepatotoxicant treated adult zebrafish can be detected in whole ZFE as well. Overall design: Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. postwards the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled one sample consists of 15 embryos and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al 2009. and then equal amounts of every sample is pooled. The two pools one for the adult zebrafish liver the other for the whole zebrafish embryo are sequenced. | Adult zebrafish liver | GSM932886 | source name:Adult zebrafish liver|tissue:liver|developmental stage:adult|treatment:exposed for 48h t2 xxx known human hepatotoxicants including paraquat acetaminophen thioacetamide cyclosporine A 17a ethynylestradiol chlorpromazine amiodar1 tetracycline and valproic acid | Adult zebrafish liver | Illumina Genome Analyzer pipeline. Genome build: Ensemble Zv8 Release 59 August 2010. Supplementary files format and content: RPKM | Adult zebrafish liver | Zebrafish are exposed for 48h ttwo xxx known human hepatotoxicants including paraquat acetaminophen thioacetamide cyclosporine A 17a ethynylestradiol chlorpromazine amiodarone tetracycline and valproic acid. | Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. postwards the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled one sample consists of 15 embryos and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al 2009. and then equal amounts of every sample is pooled. The two pools one for the adult zebrafish liver the other for the whole zebrafish embryo are sequenced. | tissue:liver|developmental stage:adult|treatment:exposed for 48h t2 xxx known human hepatotoxicants including paraquat acetaminophen thioacetamide cyclosporine A 17a ethynylestradiol chlorpromazine amiodar1 tetracycline and valproic acid | GSM932886 | GSM932886: Adult zebrafish liver; Danio rerio; RNA Seq | GSM932886 2 | GSM932886: Adult zebrafish liver | 1 | GEO Accession:GSM932886 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina Genome Analyzer IIx | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>100</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>51</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP013245 | s_1_2_sequence-ZFPOOL.txt s_1_1_sequence-ZFPOOL.txt | fastq fastq | 928783500.0 | 9287835.0 | GSM932886 r1 | 0:50 1:50 | A:252619394;C:208590239;G:209788766;T:257119544;N:665557 | 50 | 50 | 252619394 | 208590239 | 209788766 | 257119544 | 665557 | SRX148642 | SRS334220 | SRA052989 | GEO | Laboratory for Health Protection Research, National Institute of Public Health and the Environment (RIVM) | 2 | 0.88557 | 0.88335 | 0.08801 | 0.0874 | 0.79131 | 0.79133 | 0.4709 | 0.47049 | 50 | 50 | B | B | biological fallback assumption | illumina | early_illumina | unknown | random_priming | unknown | bulk | unknown | unknown | Netherlands | 2012-05-17 | Adult | Adult | Liver | Liver and Biliary System |