run_metadata: 36337
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36337 | SRR390720 | SRX112004 | SRS282725 | SRP009863 | PRJNA151317 | A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver | GSE34493 | Transcriptome Analysis | We sequenced mRNA from each transgenic zebrafish line including WT HBx HCP and HBx+HCP. Overall design: Examination of mRNA levels in individual line at three month of age. | mRNA from HCP transgenic line | GSM850200 | source name:zebrafish liver|phenotype:n1|strain:HCP transgenic|tissue:liver | mRNA from HCP transgenic line | HCP count.txt; genome build: Zv9 Counts: Sequence reads were obtained and mapped to the zebrafish Zv9 genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained. | zebrafish liver | Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis | The total RNA from liver tissue was extracted using a TRIzol Reagent kit Invitrogen. For transcriptome sequencing the polyA RNA from total RNA was isolated by using the PolyAPuristTM MAG Kit Ambion. post construction of whole transcriptome library and template beads preparation the sequencing run was performed by using SOLiD 3 System. Data analysis was performed with SOLiD Analysis Tool Pipeline. | Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C. | phenotype:n1|strain:HCP transgenic|tissue:liver | GSM850200 | GSM850200: mRNA from HCP transgenic line; Danio rerio; RNA Seq | GSM850200 1 | GSM850200: mRNA from HCP transgenic line | 1 | GEO Accession:GSM850200 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ABI_SOLID | AB SOLiD System 3.0 | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</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> | SRP009863 | HCP.qual HCP.csfasta | SOLiD_native SOLiD_native | 4104044600.0 | 82080892.0 | GSM850200 r1 | 0:50 | 0:944238890;1:1172273582;2:1207771613;3:775967445;.:3793070 | 50 | SRX112004 | SRS282725 | SRA048698 | GEO | Institute of Cellular and Organismic Biology, Academia Sinica | 1 | 0.70132 | 0.05286 | 0.94422 | 0.26785 | 50 | B | usable mapping rate | legacy | early | full_length | random_priming | unknown | bulk | unknown | unknown | Taiwan | 2011-12-16 | Undetermined | Adult | Liver | Liver and Biliary System |