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Sample GSM850201 Query DataSets for GSM850201
Status Public on Dec 02, 2014
Title mRNA from HBx+HCP transgenic line
Sample type SRA
 
Source name zebrafish liver
Organism Danio rerio
Characteristics phenotype: intrahepatic cholangiocarcinoma
strain: HBx+HCP transgenic
tissue: liver
Treatment protocol Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis
Growth protocol Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.
Extracted molecule total RNA
Extraction protocol The total RNA from liver tissue was extracted using a TRIzol Reagent kit (Invitrogen). For transcriptome sequencing, the poly(A) RNA from total RNA was isolated by using the Poly(A)PuristTM MAG Kit (Ambion). After 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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD System 3.0
 
Description HBx+HCP
Data processing HBx+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.
 
Submission date Dec 16, 2011
Last update date May 15, 2019
Contact name Wangta Liu
Organization name Institute of Cellular and Organismic Biology, Academia Sinica
Street address Academia Rd.
City Taipei
ZIP/Postal code 115
Country Taiwan
 
Platform ID GPL10658
Series (1)
GSE34493 A zebrafish model of intrahepatic cholangiocarcinoma by dual expression of hepatitis B virus X and hepatitis C virus core protein in liver
Relations
SRA SRX112005
BioSample SAMN00766282

Supplementary file Size Download File type/resource
GSM850201.txt.gz 1.7 Mb (ftp)(http) TXT
GSM850201_HBx+HCP.stats.txt.gz 32.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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