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Sample GSM2465776 Query DataSets for GSM2465776
Status Public on Jan 24, 2017
Title Norm
Sample type SRA
 
Source name Normal liver of transgenic fishes
Organism Danio rerio
Characteristics tissue: Normal liver
genotype: Tg(fabp10:LexPR-LexA:EGFP; cryB:mCherry-NLS-Cre; fabp10:loxP-mCherry-loxP-EGFP-krasV12) line
Treatment protocol One-month-old transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone-free water.
Extracted molecule total RNA
Extraction protocol mRNA was purified using Dynabeads Oligo(dT) EcoP (Invitrogen)
Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA-SAGE (serial analysis of gene expression) sequencing was performed on ABI SOLiD platform by Mission Biotech (Taiwan) according to manufacturer’s protocol and 10–23 million reads were generated from each sample
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD System 3.0
 
Description anchor: NlaIII
tag count: 25884343
tag length: 27
Data processing The SOLiD-generated RNA-Seq reads was in 27 bp length and an initial filtering process was taken to remove any non-desirable contamination sequences.
The reads were mapped to the zebrafish NCBI RefSeq (Reference Sequence) mRNA database with a criterion of maximum 2 nucleotide mismatches.
The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript.
Genome_build: danRer7
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
 
Submission date Jan 23, 2017
Last update date May 15, 2019
Contact name Ekaterina Matyunina
E-mail(s) ekmatyunina@gmail.com
Organization name The Biomedical Center
Street address Pudogsakya str 7
City Saint-Petersburg
ZIP/Postal code 197110
Country Russia
 
Platform ID GPL10658
Series (1)
GSE93965 Transcriptomic analyses of Kras induced zebrafish liver cancer
Relations
BioSample SAMN06251149
SRA SRX2511743

Supplementary file Size Download File type/resource
GSM2465776_M1_2_norm.txt.gz 114.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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