|
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 |