|
| Status |
Public on Jan 24, 2017 |
| Title |
Carcinoma |
| Sample type |
SRA |
| |
|
| Source name |
Hepatocellular carcinoma of transgenic fishes
|
| Organism |
Danio rerio |
| Characteristics |
tissue: Hepatocellular carcinoma
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: 21,749,743
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 |
SAMN06251151 |
| SRA |
SRX2511745 |
