|
| Status |
Public on May 29, 2019 |
| Title |
GC11 WT_Female_2 |
| Sample type |
SRA |
| |
|
| Source name |
liver, DMSO
|
| Organism |
Danio rerio |
| Characteristics |
tissue: liver
developmental stage: adult
genotype: Wild-type
|
| Treatment protocol |
Zebrafish were raised until at 3 months post fertilization. Fish were then treated daily with DMSO or β-Estradiol for a period of 6 weeks.
|
| Growth protocol |
All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines (IACUC). At 3 months post fertilization, a selected group of wild-type male and female zebrafish were seperated into individual tanks to control food consumption.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol (Life Technologies), isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA-free kit (Life Technologies) and RNA quality and quantity were determined using Qubit (Thermo Fisher) and bioanalyzer (Agilent).
For library construction, NEBNext Directional RNA Library Prep Kit for Illumina (#E7420L) was used according to the company's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: danRer7
Supplementary_files_format_and_content: excel files include RPKM values for each Sample
|
| |
|
| Submission date |
Dec 19, 2016 |
| Last update date |
May 29, 2019 |
| Contact name |
Leonard Zon |
| E-mail(s) |
zon@enders.tch.harvard.edu
|
| Organization name |
Boston Children's Hospital
|
| Department |
Oncology/Hematology
|
| Street address |
1 Blackfan Circle
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (1) |
| GSE92544 |
Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer |
|
| Relations |
| BioSample |
SAMN06163331 |
| SRA |
SRX2435214 |
