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Sample GSM2432115 Query DataSets for GSM2432115
Status Public on May 29, 2019
Title GC22 WT_Female_E2_1
Sample type SRA
 
Source name liver, β-Estradiol
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 SAMN06163322
SRA SRX2435219

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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