|
| Status |
Public on May 18, 2021 |
| Title |
tgmel.67_WF_trametinib-20nM |
| Sample type |
SRA |
| |
|
| Source name |
whole fish
|
| Organism |
Oryzias latipes |
| Characteristics |
genotype: xmrk transgenic
age: 3-4 weeks old
length: 10mm
treatment: trametinib-20nM
|
| Treatment protocol |
Fish were placed in petri dish and were treated with vehicle control (saline, or DMSO), or Cisplatin/Trametinib for 5 days. An independent group of wild type and xmrk transgenic medaka that were not treated with vehicle or durg, but maintained under regular animal housing conditons were also inlcuded in the study.
|
| Growth protocol |
Fertilized medaka eggs were collected from fish tanks that are dedicated for matings, and were transferred to rearing solution. After hatching, fries were transferred to regulatr fish tank and were maintained following animal facility protocol
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fish samples were homogenized in TRI reagent followed by addition of 200 μl/ml chloroform and the samples vigorously shaken and subjected to centrifugation at 12,000 g for 15 min at 4 °C. Total RNA was furhter purified using RNeasy mini RNA isolation kit (Qiagen, Valencia, CA, USA). Residual DNA was eliminated by incubating RNA samples with DNase for DNA digestion at 25°C for 15 min.Totall RNA concentration was determined using a Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY, USA). RNA quality was verified on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) to confirm that RIN scores were above 8.0 prior to sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MS-67
|
| Data processing |
Adaptor sequences were first removed from raw sequencing files. Low quality section of sequencing reads, and low qulaity basecalls were further removed from raw sequencing files. All filtering steps were performed using a custom perl script.
Processed sequencing reads were mapped to medaka genome using Tophat2 (v.2.2.4)
FeatureCounts was used to qunatify sequencing reads that were mapped to gene models.
Genome_build: Ensembl release 92 oryzias latipes
Supplementary_files_format_and_content: comma seperated format/Sequncing read counts
|
| |
|
| Submission date |
May 08, 2018 |
| Last update date |
May 18, 2021 |
| Contact name |
Yuan Lu |
| Organization name |
Xiphophorus Genetic Stock Center
|
| Street address |
university drive
|
| City |
San Marcos |
| State/province |
TX |
| ZIP/Postal code |
78666 |
| Country |
USA |
| |
|
| Platform ID |
GPL17089 |
| Series (1) |
| GSE114190 |
Modulation of medaka transcriptome by trametinib and cisplatin |
|
| Relations |
| BioSample |
SAMN09093077 |
| SRA |
SRX4055489 |
