|
| Status |
Public on Feb 10, 2017 |
| Title |
CP_1mg_CuSO4_24h |
| Sample type |
SRA |
| |
|
| Source name |
Marine dinoflagellate cells
|
| Organism |
Margalefidinium polykrikoides |
| Characteristics |
strain: CP-01
treatment: the cells were treated with 1 mg CuSO4 and harvested at 24 h after expousre to CuSO4 (exponential stage of growth)
|
| Growth protocol |
C. polykrikoides cultures cultured in f/2 medium at 20°C under a 12:12-h light-dark cycle with a photon flux density of about 65 mol photons m-2 s-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
C. polykrikoides cultures were harvested using centrifugation at 1,000 g for 6 min, immediately frozen in liquid nitrogen, and stored at -80°C until RNA extraction. Preserved cells were physically broken by freeze-thawing in liquid nitrogen, and further homogenized with a mini-beadbeater (BioSpec Products Inc., Bartlesville, OK) with zirconium beads (0.1 mm diameter). Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA), and purified using Mini Spin Columns from RNeasy Mini Kits (Qiagen, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
The quality of raw reads was checked with FastQC_v0.10.0 . The raw data were cleaned and trimmed by removing adaptor and low quality reads, and then reads were assembled using Trinity software
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated by using RSEM (Li and Dewey, 2011)
Supplementary_files_format_and_content: excell file include FPKM values for each Sample .
|
| |
|
| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jang-Seu Ki |
| E-mail(s) |
kijs@smu.ac.kr
|
| Organization name |
Sangmyung University
|
| Department |
Department of Life Science, College of Natural Sciences
|
| Street address |
20, Hongimun 2-Gil, Jongno-gu
|
| City |
SEOUL |
| State/province |
SEOUL |
| ZIP/Postal code |
03016 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21180 |
| Series (1) |
| GSE75463 |
Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides (Cp) when exposed to the algicide copper sulfate |
|
| Relations |
| BioSample |
SAMN04299678 |
| SRA |
SRX1453664 |
