|
| Status |
Public on Nov 16, 2018 |
| Title |
11_13_16_5% |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Trachemys scripta elegans |
| Characteristics |
tissue: liver
age: two years
practical salinity units: 5%
|
| Growth protocol |
nine healthy T. s. elegans (BW: 424-478g, 2 years old) were divided into 3 groups in pools (190 cm × 65 cm × 32 cm) of differing salinity: one in freshwater serving as the control (0 practical salinity units, psu), and the other two challenged with 5 ‰ (5 psu) or 15 ‰ (15 psu) saltwater. Turtles were fed a commercial diet each Monday and Thursday and 24 h after feeding, unused feed was siphoned out followed by replacement of one-third of the water in each tank volume. Water salinity was measured every day and then adjusted to the proper salinity as needed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA from liver samples used TRIzol® Reagent, following manufacturer’s instructions. Total RNA purity and concentration were determined using a NanoDrop 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then use Trinity(version:trinityrnaseq_r20140413) software for de novo assembly.
The clean reads obtained by sequencing are mapped to the assembled transcriptome by using the software Bowtie.
RSEM uses bowtie's alignment results to perform expression statistics. Get the number of read counts that per sample compared to each gene, and then FPKM conversion is performed to obtain the gene expression level.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Jul 19, 2018 |
| Last update date |
Nov 16, 2018 |
| Contact name |
Na Li |
| E-mail(s) |
990784506@qq.com
|
| Phone |
13178956260
|
| Organization name |
College of Life Science
|
| Department |
Hainan normal university
|
| Lab |
602
|
| Street address |
No. 99, longkun south road
|
| City |
HaiKou |
| State/province |
HaiNan |
| ZIP/Postal code |
570100 |
| Country |
China |
| |
|
| Platform ID |
GPL25350 |
| Series (1) |
| GSE117354 |
Transcriptomes and molecular pathway analysis of the liver in the red-eared slider turtle Trachemys scripta elegans under chronic salinity stress |
|
| Relations |
| BioSample |
SAMN09691330 |
| SRA |
SRX4408098 |
