|
| Status |
Public on Feb 13, 2018 |
| Title |
Nsk3 |
| Sample type |
SRA |
| |
|
| Source name |
non-infected skin
|
| Organism |
Epinephelus coioides |
| Characteristics |
tissue: skin
|
| Treatment protocol |
E. coioides was local infected with C. irritans
|
| Growth protocol |
Infected and control E. coioides were bred in flow-through water system
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA from all samples was extracted using the RNAiso Plus Total RNA extraction reagent (TAKARA)
RNA-Seq library was constructed using the TruSeq™ RNA Sample Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The raw data (raw reads) generated from Illumina sequencing experiment was first quality-fultered to eliminate adaptor sequences, low-quality bases (Q < 20) and unpaired reads based on the FastX toolkit program
The quality-filtered reads were mapped back to C. irritans and Tetrahymena thermophila database to remove protozoa contamination using soft bowtie2
The trimmed final clean reads were de novo assembled into contigs using Trinity package with k-mer length of 25
The assembled contigs of all the samples were cleaned by removing redundancies and were further assembled as primary unigenes with CD-HIT software. The final clean reads were aligned to the primary unigenes using FNASe2. The primary unigenes with at least 10 mapped reads were considered reliable unigenes.
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample
|
| |
|
| Submission date |
Apr 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
yazhou hu |
| E-mail(s) |
949186029@qq.com
|
| Phone |
15625172297
|
| Organization name |
Sun Yat-sen University
|
| Street address |
xingang west road no. 135
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510275 |
| Country |
China |
| |
|
| Platform ID |
GPL22973 |
| Series (1) |
| GSE97397 |
Expression data from infected skin and non-infected skin of Epinephelus coioides infected with Cryptocaryon irritans (C. irritans) and normal skin of E. coioides |
|
| Relations |
| BioSample |
SAMN06684348 |
| SRA |
SRX2708541 |
