|
| Status |
Public on Aug 20, 2017 |
| Title |
1h_25psu_26gen_Amill |
| Sample type |
SRA |
| |
|
| Source name |
adult coral
|
| Organism |
Acropora millepora |
| Characteristics |
Stage: adult coral
treatment: 25 PSU
time: 1h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using 3ml TRIzol Reagent for the coral adults and using RNAaqueous-Micro total RNA isolation kit (AMBION) for the juveniles.
Libraries were constructed using the NEB Next Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420S) following the manufacturers recommended protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file column: B3
|
| Data processing |
Reads were mapped onto the Acropora millepora genome using TopHat2 --read-mismatches 5 --read-gap-length 4 --read-edit-dist 6 --read-realign-edit-dist 5 --min-intron-length 30 --min-segment-intron 30 --library-type fr-firststrand --GTF --b2-very-sensitive
Counts were generated using htseq-count
Differentially gene expression analysis was done using DESeq2
gene annotations for the processed data files are located at: http://dna.anu.edu.au/~huaying/amil_v1.0/
|
| |
|
| Submission date |
Mar 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Catalina Aguilar |
| E-mail(s) |
catalina.aguilarhurtado@my.jcu.edu.au
|
| Organization name |
James Cook University
|
| Department |
Collegue of Public Health, Medical and Veterinary Sciences
|
| Lab |
Coral Genomics
|
| Street address |
1 James Cook Dr.
|
| City |
Townsville |
| State/province |
Queensland |
| ZIP/Postal code |
4811 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23215 |
| Series (1) |
| GSE96916 |
Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals |
|
| Relations |
| BioSample |
SAMN06639184 |
| SRA |
SRX2669907 |
