|
| Status |
Public on Apr 03, 2016 |
| Title |
control_48h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
coral larvae_control 48h
|
| Organism |
Acropora digitifera |
| Characteristics |
tissue: larvae
infection status: not infected
time point: 48h
|
| Treatment protocol |
Symbiodinium was inoculated and larvae were collected for RNA isolation 4, 12, 48 h post infection
|
| Growth protocol |
Coral larvae were reared in 0.2 uM FSW under ambient conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIZOL
libraries were prepared using TruSeq sample preparation kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data: 48_Negative_control_2/48H_matrix.TMM.fpkm.matrix; 48_Negative_control_2/48H_matrix.counts.matrix
|
| Data processing |
Reads were mapped using BOWTIE version 0.12.7
Transcripts abundance was estimated using RSEM version 1.1.17
Differential expression was performed using the r package edgeR comparining Symbiodinium-infected samples to control at 4, 12, and 48h timepoints
Genome_build: Adig_1.0; Acropora digitifera reference transcriptome assembly Shinzato et al 2011, PMID: 21785439; transcriptome assembly is available at: http://marinegenomics.oist.jp/coral/viewer?project_id=3
Supplementary_files_format_and_content: count matrix containing expression values (FPKM;Fragments Per Kilobase of transcript per Million) and raw count matrix
|
| |
|
| Submission date |
Jan 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Amin Roushdy Mohamed |
| E-mail(s) |
am_rd85@yahoo.com
|
| Organization name |
CSIRO
|
| Department |
Agriculture and Food
|
| Lab |
Aquaculture Genomics
|
| Street address |
306 Carmody Rd, University of Queensland
|
| City |
Brisbane |
| State/province |
Queensland |
| ZIP/Postal code |
4067 |
| Country |
Australia |
| |
|
| Platform ID |
GPL21348 |
| Series (1) |
| GSE76976 |
The transcriptomic response of the coral Acropora digitifera to a competent Symbiodinium strain: the symbiosome as an arrested early phagosome |
|
| Relations |
| BioSample |
SAMN04421950 |
| SRA |
SRX1534831 |
