|
| Status |
Public on Mar 01, 2024 |
| Title |
Coral, col_L, temp_AMB, sym_SS1, rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
P. daedalea colonies
|
| Organism |
Platygyra daedalea |
| Characteristics |
cell type: P. daedalea colonies
temperature treatment: Ambient
coral genotype: Colony L
inoculation treatment: SS1
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using a RNEasy Plant Mini Kit (Qiagen). The purified total RNA was normalised to a concentration of 50 ng/µl.
Messenger RNA libraries were constructed using Illumina Stranded mRNA Prep kit with 500 ng of starting input.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Each sample was run on two NovaSeq 600 S4 lanes (L001 and L002)
|
| Data processing |
Quality of the raw sequences was verified using FastQC (version 0.12.0)
End-trimming of sequences was carried out using fastp (version 0.23.2)
Concatanation of reads from lanes 1 and 2 for each sample and read direction
Trimmed sequences were first mapped to a P. daedalea reference genome using STAR (version 2.7.10b). This provided the gene count matrix for the coral host reads (processed file: "gene_counts_matrix_pdae.txt")
Unassigned sequences were then mapped to a C. proliferum reference genome using STAR (version 2.7.10b). This provided the gene count matrix for the photosymbiont reads (processed file: "gene_counts_matrix_cpol.txt")
Assembly: P. daedalea reference genome retrieved from: http://pdae.reefgenomics.org/. C. proliferum reference genome retrived from: https://espace.library.uq.edu.au/view/UQ:fba3259
Supplementary files format and content: Tab-delimited raw exon counts. Each column corresponds to a sample. One file for coral host reads, the second for photosymbiont reads.
|
| |
|
| Submission date |
Feb 21, 2024 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Hugo Scharfenstein |
| E-mail(s) |
hugo.scharfenstein@gmail.com
|
| Organization name |
The University of Melbourne
|
| Street address |
Grattan Street
|
| City |
Parkville |
| State/province |
VIC |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL34218 |
| Series (1) |
| GSE256269 |
Differential transcriptomic responses to heat in wild-type and heat-evolved Symbiodiniaceae in corals |
|
| Relations |
| SRA |
SRX23655003 |
| BioSample |
SAMN39981324 |
