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Status |
Public on Mar 01, 2024 |
Title |
Coral, col_L, temp_AMB, sym_C, 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: C
|
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.
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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|
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.
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|
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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 |
SRX23655032 |
BioSample |
SAMN39981315 |