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| Status |
Public on Aug 26, 2022 |
| Title |
SD8 elevated temperature |
| Sample type |
SRA |
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| Source name |
pigmented tissue
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| Organism |
Sporolithon durum |
| Characteristics |
tissue: pigmented tissue
treatment: elevated temperature
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| Treatment protocol |
Fragments of CCA (20 per species) were divided across four treatments [“control” (unmanipulated seawater conditions, 27.2 ºC, 8.0 pH/450 µatm pCO2), “T” (elevated temperature and ambient pH, 29.5 ºC, 8.0 pH/450 µatm pCO2), “pH” (reduced pH and ambient temperature, 27.2 ºC, 7.7 pH/1000 µatm pCO2), or “T+pH” (elevated temperature and reduced pH, 29.5 ºC, 7.7 pH/1000 µatm pCO2)] with five biological replicates (n = 5) per treatment for a duration of three months.
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| Growth protocol |
Coralline algae were cultured for three months in flow through aquarium where temperature and pH were altered.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fragments of CCA were thoroughly cleaned prior to sampling for molecular analysis under a microscope and all epiphytes, as far as possible, were removed. CCA were rinsed with filtered seawater and RNAlater® and then blotted with a kimwipe to remove bacterial film. RNA was extracted following a modified TRIzol protocol.
cDNA synthesis, library preparation, and sequencing followed the single-cell sequencing (CEL-Seq2) protocol detailed in Hashimonshony et al. 2016
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
SD8_temp
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| Data processing |
Customised sequencing was performed on a single lane of an Illumina NovaSeq 6000, sequencing 26 bp on read 1, and 100 bp on read 2.
Raw sequence data were processed using Illumina BCL2FASTQ.
Quality control was performed with FastQC.
CEL-Seq-pipeline (https://github.com/yanailab/CEL-Seq-pipeline) for demultiplexing and mapping.
Assembly: Reference transcriptomes were created using transcriptomes for P. onkodes and S. durum (NCBI BioProject PRJNA518156, accession numbers GHIN00000000.1 and GHIO00000000.1 for S. cf. durum and P. cf. onkodes, respectively).
Supplementary files format and content: csv matrix of counts data for Porolithon onkodes
Supplementary files format and content: csv matrix of counts data for Sporolithon durum
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| Submission date |
Aug 23, 2022 |
| Last update date |
Aug 26, 2022 |
| Contact name |
Tessa M Page |
| E-mail(s) |
tessa.page@griffith.edu.au
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| Organization name |
Griffith University
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| Department |
Science and Environment
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| Street address |
170 Kessels Road
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| City |
Nathan |
| State/province |
QLD |
| ZIP/Postal code |
4111 |
| Country |
Australia |
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| Platform ID |
GPL32593 |
| Series (1) |
| GSE211882 |
Transcriptomic responses of coralline algae |
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| Relations |
| BioSample |
SAMN30467709 |
| SRA |
SRX17247071 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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