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| Status |
Public on Sep 28, 2016 |
| Title |
SM_day 9_27C_sample 4 [re-analysis] |
| Sample type |
SRA |
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| Source name |
SM_day 9_27C
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| Organism |
Cladocopium sp. C1 |
| Characteristics |
population source: South Molle Island, Great Barrier Reef
sample type: cell culture
medium: filtered sea water + IMK nutrient supplement
coral host from which it was isolated: Acropora tenuis
sampling time point: day 9
temperature treatment: 27C
incubator: incubator 2
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| Treatment protocol |
Two flasks per population were randomly assigned to each of four experimental incubators and acclimated at 27°C for two weeks. Transcriptomes were sampled on day -1 to confirm that there were no significant pre-experimental differentially expressed genes before heating. Two incubators were ramped on day 0 at 0.5°C/h to 32°C for the heat stress temperature treatment, while two incubators remained at 27°C. Transcriptomes were sampled on day 9 and day 13.
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| Growth protocol |
The thermal sensitive South Molle (SM) Symbiodinium population and thermal tolerant Magnetic Island (MI) Symbiodinium population were cultured in filtered seawater supplemented with Daigo IMK (Wako Pure Chemical Industries, Ltd.). For this study, 5x107 cells (1.5x106 cells/ml) of each population were added to eight replicate culture flasks per population. Light was provided at an intensity of 30 µmol quanta m-2 s-1 with a 12:12 h light:dark cycle.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Precisely after six hours of light exposure, 2-4 x 106 cells per population were immediately snap frozen in liquid nitrogen within 10 s of removal from experimental incubators and stored at -80°C. Snap frozen cells were thawed at room temperature and pelleted at 4°C (3,000 x g, 5 min). Media was removed, and pellets were lysed in buffer RLT (RNeasy plant mini kit, Qiagen) containing β-mercaptoethanol by bead beating with 0.3 g of 710-1,180 µm acid-washed glass beads (Sigma) using a TissueLyser II (Qiagen) for 90 s at 30 Hz. RNA was extracted and purified using the RNeasy plant mini kit (Qiagen) with an added on-column DNase I treatment (Qiagen).
Total RNA (150-500 ng) of each sample was sent to the Australian Genome Research Facility for confirmation of high quality RNA on an Agilent 2100 bioanalyzer, polyA-purification, Illumina TruSeq stranded library preparation, and sequencing on an Illumina HiSeq2500 (single end 100 bp, ~107 reads per sample)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
processed data files: day9_SM_RSEMmatrix_isoforms.min250_nr*matrix.txt
reanalysis of GSM1872160
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| Data processing |
Illumina Truseq (TruSeq3-SE) adapters were removed from sequence reads using Trimmomatic.
Prinseq was used to remove poly-A tails (min 6-A tail) and to filter short (min length 60 bases), low quality (min mean quality score 20, 4 base window, 1 base step), and low complexity sequences (dust method threshold 7).
Genome_build: RNA sequences from the 24 samples per population (four replicates, two temperature treatments, three time points) were combined for de novo assembly of the SM and MI transcriptomes using Trinity (version: 2.0.6).
Genome_build: SM_min250_nr.fasta;South Molle population de novo transcriptome, non redundant transcripts ≥ 250 bp
Genome_build: MI_min250_nr.fasta; Magnetic Island population de novo transcriptome, non redundant transcripts ≥ 250 bp
Genome_build: transcript annotation is provided in the *annotation_report.complete.5.xls
transcripts shorter than 250 bp were removed from the assembeled transcriptomes
redundant transcripts (similarity ≥ 99%) were removed from the assembled transcriptomes using cd-hit-est
Supplementary_files_format_and_content: tab-delimited text files include expression matrices for fpkm and counts of each sample at each time point
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| Submission date |
Feb 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rachel Levin |
| E-mail(s) |
[email protected]
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| Organization name |
University of New South Wales
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| Street address |
UNSW
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| City |
Sydney |
| State/province |
New South Wales |
| ZIP/Postal code |
2052 |
| Country |
Australia |
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| Platform ID |
GPL20890 |
| Series (1) |
| GSE77911 |
Evidence for a role of viruses in the thermal sensitivity of coral photosymbionts |
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| Relations |
| Reanalysis of |
GSM1872160 |
| SRA |
SRX1589625 |
| BioSample |
SAMN04504768 |
| 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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