Experiment Detail
| Title | Illumina HiSeq 1000 paired end sequencing; Cymodocea nodosa response to simulated CO2-driven ocean acidification |
| Design Description | Cymodocea nodosa response to simulated CO2-driven ocean acidification |
| Organism | Cymodocea nodosa |
Library Description
| Name | T7R6_1 |
| Strategy | RNA-Seq |
| Source | TRANSCRIPTOMIC |
| Selection | cDNA |
| Layout | PAIRED |
| Orientation | |
| Nominal Length | 450 |
| Nominal Sdev | 100 |
| Construction Protocol | Prior to start the CO2 treatment plants were left to recover from transportation, and monitored for five days after transplantation (i.e. acclimated). At the end of the acclimation period (t0), C. nodosa was either kept under present day (400 ppm), or pCO2 elevated to 1,200 ppm, close to the IPCC business as usual scenario for 2100. In total, five tanks were set at 400 ppm whereas the other five were maintained at pCO2 of 1,200 ppm. Plant material for RNA extraction and subsequent transcriptome sequencing was sampled at t0, and after 12 days of exposure to current or elevated pCO2 (t1) from three of the five experimental tanks treatment. All samples were taken between 11 and 13 h to avoid circadian modulation of gene expression, rapidly cleaned of epiphytes and entirely submerged in RNAlater tissue collection (Ambion, life technologies), to inhibit RNA degradation. After let the solution penetrate throughout the tissue for one night at 4C, leaf samples were definitely stored at -20C until RNA extraction. Total RNA from youngest fully developed leaves of Cymodocea nodosa ramets, was extracted with AurumTM Total RNA Mini Kit (BIO-RAD) following manufacturers protocol. Qualified RNA samples were sent to Personal Genomics s.r.l. (Verona, Italy) for libraries preparation and sequencing. Nine cDNA libraries were constructed according to the Illumina TruSeq Stranded mRNA library protocol outlined in TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031047; Rev. E; October 2013), from 2.5 g total RNA. The libraries were subsequently size selected using the Pippin Prep automated gel electrophoresis system (Sage Science) for 350 to 550 bp. |
Platform
| Platform | ILLUMINA |
| Instrument Model | Illumina HiSeq 1000 |
Processing
| Base Calls | |
|---|---|
| Sequence Space | |
| Base Caller | |
Spot Information
| Number of Reads per Spots | 0 |
| Spot Length | 200 |
Read Spec
| Read Index 0 | |
|---|---|
| Read Label | |
| Read Class | Application Read |
| Read Type | Forward |
| Base Coord | 1 |
| Read Index 1 | |
| Read Label | |
| Read Class | Application Read |
| Read Type | Reverse |
| Base Coord | 101 |
Navigation
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Submission | ERA552200 |
 FTP
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Study | ERP013843 | ||
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Sample | ERS1031933 | ||
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Run | ERR1211092 |
FASTQ
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SRA
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