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| Status |
Public on May 11, 2016 |
| Title |
A54Lib16 |
| Sample type |
SRA |
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| Source name |
yeast strain, 12-rep3-11
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: 11
time point: 12
single-mixed original culture: Single culture
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| Treatment protocol |
Samples were rapidly centrifuged to eliminate the must fractions and RNAlater (Ambion, Monza) was added and immediately frozen in liquid nitrogen. Samples were kept at -80ｰC until flow cytometry separation. Cells were sorted with a MoFlo (Dako cytomation, Glostrup, Denmark) cytometer, on the basis of labels according to fluorescence intensities of the populations. The cytometer was equipped with two lasers: 488nm (for GFP exitation) and 345 nm (for Sapphire exitation). For GFP and Sapphire FL7 570/20 and FL1 530/20 channels were respectively used. Separation was performed with a sorting rate up to 20000 events per second for the time necessary to reach between 500000 and 1000000 cells. Cells were collected in tubes containing PBS buffer and directly put in dry ice to flash freeze them at the exit of the cytometer. Frozen samples were kept at -80ｰC and thawed in ice for the subsequent RNA extraction
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| Growth protocol |
Single and mixed fermentations, including strain-dye swap, were performed in triplicate. Dominant and non-dominant strains were inoculated reaching the same cell density (0.1 OD) in 10 ml of Nebbiolo natural must (Fig. 1A). Fermentations were carried out at 25°C with continuous shaking. Samples of 1 ml were taken at 3 points of the fermentation. The first sample was taken at the beginning of the exponential growth phase, the second in the middle of the exponential growth phase and the last at the beginning of the stationary phase.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA Mini Kit (Qiagen, Madrid) was used following manufacturer’s instructions. RNA quality was checked using the Bioanalyser (Agilent Technologies Spain, Madrid) and samples with good quality RNA, showing 5 as minimum of RNA Integrity Number (RIN) were sequenced
Illumina RNA amplification kit (Thermo-Fisher) was used in order to amplify the low amount of RNA extracted from cells separated by cytometry. Sequencing was performed with the 5500 SOLiD system (Life Technologies, Madrid). Libraries were performed using standard SOLID protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500 Genetic Analyzer |
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| Data processing |
Sequencing was performed with the 5500 SOLiD system (Life Technologies, Madrid). Seventy-eight million reads per strain were obtained and short sequences (75bp) were assembled and aligned using a reference S. cerevisiae strain (Saccer2). Values of FPKM (Fragments Per Kilobase of exon per Million fragments mapped) were transformed for the statistical test as log2 (FPKM1/FPKM2) and uploaded on Cuffdiff (Cufflinks V1.3.0, http://cufflinks.cbcb.umd.edu/) where FPKM1 represents data of 12 strain and FPKM2 represent data of 11 strain. The FPKM parameter was used for pair end RNA-Seq experiments, where fragments were sequenced from both ends, providing two reads for each fragment. The Q value, representing significance value for statistical analysis performed through the use of cufflink platform was calculated and significant transcriptome differences were identified
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| Submission date |
May 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Roberto Pérez |
| E-mail(s) |
rober@iata.csic.es
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| Phone |
0034963900022
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| Organization name |
Centro Superior de Investigaciones Científicas
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| Street address |
Av Agustín Escardino 7
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| City |
Paterna |
| State/province |
Valencia |
| ZIP/Postal code |
46980 |
| Country |
Spain |
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| Platform ID |
GPL16234 |
| Series (1) |
| GSE81270 |
Transcriptome of two S. cerevisiae strain in competition in natural must |
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| Relations |
| BioSample |
SAMN04966331 |
| SRA |
SRX1753789 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2148006_A54Lib16.coverage.wig.tar.gz |
24.2 Mb |
(ftp)(http) |
TAR |
| GSM2148006_A54Lib16.exon.counts.gtf.gz |
135.3 Kb |
(ftp)(http) |
GTF |
| GSM2148006_A54Lib16.gene.counts.tab.gz |
132.2 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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