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Status |
Public on Dec 01, 2016 |
Title |
S2052 exp C bio1 |
Sample type |
SRA |
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Source name |
Vibrio coralliilyticus
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Organism |
Vibrio coralliilyticus |
Characteristics |
strain: S2052 carbon source: Growth on chitin growth phase: Exponential phase
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Treatment protocol |
At the harvesting time points, subsamples of the bacterial cultures were taken and mixed with 0.2 volumes of ice-cold STOP solution (95% [v/v] ethanol, 5% [v/v] phenol), incubated for 5 minutes on ice and pelleted by centrifugation. Cell pellets were stored at -80 degrees until RNA extraction.
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Growth protocol |
Strains were inoculated in 10 ml of ½ YTSS in a 50 ml Erlenmeyer flasks and grown aerated (200 rpm) at 25 degrees for 24 hours. 100 ul of the 24 hours cultures were used to inoculate 10 ml of fresh ½ YTSS, and these cultures were grown for 24 hours, 200 rpm at 25 degrees. 50 ml of the glucose containing medium (SSBG, 2% Sigma Sea Salts, 0.3% casamino acids, 40mM MOPS, 0.2% glucose) and of the chitin containing medium (SSBC, 2% Sigma Sea Salts, 0.3% casamino acids, 0.2% colloidal chitin) were inoculated at a cell density of approximately 10^3 CFU/ml. Cultures were run in 250 ml Erlenmeyer flasks, 200 rpm, 25 degrees. Samples for gene expression and bacterial counts were taken in the late exponential phase (cell density 10^8 CFU/ml) and in the stationary phase (24 hours old cultures, approx 10^9 CFU/ml)
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted using the RNeasy kit(Qiagen), following manufacturer's instructions. DNA was removed on column with the Rnase-free Dnase set (Qiagen). Integrity and quality of total RNA were assesses with a NanoDrop spectrometer and an Agilent 2100 Bioanalyzer. Total RNA samples were sent to the Beijing Genome Institute (BGI, Hong Kong), where rRNA was removed using the Ribo-Zero rRNA removal kit Library where constructed by BGI with the TruSeq RNA Library Preparation kit (Illumina) and 100 bp paired-enf sequenced on a HiSeq 2000
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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Data processing |
Data received from BGI were already sorted according to their respective adaptor sequences, and linker sequences had already been removed. RNA seq data was analyzed using the CLC genomics workbench software (CLC Aarhus, version 8.5). Quality and quantity of RNA sequence data was evaluated by the number of reads, GC%, PHRED-score, nucleotide contribution, quality distribution and enriched 5mers sequences. Reads were trimmed removing the first 15 nucleotides when nucleotide contribution was not normally distributes. Reads were then mapped to the reference genomes and expression values were calculated as RPKM. Gene expression profiles of biological samples were merged and, for each strain at each time point, the profiles deriving from the two media were compared. The quality of the transcriptomic data was evaluated using hierarchical clustering and principal component analysis. Statistically significant gene expression differences were assesses through a Baggerley's test using p-value<0.05 and q-values<0.05 Genome_build: V. coralliilyticus S2052 genome (JXXR01) Supplementary_files_format_and_content: xslx files including total gene reads, RPKM values etc. for each sample
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Submission date |
Apr 28, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Sonia Giubergia |
Organization name |
Technical University of Denmark
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Street address |
Matematiktorvet 301
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City |
Kgs. Lyngby |
ZIP/Postal code |
2800 |
Country |
Denmark |
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Platform ID |
GPL21793 |
Series (2) |
GSE80781 |
Influence of chitin on the transcriptome of Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753 (V. coralliilyticus) |
GSE80783 |
Influence of chitin on the transcriptome of Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753 |
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Relations |
BioSample |
SAMN04913758 |
SRA |
SRX1735930 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2136990_S2052_exp_C_bio1.xlsx |
277.3 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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