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Sample GSM2136990 Query DataSets for GSM2136990
Status Public on Dec 01, 2016
Title S2052 exp C bio1
Sample type SRA
 
Source name Vibrio coralliilyticus
Organism Vibrio coralliilyticus
Characteristics strain: S2052
carbon source: Growth on chitin
growth phase: Exponential phase
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.
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)
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
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
 
Submission date Apr 28, 2016
Last update date May 15, 2019
Contact name Sonia Giubergia
Organization name Technical University of Denmark
Street address Matematiktorvet 301
City Kgs. Lyngby
ZIP/Postal code 2800
Country Denmark
 
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
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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