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Sample GSM1673540 Query DataSets for GSM1673540
Status Public on Jun 22, 2015
Title Streptococcus gordonii in Candida albicans media R1
Sample type SRA
 
Source name Streptococcus gordonii cells
Organism Streptococcus gordonii
Characteristics strain: Challis Substr. CH1
sample type: C. albicans in hypha inducing conditions for two hours, C. albicans cells removed, media added to S. gordonii cells for one hour
Growth protocol C. albicans wild-type strain SC5314 was grown aerobically for 16 h in YPD medium (2% yeast extract, 1% Bacto peptone, 2% glucose) at 37 degrees, with shaking at 220-rpm. Cells were then harvested by centrifugation (5000 x g for 5 min), washed twice in YPT medium (1 x Difco yeast nitrogen base, 20 mM phosphate buffer pH 7.1, 0.1% Bacto tryptone) by alternate centrifugation (5000 x g for 5 min) and suspension, and finally suspended at optical density 600 nm (OD600) = 1.0 (approximately 1 x 107 cells ml-1) in YPT medium. Aliquots (10 ml; 1 x 107 cells ml-1) were transferred into conical flasks containing YPT medium (90 ml) supplemented with 0.4% glucose (YPT-Glc). The cultures were then incubated at 37 degrees for 2 h with shaking at 50-rpm to induce hypha formation. S. gordonii cells were grown anaerobically for 16 h in 10 ml BHY medium (per litre: 37g Brain Heart infusion broth, 5 g yeast extract) and then harvested by centrifugation (5000 x g for 7 min). The bacterial cells were washed twice with YPT (no glucose) and finally suspended at OD600 = 0.5 (2 x 108 cells ml-1) in YPT-Glc medium.
Extracted molecule total RNA
Extraction protocol Cells were harvested by centrifugation, flash frozen and stored at -70 °C. RNA was extracted using a Qiagen RNeasy Mini Kit following the manufacturer's instructions for yeast using mechanical disruption. An on-column DNase digest using RNase-free DNase (Qiagen) was performed.
ERCC RNA Spike-In Control Mix (Ambion) was mixed with 2.5 µg RNA. Riobsomal RNA was depleted with RiboZero Magnetic Gold Kit (Epicentre) and Illumina sequencing libraries were prepared using ScriptSeq v2 (Epicentre).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description C. albicans in hypha inducing conditions for two hours, C. albicans cells removed, media added to S. gordonii cells for one hour
Data processing Base calling was carried out using CASAVA v1.8.2
Reads were filtered for quality and adapters removed using fastq-mcf with the parameters -q 20 -l 35 -p 15 -m 3
ERCC transcripts were removed by alignment to the ERCC reference using Bowtie v 1.0.0
Remaining reads were aligned to the C. albicans and S. gordonii reference genomes using Tophat v 2.0.8 with the following parameters: -G <gff> --library-type fr-secondstrand -l 10000 -r 50 --mate-std-dev 100 -p 8
Bedtools multicov was used to quantify the number of reads aligned at each annotated feature.
Differential expression comparisons were carried out using DESeq v.1.12.1 with default parameters.
Genome_build: Ca21_C_albicans_SC5314 genome
Genome_build: NC_009785 S gordonii CH1 genome
Supplementary_files_format_and_content: Tab delimited matrix containing the number of reads aligned to each feature in each sample.
 
Submission date May 01, 2015
Last update date May 15, 2019
Contact name Sophie Shaw
E-mail(s) s.shaw@abdn.ac.uk
Organization name University of Aberdeen
Department Centre for Genome Enabled Biology and Medicine
Street address 23 St. Machar Drive
City Aberdeen
State/province Aberdeen City
ZIP/Postal code AB24 3RY
Country United Kingdom
 
Platform ID GPL20134
Series (1)
GSE68477 Transcriptional landscape of transkingdom communication between Candida albicans and Streptococcus gordonii
Relations
BioSample SAMN03579679
SRA SRX1015921

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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