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| Status |
Public on May 03, 2016 |
| Title |
USA300 JE 2 |
| Sample type |
SRA |
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| Source name |
USA300_in vitro culture
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| Organism |
Staphylococcus aureus |
| Characteristics |
strain: USA300 JE2
tissue source: in vitro
replicate: 2
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| Growth protocol |
Staphylococcus aureus strains isolated from human samples were grown on Tryptic Soy agar (TSA), Trypticase soy broth supplemented with glucose (TSB + Glc) (0.25%, wt/vol), B2 medium (1% casein hydrolysate, 2.5% yeast extract, 2.5% NaCl, 0.1% K2HPO4, and 0.5% glucose [wt/vol]) with appropriate antibiotics wherever needed. Nasal swabs were plated on SASelect agar (BioRad) overnight at 37 ºC, and individual colonies were subcultured onto horse blood agar (Oxoid). Blood cultures used the BD Bactec system; media from the positive bottles was plated on horse blood agar, and colonies were picked from each bottle for sequencing. For RNA extraction, cultures of all samples listed above were prepared by picking 4 colonies from HBA to inocculate TSB and incubate overnight until stationary phase.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Protect Bacteria Kit (Qiagen) according to the manufacturer instructions (protocol 4). DNase I (DNAfree kit, Ambion) was used to remove remaining DNA. The concentration of the RNA was determined by spectrophotometry via fluorometry using the Qubit Fluorometer RNA BR Kit (Invitrogen). Quality and quantity of the RNA was examined by analysis on Tapestation (Agilent Technologies).
Sequencing libraries were constructed using the NEBNext Ultra Directional Library Preparation Kit for Illumina (#E7420 ,NEB)
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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 |
Illumina Casava v1.8 was used for basecalling.
Reads were adapter removed and trimmed to 70Bp using trimmomatic 0.32 with parameters ILLUMINACLIP:/Trimmomatic-0.32/adapters/TruSeq3-PE-2.fa:2:30:10 HEADCROP:15 CROP:70 SLIDINGWINDOW:6:5 MINLEN:70
Sequences were mapped to USA300_FPR3757 using bowtie2 v2.2.2 with parameters -N 0 --sensitive --fr -q --no-mixed --no-discordant --no-unal
Genome_build: Staphylococcus aureus subsp. aureus USA300_FPR3757, assembly GCA_000013465.1
Supplementary_files_format_and_content: tab-delimited text files include per gene read counts. Counts were calculated using htseq-count from the HT-Seq package v0.6.1 with parameters: -f bam -r pos -s reverse -a 10 -t gene -i Name -m union
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| Submission date |
Mar 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Julius Muller |
| E-mail(s) |
mail@jmuller.eu
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| Organization name |
The Jenner Institute, University of Oxford
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| Department |
Nuffield Department of Medicine
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| Lab |
Prof. Adrian Hill
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| Street address |
ORCRB, Roosevelt Drive
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| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7DQ |
| Country |
United Kingdom |
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| Platform ID |
GPL17452 |
| Series (1) |
| GSE67448 |
A master virulence regulator of S. aureus inactivated during carriage in man |
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| Relations |
| BioSample |
SAMN03452606 |
| SRA |
SRX974229 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1647143_htseq_count_287_Dbxref_rX.txt.gz |
12.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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