 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 22, 2020 |
| Title |
Klox_t11_bs |
| Sample type |
SRA |
| |
|
| Source name |
chronic wound
|
| Organism |
Klebsiella oxytoca |
| Characteristics |
condition: K. oxytoca + S. aureus t111 co-culture, stationary phase
origin: clinical isolate
collection date: Feb. 14, 2013
reference genome name: 571.31_Klebsiella_oxytoca
eference genome: JAAFYN000000000.1
|
| Treatment protocol |
Main cultures were started in water bath under constant shaking (80–85 rpm) at 37ºC in 120 mL pre-warmed RPMI medium. The monocultures were initiated with an OD600 of 0.05 while co-cultures were inoculated with an OD600 of 0.025 of each isolate to a total of 0.05. Samples were collected at mid-exponential phase (2-2.5 h, OD600 ±0.5) and at 90 min within the stationary growth phase (4-5 h, OD600 ±1.0). To mimic biofilm conditions, serial dilutions were performed with monocultures or mixed cultures of t111, t13595, Bt plus Ko, and these were plated onto RPMI agar and incubated at 37 ºC for 24 hr to form a homogeneous plate with coalescent individual colonies.
|
| Growth protocol |
Bacterial isolates were grown in RPMI liquid medium and RPMI agar
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Immediately after obtaining the cell pellet, 100 µl of killing buffer was added. Mechanical cell disruption was carried out with a Teflon vessel and a disruption ball filled with liquid N2 and pre-cooled in liquid N2 . The resulting cell powder was resuspended in 4 ml of lysis solution by repeated pipetting and transfer into 1 ml aliquots. Subsequently, one volume of acid phenol solution was added to cell lysate, and mixed on a tube shaker. Centrifugation and supernatant transfer into a new tube were followed by the addition of one volume acid phenol solution. This procedure was repeated twice; first by the addition of one volume chloroform/IAA and then by the addition of Na-Acetate and isopropanol for overnight precipitation. RNA extraction was carried out by centrifugation at 4°C, where the pellet was washed twice with 80% ethanol, dry at room temperature, and dissolved in nuclease-free water. DNase Digestion and RNA clean-up (Qiagen, Hilden, Germany) were performed following manufacturer’s protocol. RNA concentration was determined by Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, USA) and RNA quality assessment was carried out by Agilent 2100 Bioanalyzer.
cDNA libraries were constructed using the Ion Total RNA-Seq Kit v2 (Life Technologies, Carlsbad, CA) and the manufacturer’s recommended protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
liquid culture
Processed_data_rpkm_Klox.txt
Processed_data_rpkm_Klox.txt
|
| Data processing |
mapping of reads was done using: bowtie2 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: 1280.1984_Staphylococcus_aureus GenBank: JAAFYP000000000.1 42 rc DNA linear BCT 09-FEB-2020
Genome_build: 1428.155_Bacillus_thuringiensis Genbank: JAAFYT000000000.1
Genome_build: 571.31_Klebsiella_oxytoca GenBank: JAAFYN000000000.1 59 rc DNA linear BCT 09-FEB-2020
Genome_build: 1280.1985_Staphylococcus_aureus GenBank: JAAFYO000000000.1 37 rc DNA linear BCT 09-FEB-2020
Supplementary_files_format_and_content: Tab delimited text file
|
| |
|
| Submission date |
Feb 21, 2020 |
| Last update date |
Feb 22, 2020 |
| Contact name |
Anne de Jong |
| E-mail(s) |
anne.de.jong@rug.nl
|
| Phone |
+31 50 363 2047
|
| Organization name |
university of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL28183 |
| Series (1) |
| GSE145732 |
Pathogen-pathogen interactions, a way to soothe virulence? |
|
| Relations |
| BioSample |
SAMN14162220 |
| SRA |
SRX7779320 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4331696_Klox_4bs.rpkm.gz |
192.3 Kb |
(ftp)(http) |
RPKM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
