|
| Status |
Public on Mar 31, 2012 |
| Title |
E. coli O157:H7 EDL933 in LB at 37oC for 7 hrs incubation with honey |
| Sample type |
RNA |
| |
|
| Source name |
rna extracted from e. coli o157: H7 EDL933 cells grown (7 hrs incubation) in LB at 37ºC with 0.5% honey
|
| Organism |
Escherichia coli |
| Characteristics |
agent: 0.5% honey
|
| Extracted molecule |
total RNA |
| Extraction protocol |
E. coli O157:H7 EDL933 was inoculated in 250 ml of LB in 1000 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken with 10 g of glass wool at 100 rpm and 37°C for 7 hrs. Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C. RNA was isolated using Qiagen RNeasy mini Kit (Cat# 74104) with Qiagen RNase-free DNase I (Cat# 79254).
|
| Label |
biotin
|
| Label protocol |
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).
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| |
|
| Hybridization protocol |
Following affymetrix protocol.
Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA.
After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours.
After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).
|
| Scan protocol |
Following affymetrix protocol.
After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).
|
| Description |
RNA extracted from E. coli EDL933 cells grown on glass wool for 7 hrs in LB at 37ºC plus honey
|
| Data processing |
MAS 5.0 Expression Analysis Default Setting
|
| |
|
| Submission date |
Mar 26, 2011 |
| Last update date |
Mar 31, 2012 |
| Contact name |
Jintae Lee |
| E-mail(s) |
jtlee@ynu.ac.kr
|
| Phone |
82-53-810-2533
|
| Organization name |
Yeungnam University
|
| Department |
Chemical engineering
|
| Lab |
Biotechnology
|
| Street address |
214-1 Daedong
|
| City |
Gyeongsan-Si |
| State/province |
Gyeongsangbuk-Do |
| ZIP/Postal code |
712-749 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL3154 |
| Series (1) |
| GSE28193 |
Honeys Inhibit Virulence and Biofilm Formation in Enterohaemorrhagic Escherichia coli O157:H7, but Do not Harm Commensal Escherichia coli K-12 Biofilm |
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