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Sample GSM1198177 Query DataSets for GSM1198177
Status Public on Jul 29, 2015
Title Escherichia coli O157:H7 EDL933, 0.005 mg/ml of Ginkgolic acid
Sample type RNA
 
Source name Escherichia coli O157:H7 EDL933
Organism Escherichia coli O157:H7 str. EDL933
Characteristics treatment: 0.005 mg/ml Ginkgolic acid
Treatment protocol Sample 2 was incubated with 0.005 mg/ml of Ginkgolic acid at 37oC for 8 hrs with 250 rpm shaking
Growth protocol E. coli was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 8 h with shaking at 250 rpm with and without ginkgolic acid (0.005 mg/ml)
Extracted molecule total RNA
Extraction protocol DNA microarray analysis with one biological replicate was performed with an Affymetrix system. E. coli was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 8 h with shaking at 250 rpm with and without 0.005 mg/ml of ginkgolic acid. Before sample collection, RNase inhibitor (RNAlater, Ambion, TX, USA) was added, and the cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 s before centrifugation at 16,000 g for 2 min. The cell pellets were immediately frozen with dry ice and stored at –80°C. Total RNA was isolated using a Qiagen RNeasy mini Kit (Valencia, CA, USA) 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).
 
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 Gene expression data of E. coli O157:H7 incubated with 0.005 mg/ml of Ginkgolic acid for 8 hrs at 37oC with 250 rpm shaking
Data processing The data were analyzed with Robust Multi-array Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.5 (Agilent technologies, CA). Fold change filters included the requirement that the genes be present in at least 150% of controls for up-regulated genes and lower than 66% of controls for down-regulated genes. Hierarchical clustering data were clustered groups that behave similarly across experiments using GeneSpring GX 12.5 (Agilent technologies, CA). Clustering algorithm was Euclidean distance, average linkage.
 
Submission date Jul 30, 2013
Last update date Jul 29, 2015
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)
GSE49367 Ginkgolic acids and Ginko biloba extract inhibit Escherichia coli O157:H7 biofilm formation

Data table header descriptions
ID_REF
VALUE Quantification

Data table
ID_REF VALUE
AFFX-BioB-5_at 1.09989
AFFX-BioB-M_at 1.01492
AFFX-BioB-3_at 1.24122
AFFX-BioC-5_at 1.18724
AFFX-BioC-3_at 0.955231
AFFX-BioDn-5_at 0.894896
AFFX-BioDn-3_at 0.972802
AFFX-CreX-5_at 0.918652
AFFX-CreX-3_at 0.660991
AFFX-DapX-5_at 7.96313
AFFX-DapX-M_at 8.68329
AFFX-DapX-3_at 7.77297
AFFX-LysX-5_at 2.9842
AFFX-LysX-M_at 3.42973
AFFX-LysX-3_at 2.23574
AFFX-PheX-5_at 5.3634
AFFX-PheX-M_at 5.8489
AFFX-PheX-3_at 5.7287
AFFX-ThrX-5_at 6.15827
AFFX-ThrX-M_at 6.80397

Total number of rows: 10208

Table truncated, full table size 207 Kbytes.




Supplementary file Size Download File type/resource
GSM1198177_EGA_E_coli_2.CEL.gz 596.7 Kb (ftp)(http) CEL
GSM1198177_EGA_E_coli_2.rma.chp.gz 83.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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