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Sample GSM1141729 Query DataSets for GSM1141729
Status Public on May 25, 2015
Title P. aeruginosa PAO1, control
Sample type RNA
 
Source name P. aeruginosa PAO1, control
Organism Pseudomonas aeruginosa PAO1
Characteristics agent: control
Treatment protocol Sample 2 was incuabted with 1 mM ZnO nanoparticle at 37oC for 5 hrs with 250 rpm shaking
Growth protocol P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM).
Extracted molecule total RNA
Extraction protocol DNA microarray analysis with one biological replicate was performed with an Affymetrix system. P. aeruginosa was inoculated in 25 ml of LB medium in 250 ml shaker flasks with overnight cultures (1 : 100 dilution). Cells were cultured for 5 h with shaking at 250 rpm with and without ZnO nanoparticles (1 mM). 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 SAMPLE 1
Gene expression data of Pseudomonas aeruginosa PAO1 incubated for 5 hrs at 37oC with 250 rpm shaking
Data processing MAS 5.0 Expression Analysis Default Setting
 
Submission date May 15, 2013
Last update date May 25, 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 GPL84
Series (1)
GSE46947 Antivirulence activities of zinc ion and ZnO nanoparticle against Pseudomonas aeruginosa

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-YEL002C_WPB1_at 0.0969821 A 0.872355
AFFX-YEL018W_at 0.470587 A 0.67917
AFFX-YEL024W_RIP1_at 0.755685 A 0.267463
AFFX-YFL039C_ACT1_at 4.27652 A 0.138765
AFFX-YER148W_SPT15_at 6.58572 A 0.250724
AFFX-YER022W_SRB4_at 3.45578 A 0.138765
AFFX-Athal_GAPDH_at 1.11457 A 0.697453
AFFX-Athal_ubq_at 2.16557 A 0.541184
AFFX-Athal_actin_at 0.376714 A 0.94553
AFFX-Bsubtilis_dapB_at 1584.85 P 0.000218889
AFFX-Bsubtilis_lys_at 21.4102 P 0.00652438
AFFX-Bsubtilis_pheB_at 249.688 P 0.000218889
AFFX-Bsubtilis_thrC_at 773.257 P 0.000265621
AFFX-Bsubtilis_trpD_at 0.555049 A 0.990015
Pae_flgK_at 16.2379 A 0.276247
Pae_flgL_at 2.58602 A 0.933521
Pae_orfA_vioA_at 37.7666 A 0.649648
Pae_orfB_at 30.7582 A 0.0759781
Pae_orfC_at 9.67081 A 0.69991
Pae_orfD_at 3.1412 A 0.9768

Total number of rows: 5900

Table truncated, full table size 188 Kbytes.




Supplementary file Size Download File type/resource
GSM1141729_PA01_none_PC_.CEL.gz 713.3 Kb (ftp)(http) CEL
GSM1141729_PA01_none_PC_.YNUNIV.mas5.CHP.gz 59.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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