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Sample GSM3581261 Query DataSets for GSM3581261
Status Public on Jan 29, 2019
Title G. oxydans, 4hr, HMF, replicate 1
Sample type RNA
 
Source name G. oxydans, 4hr, HMF
Organism Gluconobacter oxydans
Characteristics strain: 621H
agent: HMF
Treatment protocol The cells were harvested at 4 h by centrifugation at 10,000 rpm, 4 oC for 10 min, then quenched by liquid nitrogen and stored at -80 oC freezer for RNA extraction.
Growth protocol G. oxydans was cultured in a 3 L bioreactor (Baoxing Biotech Co., Shanghai, China) containing one liter seed medium (80 g of sorbitol, 20 g of yeast extract, 0.5 g of MgSO4·7H2O, 1.5 g of KH2PO4, 1.5 g of (NH4)2SO4 per liter of deionized water) at 30 ºC, pH 5.5, 2.5 vvm and 500 rpm to OD₆₀₀ reached 5.0. Then the seed broth was inoculated at 10% (v/v) ratio into 250 mL flask containing 45 mL synthetic fermentation medium (80 g of glucose, 20 g of yeast extract, 0.5 g of MgSO4·7H2O, 1.5 g of KH2PO4, 1.5 g of (NH4)2SO4 per liter of deionized water) with the addition of 1.2 g/L furfural, 1.5 g/L of HMF, 0.8 g/L of HBA, 0.9 g/L of syringaldehyde or 0.8 g/L of vanillin, respectively at 30 ºC, 220 rpm.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Trizol (Invitrogen, Gaithersburg, MD, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) (GE Healthcare Cat. No. PA53021) labeled cRNAs were heat denatured and hybridized to Agilent miRNA microarray, according to manufacturer's protocol.
 
Hybridization protocol According to the Agilent miRNA Microarray Protocol (Agilent Technologies).
Scan protocol After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner (G2565CA) with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).
Description 258001210002_2_1
Gene expression with HMF treatment
151581A&150948A_HMF1
Data processing Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software V13 (Agilent) was used to calculate the difference of gene expression and statistical significance p value
The normalized value of 75 percentile was calculated (log2). Note: Normalization is done using the Percentile75 method (the ratio is obtained by dividing the 75 bits value of the data expressed by each chip itself), and then the value generated after the logarithm of the log2 is taken.
 
Submission date Jan 28, 2019
Last update date Jan 29, 2019
Contact name Jie Bao
Organization name East China University of Science and Technology
Street address 130 Meilong Road
City Shanghai
ZIP/Postal code 200237
Country China
 
Platform ID GPL26106
Series (1)
GSE125739 Transcriptome response of Gluconobacter oxydans against five typical aldehyde inhibitors

Data table header descriptions
ID_REF
VALUE normalized value of 75 percentile

Data table
ID_REF VALUE
(-)3xSLv1 -8.626997998
(+)E1A_r60_1 1.975017769
(+)E1A_r60_3 -8.592670598
(+)E1A_r60_a104 -8.644780007
(+)E1A_r60_a107 -8.579423428
(+)E1A_r60_a135 -6.781794449
(+)E1A_r60_a20 -6.463235999
(+)E1A_r60_a22 -3.299966645
(+)E1A_r60_a97 -2.157536802
(+)E1A_r60_n11 -0.591071715
(+)E1A_r60_n9 1.396563167
(+)eQC-39 -8.616708823
(+)eQC-40 -8.67064805
(+)eQC-41 -8.571659334
(+)eQC-42 -8.653747729
CUST_1_PI430852443 -1.361910067
CUST_10_PI430852443 1.145502787
CUST_100_PI430852443 -6.555969814
CUST_1000_PI430852443 -3.774444998
CUST_1001_PI430852443 -1.445358132

Total number of rows: 2724

Table truncated, full table size 89 Kbytes.




Supplementary file Size Download File type/resource
GSM3581261_US10313827_258001210002_S01_GE1_1105_Oct12_2_1.txt.gz 769.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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