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Sample GSM1202703 Query DataSets for GSM1202703
Status Public on Oct 14, 2014
Title ZM4 (ATCC31821) treated by 220 g/L glucose and 10mM sorbitol for 6 hours rep-2
Sample type RNA
 
Source name ZM4 (ATCC31821)treated by 220 g/L glucose and 10mM sorbitol for 6 hours rep-2
Organism Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
Characteristics genotype: wild type
Treatment protocol The fresh cultures were subcultured to the inoculum media with 5% of the inoculation and cultivated for 16 h at 30°C.Then the appropriate amount of glucose and sorbitol was added when the ZM4 reached the midexponential phase. The initial concentrations were nearly 0, 220 g/L of glucose, 220 g/L of glucose and 10mM of sorbitol. The time of taking samples was set at 6 hrs(0 g/L glucose), 8 hrs(220 g/L of glucose), 12 hrs(220 g/L of glucose and 10 mM of sorbitol), 20 hrs(220 g/L of glucose) after treatment, respectively.
Growth protocol Z. mobilis ZM4 (ATCC31821) was cultured in Rich Media (RM) at 30°C for 24-48 hours without shaking.Goodman AE, Rogers PL, Skotnicki ML. Appl Environ Microbiol. 1982, 44(2):496 –498.
Extracted molecule total RNA
Extraction protocol Twelve samples representing four patterns of growth conditions in the exponential phase from ZM4 cultures were harvested by centrifugation and total cellular RNA was isolated using an RNA extraction kit (Kangwei century Biotech Co., Ltd., China).The remaining genomic DNA in the RNA samples was erased by following the manufacturer’s protocol (Takara Biotechnology (Dalian) Co., Ltd.). The RNA quality was evaluated by agarose gel electrophoresis and the ratio of its OD 260 to OD280 by a spectrophotometer, respectively.
Label Cy3
Label protocol The purified RNA from each sample was used as the template to generate cDNAs while labeled with Cy3-dUTP (CapitalBio).
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Description This sample is of wild-type ZM4. It is the second of three wild-type biological replicates treated by 220 g/L glucose and 10mM sorbitol for 6 hours , each from separate cultures.
Data processing Image signals were transformed into digital signals by NimbleScan 2.6 software and corrected by normalization method of RMA (Robust Multichip Analysis) to remove variations. It’s necessary to note that the group will be filtered if all digital signals of its four types for any gene were below 400 of cutoff. In a comparison analysis, the significant analysis of microarray software (SAM, version 3.02) was performed to identify significantly differentially expressed genes between treated and control groups.
Genes were determined to be significantly differentially expressed with a selection threshold of false discovery rate: FDR <5 % and fold change ≥2 (significant induction) or ≤0.5 (significant repression).
 
Submission date Aug 07, 2013
Last update date Oct 15, 2014
Contact name kun zhang
E-mail(s) kunkunzhangok@163.com
Organization name Sichuan University
Department College of Life Sciences
Lab Sichuan Key Laboratory of Molecular Biology and Biotechnology
Street address section 29,Wangjiang Rd.
City chengdu
State/province sichuan
ZIP/Postal code 610064
Country China
 
Platform ID GPL17542
Series (1)
GSE49620 Transcriptional analysis of adaptation to high glucose concentration in Zymomonas mobilis

Data table header descriptions
ID_REF
VALUE RMA

Data table
ID_REF VALUE
ZMO0001110200000001 314.2111
ZMO0002110200000002 196.8740
ZMO0003110200000003 1882.0339
ZMO0004110200000004 1908.4317
ZMO0005110200000005 1392.5694
ZMO0006110200000006 2294.3193
ZMO0007110200000007 5969.1023
ZMO0008110200000008 3394.4291
ZMO0009110200000009 3909.5763
ZMO0010110200000010 1304.0350
ZMO0011110200000011 2262.9098
ZMO0012110200000012 1323.3987
ZMO0013110200000013 3766.7364
ZMO0014110200000014 4190.1200
ZMO0015110200000015 4943.6566
ZMO0016110200000016 8919.4555
ZMO0017110200000017 5127.4192
ZMO0018110200000018 3684.2546
ZMO0019110200000019 2267.5193
ZMO0020110200000020 4858.7676

Total number of rows: 1918

Table truncated, full table size 56 Kbytes.




Supplementary file Size Download File type/resource
GSM1202703_472471A08_2012-09-19_532.pair.gz 2.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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