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Sample GSM1202699 Query DataSets for GSM1202699
Status Public on Oct 14, 2014
Title ZM4 (ATCC31821) treated by 220 g/L glucose for 14 hours rep-1
Sample type RNA
 
Source name ZM4 (ATCC31821)treated by 220 g/L glucose for 14 hours rep-1
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 first of three wild-type biological replicates treated by 220 g/L glucose for 14 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 499.3930
ZMO0002110200000002 271.8713
ZMO0003110200000003 3809.4533
ZMO0004110200000004 3323.7431
ZMO0005110200000005 2485.9602
ZMO0006110200000006 5677.9630
ZMO0007110200000007 6255.0142
ZMO0008110200000008 3445.8418
ZMO0009110200000009 4325.4460
ZMO0010110200000010 1694.2637
ZMO0011110200000011 2385.5774
ZMO0012110200000012 1939.6669
ZMO0013110200000013 4819.3427
ZMO0014110200000014 5903.0992
ZMO0015110200000015 4839.7982
ZMO0016110200000016 8695.4794
ZMO0017110200000017 6082.7809
ZMO0018110200000018 3089.3543
ZMO0019110200000019 1741.7805
ZMO0020110200000020 4028.6795

Total number of rows: 1918

Table truncated, full table size 56 Kbytes.




Supplementary file Size Download File type/resource
GSM1202699_472471A10_2012-09-19_532.pair.gz 2.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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