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Sample GSM2175829 Query DataSets for GSM2175829
Status Public on Jan 02, 2017
Title DG-8052 in P2 vs. DG-8052 in P2 with CaCO3 at 12h replicate 3
Sample type RNA
 
Channel 1
Source name collected the whole fermentation cells_P2 with CaCO3 at 12h
Organism Clostridium beijerinckii NCIMB 8052
Characteristics strain: degenerated strain
culture media: P2 medium with 4g/L CaCO3
culture duration: 12 hrs
Growth protocol DG-8052 cells were grown at P2 medium/ P2 meidum with 4g/L CaCO3 in anaerobic chamber at 35 °C.
Extracted molecule total RNA
Extraction protocol Total cellular RNA was extracted from homogenized cells using RiboPureTM RNA Purification Kit, bacteria (Ambion®, Life Technologies, Inc., US) according to the manufacturer’s instructions.
Label Cy5
Label protocol The Crystal Core® cDNA amplified RNA labelling kit (CapitalBio, Beijing, China) were used as the protocol. 1 µg of total RNA were primed with 1 µl of 100 µM T7 Oligo (dT) DNA primer at 70°C for 10 min to get the 1st strand cDNA, then transcribed into cRNA at 37°C for 4 h in the presence of T7 enzyme Mix, and the 2µg of cRNA were reversed transcribed into cDNA at 25°C for 10min, 37°C for 1.5 h in the presence of 1.5 µl CbcScript II RTase (CapitalBio) with 4µl Random Primer; and 1 µg of cDNA,100 µM each dATP, dTTP, dGTP, with 25 µM dCTP Cy3-label (Cy5-label) were used for labeling by 4µl Random Primer and1.2 µl Klenow Fragment .
 
Channel 2
Source name collected the whole fermentation cells_P2
Organism Clostridium beijerinckii NCIMB 8052
Characteristics strain: degenerated strain
culture media: P2 medium
culture duration: 12 hrs
Growth protocol DG-8052 cells were grown at P2 medium/ P2 meidum with 4g/L CaCO3 in anaerobic chamber at 35 °C.
Extracted molecule total RNA
Extraction protocol Total cellular RNA was extracted from homogenized cells using RiboPureTM RNA Purification Kit, bacteria (Ambion®, Life Technologies, Inc., US) according to the manufacturer’s instructions.
Label Cy3
Label protocol The Crystal Core® cDNA amplified RNA labelling kit (CapitalBio, Beijing, China) were used as the protocol. 1 µg of total RNA were primed with 1 µl of 100 µM T7 Oligo (dT) DNA primer at 70°C for 10 min to get the 1st strand cDNA, then transcribed into cRNA at 37°C for 4 h in the presence of T7 enzyme Mix, and the 2µg of cRNA were reversed transcribed into cDNA at 25°C for 10min, 37°C for 1.5 h in the presence of 1.5 µl CbcScript II RTase (CapitalBio) with 4µl Random Primer; and 1 µg of cDNA,100 µM each dATP, dTTP, dGTP, with 25 µM dCTP Cy3-label (Cy5-label) were used for labeling by 4µl Random Primer and1.2 µl Klenow Fragment .
 
 
Hybridization protocol The labelled DNA was dissolved into hybridization buffer (2×GEx Hyb buffer (HI-RPM), Agilent In Situ Hybridization Kit; 25% formamide) at 45°C overnight. After hybridization, the slides were washed in 0.2% SDS and 2× SSC at 42°C for 5min, then washed in 0.2× SSC at room temperature for 5min. Finally the slides were drying for microarray scan.
Scan protocol Scanned on an Agilent G2565CA scanner
Description Biological replicate 3 of 3. degenerated strain in P2 vs degenerated strain in P2 with CaCO3, 12h culture cells
B3vsA3; B-3vsA-3:cy5ByCy3Signal(normalized)
Data processing Quantile normalized,background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
 
Submission date May 24, 2016
Last update date Jan 02, 2017
Contact name Bei Han
E-mail(s) hanbei@mail.xjtu.edu.cn
Organization name Xi'an Jiaotong University
Department School of Public Health
Street address NO 76 Yanta West Road
City Xi'an
State/province Shaanxi
ZIP/Postal code 710061
Country China
 
Platform ID GPL19469
Series (1)
GSE81808 Calcium effect to the Clostridium beijerinckii NCIMB 8052 degenerate strain for the solvent producing recovery

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
CUST_1_PI429219921 0.044836164
CUST_2_PI429219921 0.6648408
CUST_3_PI429219921 -0.31114006
CUST_4_PI429219921 0.5157346
CUST_5_PI429219921 0.6579847
CUST_6_PI429219921 0.21443178
CUST_7_PI429219921 0.4884101
CUST_12_PI429219921 0.703906
CUST_13_PI429219921 -0.44863036
CUST_14_PI429219921 -0.7096204
CUST_15_PI429219921 -0.26102644
CUST_18_PI429219921 -0.026156481
CUST_19_PI429219921 0.6489029
CUST_20_PI429219921 -0.17429537
CUST_21_PI429219921 1.2790556
CUST_22_PI429219921 0.040723328
CUST_23_PI429219921 -0.8702412
CUST_25_PI429219921 -0.7265739
CUST_26_PI429219921 -1.2521801
CUST_27_PI429219921 -0.64126015

Total number of rows: 5168

Table truncated, full table size 165 Kbytes.




Supplementary file Size Download File type/resource
GSM2175829_B3vsA3.txt.gz 1.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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