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| Status |
Public on Jul 23, 2012 |
| Title |
Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018 |
| Platform organism |
Clostridium acetobutylicum |
| Sample organisms |
Clostridium acetobutylicum ATCC 824; Clostridium acetobutylicum EA 2018 |
| Experiment type |
Expression profiling by array
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| Summary |
Transcriptomic profiling of gene expression in EA 2018 relative to that of ATCC824 revealed several key genes related to solvent formation. For example, spo0A and adhEII have higher expression level, and most of the acid formation related genes have lower expression level in EA 2018.
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| Overall design |
Cells for RNA isolation were grown on P2 medium and collected at 9 h, 13 h, 17 h, 21 h, 24 h and 30 h by centrifugation at 4°C and 4500 x g for 10 min. Total RNA was extracted and purified by using Trizol (Invitrogen, Carlsbad, CA, USA) and RNeasy cleanup kit (Qiagen, Inc., Valencia, CA, USA) according to the manufacturer’s protocol. The total RNA yield was quantified by spectrophotometric analysis (NanoDrop Technology, Cambridge, UK) and the quality was verified by gel electrophoresis. Agilent oligonucleotide microarrays technology was used for monochromic analysis, in which probes (size: 60bp; three replicates for each ORF) from the two groups were labeled by incorporation of cyanine 3 (Cy3) (Agilent Technologies, Palo Alto, CA, USA). Average linkage hierarchical clustering was performed using Cluster 3.0, and gene clusters were visualized in Treeview
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| Contributor(s) |
Hu S, Zheng H, Gu Y, Zhao J, Zhang W, Yang Y, Wang S, Zhao G, Yang S, Jiang W |
| Citation(s) |
21284892 |
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| Submission date |
Jul 21, 2010 |
| Last update date |
Sep 25, 2019 |
| Contact name |
Shiyuan Hu |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of plant physiology and ecology, Shanghai institutes for biological sciences, Chinese academy of sciences
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| Lab |
Laboratory of synthetic biology
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| Street address |
300# fenglin road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platforms (1) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA131675 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE23071_RAW.tar |
25.8 Mb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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