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| Status |
Public on Mar 15, 2018 |
| Title |
High-resolution analysis of the pneumococcal transcriptome under a wide range of infection-relevant conditions |
| Organism |
Streptococcus pneumoniae D39 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Streptococcus pneumoniae is an opportunistic human pathogen that typically colonizes the nasopharyngeal passage and causes lethal disease in other host niches such as the lung or the meninges. How pneumococcal genes are expressed and regulated at the different stages of its life cycle, as commensal or as pathogen, has not been entirely described. To chart the transcriptional responses of S. pneumoniae, we quantified the transcriptome under 22 different infection-relevant conditions. The transcriptomic compendium exposed a high level of dynamic expression and, strikingly, all annotated pneumococcal genomic features were expressed in at least one of the studied conditions. By computing the correlation of gene expression of every two genes across all studied conditions, we created a co-expression matrix that provides valuable information on both operon structure and regulatory processes. The co-expression data is highly consistent with well-characterized operons and regulons, such as the PyrR, ComE and ComX regulons, and had allowed us to identify a new member of the competence regulon. Finally, we created an interactive data center (www.veeninglab.com/pneumoexpress) that enables users to access the expression data as well as the co-expression matrix in an intuitive and efficient manner, providing a valuable resource to the pneumococcal research community.
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| Overall design |
17 conditions of 2 biological replicates, totalling in 34 individual samples
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| Contributor(s) |
Aprianto R, Slager J, Holsappel S, Veening J |
| Citation(s) |
30165663, 30885934 |
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| Submission date |
Dec 13, 2017 |
| Last update date |
Jul 02, 2019 |
| Contact name |
Rieza Aprianto |
| E-mail(s) |
[email protected]
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| Phone |
+31503632409
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| Organization name |
University of Groningen
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| Department |
Molecular Genetics Department
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| Lab |
Veening
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| Street address |
Nijenborg 7
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| City |
Groningen |
| State/province |
Groningen |
| ZIP/Postal code |
9747AG |
| Country |
Netherlands |
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| Platforms (1) |
| GPL24384 |
Illumina NextSeq 500 (Streptococcus pneumoniae D39) |
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| Samples (34)
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| GSM2887735 |
A04: ND6, biol. repl. 2 |
| GSM2887736 |
A05: NDN, biol. repl. 1 |
| GSM2887737 |
A06: NDN, biol. repl. 2 |
| GSM2887738 |
A07: C2N, biol. repl. 1 |
| GSM2887739 |
A08: C2N, biol. repl. 2 |
| GSM2887740 |
A09: NEP, biol. repl. 1 |
| GSM2887741 |
A10: NEP, biol. repl. 2 |
| GSM2887742 |
B05: CEP, biol. repl. 1 |
| GSM2887743 |
B06: CEP, biol. repl. 2 |
| GSM2887744 |
B07: C03, biol. repl. 1 |
| GSM2887745 |
B08: C03, biol. repl. 2 |
| GSM2887746 |
B09: C10, biol. repl. 1 |
| GSM2887747 |
B10: C10, biol. repl. 2 |
| GSM2887748 |
B11: C20, biol. repl. 1 |
| GSM2887749 |
B12: C20, biol. repl. 2 |
| GSM2887750 |
C01: N2L, biol. repl. 1 |
| GSM2887751 |
C02: N2L, biol. repl. 2 |
| GSM2887752 |
C07: LEP, biol. repl. 1 |
| GSM2887753 |
C08: LEP, biol. repl. 2 |
| GSM2887754 |
D03: B2C, biol. repl. 1 |
| GSM2887755 |
D04: B2C, biol. repl. 2 |
| GSM2887756 |
D05: F40, biol. repl. 1 |
| GSM2887757 |
D06: F40, biol. repl. 2 |
| GSM2887758 |
D07: FEP, biol. repl. 1 |
| GSM2887759 |
D08: FEP, biol. repl. 2 |
| GSM2887760 |
D11: N2F, biol. repl. 1 |
| GSM2887761 |
D12: N2F, biol. repl. 2 |
| GSM2887762 |
E03: N2B, biol. repl. 1 |
| GSM2887763 |
E04: N2B, biol. repl. 2 |
| GSM2887764 |
E05: BEP, biol. repl. 1 |
| GSM2887765 |
E06: BEP, biol. repl. 2 |
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| Relations |
| BioProject |
PRJNA422256 |
| SRA |
SRP126660 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE108031_count_compendium.txt.gz |
185.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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