|
| Status |
Public on Apr 10, 2014 |
| Title |
Transcriptome and marker frequency analysis of E. coli (control vs. Trimethoprim) and S. pneumoniae (control vs. HPUra/Kanamycin) |
| Organisms |
Escherichia coli; Streptococcus pneumoniae |
| Experiment type |
Genome variation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
We show that treatment with HPUra (for S. pneumoniae) and trimethoprim (for E. coli) leads to a skewed gene dosage profile (increase around the origin of replication), which is also propagated to the transcriptome level. Kanamycin, however, does not have this effect. In case of S. pneumoniae this shift in gene dosage distribution leads to the population-wide activation of competence.
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| Overall design |
Pairwise comparison of untreated and antibiotic-treated cells (either RNA-seq or DNA-seq). It was performed with deep sequencing, using an Illumina HiSeq 2000 machine with 100 nt paired-end reads. Control (E. coli and S. pneumoniae), HPUra- (S. pneumoniae) and Trimethoprim-treated (E. coli) samples were analysed from duplicate samples, while other conditions were from single samples.
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| Contributor(s) |
Slager J, Kjos M, Attaiech L, Veening JW |
| Citation(s) |
24725406, 35877768 |
| Submission date |
Jan 17, 2014 |
| Last update date |
Aug 16, 2022 |
| Contact name |
Jelle Slager |
| E-mail(s) |
j.slager@rug.nl
|
| Organization name |
University of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747AG |
| Country |
Netherlands |
| |
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| Platforms (2) |
| GPL14548 |
Illumina HiSeq 2000 (Escherichia coli) |
| GPL18183 |
Illumina HiSeq 2000 (Streptococcus pneumoniae) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA235855 |
| SRA |
SRP035502 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE54199_EC_Cont_DNA.txt.gz |
104.8 Kb |
(ftp)(http) |
TXT |
| GSE54199_EC_Cont_RNA.txt.gz |
89.7 Kb |
(ftp)(http) |
TXT |
| GSE54199_EC_Trim_DNA.txt.gz |
105.2 Kb |
(ftp)(http) |
TXT |
| GSE54199_EC_Trim_RNA.txt.gz |
86.5 Kb |
(ftp)(http) |
TXT |
| GSE54199_SP_Cont_DNA.txt.gz |
42.0 Kb |
(ftp)(http) |
TXT |
| GSE54199_SP_Cont_RNA.txt.gz |
44.8 Kb |
(ftp)(http) |
TXT |
| GSE54199_SP_HPUra_DNA.txt.gz |
42.0 Kb |
(ftp)(http) |
TXT |
| GSE54199_SP_HPUra_RNA.txt.gz |
44.3 Kb |
(ftp)(http) |
TXT |
| GSE54199_SP_Kan_DNA.txt.gz |
34.6 Kb |
(ftp)(http) |
TXT |
| GSE54199_SP_Kan_RNA.txt.gz |
38.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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