|
| Status |
Public on Mar 17, 2015 |
| Title |
∆pnp_RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Culture cells
|
| Organism |
Escherichia coli |
| Characteristics |
strain: K12-MG1693
growth phase: Exponential Phase
genotype: PNPase mutant
|
| Growth protocol |
Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.3) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA.
RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 4
|
| Data processing |
Vertis Biotechnologie AG bioinformatics department did a preliminary analysis of the high-throughput sequencing results which included the mapping of the reads against E. coli genome (NC_000913 downloaded from NCBI genome database).
We then used the mapped files to run Cufflinks (estimates the relative abundance of the transcripts) and after Cuffdiff to find significant changes in transcript expression when comparing two samples (Trapnell, Williams et al. 2010).
Genome_build: ASM584v2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …
|
| |
|
| Submission date |
Aug 05, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Cecilia M. Arraiano |
| E-mail(s) |
[email protected]
|
| Phone |
+351214469547
|
| Organization name |
Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa
|
| Street address |
Av. Republica, Apt 127
|
| City |
Oeiras |
| ZIP/Postal code |
2781-901 |
| Country |
Portugal |
| |
|
| Platform ID |
GPL14548 |
| Series (1) |
| GSE60107 |
Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli |
|
| Relations |
| BioSample |
SAMN02952128 |
| SRA |
SRX669656 |
