|
| Status |
Public on Oct 09, 2024 |
| Title |
JS006 prm1 void replica 2 |
| Sample type |
SRA |
| |
|
| Source name |
bacteria
|
| Organism |
Escherichia coli |
| Characteristics |
strain: JS006
cell type: bacteria
genotype: MG1655 [delta]araC [delta]lacI KanS
plasmid: pRM1 void plasmid
|
| Treatment protocol |
Cells were harvested from 200 mL of culture by rapid filtration through a Kontes 90 mm filtration apparatus with 0.45 μm nitrocellulose filters (Whatman)
|
| Growth protocol |
E. coli JS006 cells transformed with pRM1+ or with a void plasmid (in duplicate) were grown in LB medium at 37 ºC to reach an OD600 around 0.4
|
| Extracted molecule |
other |
| Extraction protocol |
Aliquots were lysed in Tris-based ice-cold polysome lysis buffer (Tris-based) by bead beating . Lysates were clarified by centrifugation and ribosomes were subsequently pelleted from lysates by ultracentrifugation. Samples were then digested with MNase, RNA was purified and ribosome-protected mRNA fragments ranging 20-40 nt in length were selected for size using 15% urea PAGE gels. rRNA was depleted from samples using custom biotinylated rRNA depletion oligos for E. coli.
mRNAs were fractionated and converted into Illumina compatible cDNA libraries
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The BioConductor R package DESeq2 was used to perform the differential gene expression analysis.
The statistical significance was evaluated by means of a Wald test in pair-wise data (i.e., two conditions) with a correction for multiple testing using the Benjamini-Hochberg’s FDR.
Assembly: NZ_CP009273.1 Escherichia coli BW25113 strain K-12 chromosome
Supplementary files format and content: tab-delimited text file includes counts for each gene in samples
Supplementary files format and content: tab-delimited text file includes fold change and p-values for each gene in samples
Library strategy: Ribo-seq
|
| |
|
| Submission date |
Aug 23, 2024 |
| Last update date |
Oct 09, 2024 |
| Contact name |
Guillermo Rodrigo |
| E-mail(s) |
guillermo.rodrigo@csic.es
|
| Organization name |
Agencia Estatal Consejo Superior de Investigaciones Científicas
|
| Street address |
Calle del Catedrático Agustín Escardino Benlloch, 9
|
| City |
Paterna |
| ZIP/Postal code |
46980 |
| Country |
Spain |
| |
|
| Platform ID |
GPL25368 |
| Series (1) |
| GSE275581 |
Probing the orthogonality and robustness of the mammalian RNA-binding protein Musashi-1 in Escherichia coli [Ribo-seq] |
|
| Relations |
| BioSample |
SAMN43323094 |
| SRA |
SRX25815609 |
