|
| Status |
Public on Nov 16, 2021 |
| Title |
R-gly-1, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Culture in fed-batch bioreactor
|
| Organism |
Escherichia coli |
| Characteristics |
strain: BW25113
genotype: R-gly
time point (h): 4.1
od600: 5.36
|
| Treatment protocol |
500 μL of the culture broth was placed in 500 μL of phenol/ethanol (5:95 v/v), then mixed by inverting the tube and kept at -80°C until further use
|
| Growth protocol |
Growth in a 2 L-bioreactor in fed-batch mode, M9 medium with glucose, 37 C and pH 6.8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribodepletion and sequencing (200pb oriented single end) with the Ion 540 kit on the Ion S5 using the Ion 540 chip
Oriented RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent S5 |
| |
|
| Description |
ribodepleted RNA
Ion010_RGly_1_1
|
| Data processing |
Basecalling with IonTorrent Suite software v5.0.4
reads were aligned with IonTorrent Suite Software v5.0.4 (Tmap from Thermofisher)
reads count with htseq-count (v 0.9.1) (option -f bam –stranded=yes -t gene -m intersection-nonempty -a 0)
Stastitical analysis was made with R and the package edgeR, the data were log2 transformed and normalized with RLE and Bonferroni correction for the differential analysis between samples (adjusted pvalue <1%).
Genome_build: E coli BW25113 (CP009273.1)
Supplementary_files_format_and_content: tab-delimited text files include raw reads count values for each Sample and matrix of normalized data
|
| |
|
| Submission date |
Mar 05, 2021 |
| Last update date |
Nov 16, 2021 |
| Contact name |
Delphine Labourdette |
| E-mail(s) |
labourd@insa-toulouse.fr
|
| Organization name |
INSA
|
| Department |
LISBP
|
| Lab |
Plateforme Biopuces
|
| Street address |
Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil
|
| City |
Toulouse |
| ZIP/Postal code |
31140 |
| Country |
France |
| |
|
| Platform ID |
GPL25140 |
| Series (1) |
| GSE168336 |
A multi-omics study of bacterial growth arrest in a synthetic biology application |
|
| Relations |
| BioSample |
SAMN18148853 |
| SRA |
SRX10244152 |
