|
Status |
Public on Nov 16, 2021 |
Title |
W-gly-2, replicate 3 |
Sample type |
SRA |
|
|
Source name |
Culture in fed-batch bioreactor
|
Organism |
Escherichia coli |
Characteristics |
strain: BW25113 genotype: W-gly time point (h): 5.7 od600: 18.4
|
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 Ion011_WGly_2_3
|
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 |
SAMN18148854 |
SRA |
SRX10244151 |