|
| Status |
Public on Jul 01, 2016 |
| Title |
Sh0012 40h |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cells
|
| Organism |
Escherichia coli |
| Characteristics |
strain: SH0012
fermentation time: 40h
agitation speed: 600 rpm
|
| Treatment protocol |
Expression of introduced enzymes for 3-HP productionm was induced by 0.05mM IPTG and 50 µM vitamin B12 when the cell reached at the early-exponential growth phase. T
|
| Growth protocol |
SH0012 and SH0003 were fermented in a 5.0L jar-fermenter with a 2.0 working voulume of modified R medium (20g/L glucose, 80 g/L glycerol, 1.4g/L MgSDo4, 13.5 g/L KH2PO4, 4.0 g/L (NH4)2HPO4 and 1.7g/L citric acid at 35°C. The agitation was at 1200 rpm and pH was maintained at 7.0 with 5N NH4OH. with the depletion of initial glucose, feeding medium of glycerol (700g/L) was throughout fermentation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The bacterial cells from 5L fermentation were collected at 20h, 30h, 40h and centrifuged for 5min to pellet the cells. The cells then mixed with 500mL of RNA protectant bacterial reagents to stabilize RNA and stored at -80°C until use. Total RNAs were isolated using RNeasy mini kit and were treated with DNase to remove DNA.
The RNA-Seq library was constructed with TruSeq RNA Preparation Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
with vitamin B12
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling with default parameter.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity sequence, then mapped to E.coli W3110 whole genome.
Data filtering was done with in-house script with the set value as follows: Removal if % of N nucleotide is more than 10%, if more than 40% of the nucleotide is Q20 or less, if average quality of the reads is less than Q20.
Read alignment was performed with BWA (version 0.6.2) with default parameter.
Transcript assembly an quantification was performed using a protocols from Trapnell et al., and Li et al. Fragments Per Kilobases of exon per million (FPKM) were calculated.
Genome_build: http://www.ncbi.nih.gov/nuccore/AP009048.1
Supplementary_files_format_and_content: Excel files include FPKM values for each sample.
|
| |
|
| Submission date |
Jul 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinsuk J. Lee |
| E-mail(s) |
jenny1008@gmail.com
|
| Organization name |
Samsung Advanced Institute Technology
|
| Street address |
130 Samsung-ro
|
| City |
Suwon-si |
| ZIP/Postal code |
443-370 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18133 |
| Series (1) |
| GSE70507 |
Transcriptome analysis using RNA-Seq reveals complex acid responsive mechanisms in 3-hydroxypropionic aicd producing strains of E. coli |
|
| Relations |
| BioSample |
SAMN03839866 |
| SRA |
SRX1081005 |
