|
| Status |
Public on Jun 23, 2022 |
| Title |
C43(DE3) [C43_DE3_LB_71] |
| Sample type |
SRA |
| |
|
| Source name |
C43(DE3)
|
| Organism |
Escherichia coli |
| Characteristics |
strain: C43(DE3) purchased from Lucigen
genotype background: F– ompT gal dcm hsdSB(rB- mB-)(DE3)
treatment: strain grown at 37C in luria broth
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Triplicate samples were grown overnight at 37 °C and used to inoculate 25mL Luria broth (LB) cultures and grown to mid-log phase (0.4-0.6).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were pelleted and total RNA was purified using RNeasy Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard MiGen protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
V300012960_L01_7-1
MGIseq-2000
|
| Data processing |
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with BWA mem aligner option (Li H et al. 2013 ) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
The reference GFF and FASTA files were downloaded from RefSeq database bl21_de3 (https://www.ncbi.nlm.nih.gov/nuccore/CP001509)
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical conts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: CP001509_bl21_de3
Supplementary_files_format_and_content: raw gene counts, summar QC metrices
|
| |
|
| Submission date |
Jun 23, 2020 |
| Last update date |
Jun 23, 2022 |
| Contact name |
Kirill Tsyganov |
| E-mail(s) |
kirill.tsyganov@monash.edu
|
| Phone |
+61399020256
|
| Organization name |
Monash University
|
| Department |
Monash Bioinformatics Platform
|
| Street address |
Wellington Road
|
| City |
Clayton |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL28756 |
| Series (1) |
| GSE153028 |
Deciphering the transcriptional changes in Escherichia coli strains C41(DE3) and C43(DE3) that makes them a superior choice for membrane protein production. |
|
| Relations |
| BioSample |
SAMN15351712 |
| SRA |
SRX8601264 |
