|
| Status |
Public on Jul 01, 2021 |
| Title |
REB057: MG1655 wt stat rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
MG1655 wt
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
strain: MG1655
growth condition: stationary phase
genotype: wt
|
| Growth protocol |
Stationary phase cells were obtained by propagating strains statically for two serial 24 hour passages at 37°C, with a 1:1000 dilution between passages (identical to the inoculum used for mouse infections). Log phase cells were obtained by diluting overnight cultures 1:100 in LB and growing to log phase (OD600 = 0.4 – 0.5) at 37°C with shaking.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction with the Qiagen RNAEasy Mini Kit; ribosomal depletion with the Ribo Zero rRNA removal kit
RNA libraries were prepared using the ScriptSeq v2 RNA-seq library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
REB057
|
| Data processing |
Raw sequencing reads were mapped to their respective reference genomes: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073 using BWA-MEM (version 0.7.10) with default parameters, then the resulting bam files were sorted and deduplicated using PicardTools v.2.2.2
HTseq was used to quantify sequencing reads mapping to predicted open reading frames (ORFs)
Ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences (based on the corresponding Genbank RefSeq annotation) were filtered out of the data set.
R (version 2.15.1) was used for differential expression analysis, using the edgeR package (samples were normalized by TMM (trimmed median of means), common and tagwise dispersion factors were estimated using a negative binomial model, and then fold change values were calculated from these normalized counts)
Genome_build: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073
Supplementary_files_format_and_content: Tab-delimited text files with normalized expression values, fold change, P-values, and FDR values.
|
| |
|
| Submission date |
Jan 25, 2021 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Swaine L Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
National University of Singapore and Genome Institute of Singapore
|
| Department |
Medicine
|
| Lab |
Bacterial Genomics
|
| Street address |
60 Biopolis Street, Genome, #02-01
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL17439 |
| Series (1) |
| GSE165421 |
Testing the impact of Type I Restriction Modification Systems on Gene Expression in Uropathogenic Escherichia coli |
|
| Relations |
| BioSample |
SAMN17527666 |
| SRA |
SRX9931062 |
