|
| Status |
Public on Jun 25, 2021 |
| Title |
ML3286 (MG1655 pKVS45-GapR-3xFLAG), in exponential phase, uninduced |
| Sample type |
SRA |
| |
|
| Source name |
Escherichia coli MG1655
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
growth stage: exponential phase
strain: ML3286
media: LB
|
| Treatment protocol |
As needed, cells were induced with 25 ng/mL anhydrous tetracycline for 2 hr.
|
| Growth protocol |
Strains were grown in LB, diluted to OD 0.3 and diluted back to OD ~0.01. Cells were grown for 2 hr (OD ~0.3) and RNA was extracted and processed into sequencing libraries as previously reported (Culviner and Laub, 2018).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted as previously reported (Culviner and Laub, 2018).
Sequencing libraries were processed as previously reported (Culviner and Laub, 2018).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were aligned to Escherichia coli MG1655 (NC_000913.2) with bowtie2 (version 2.1.0) using the default parameters.
Bowtie alignments were converted to wiggle files with custom Python scripts. The position of each alignment is evenly distributed over the length of the read.
To calculate mRNA abundance, a pseudocount was added to all positions and the number of reads mapped to a gene was divided by the length of the gene and normalized to yield the mean number of reads per kilobase per million sequencing reads (RPKM).
The change in gene expression was calculated by taking log2-RPKM ratio of each gene from the experimental condition to the control condition (GapR-3xFLAG induced / GapR-3xFLAG uninduced).
Genome_build: NC_000913.2
Supplementary_files_format_and_content: Wiggle files first column containing chromosome positions and second column containing the fraction of reads mapped to the position. For RNA-seq, two files are provided, one for forward and reverse strand.
|
| |
|
| Submission date |
Jun 19, 2020 |
| Last update date |
Jun 25, 2021 |
| Contact name |
Monica S Guo |
| E-mail(s) |
msguo@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Microbiology
|
| Lab |
Guo
|
| Street address |
750 Republican St
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
| |
|
| Platform ID |
GPL21117 |
| Series (2) |
| GSE152879 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-seq] |
| GSE152882 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
|
| Relations |
| BioSample |
SAMN15329698 |
| SRA |
SRX8586151 |
