|
| Status |
Public on Jun 25, 2021 |
| Title |
ML3285 (MG1655 pKVS45-GapR) in exponential phase, induced with aTc, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Escherichia coli MG1655
|
| Organism |
Escherichia coli str. K-12 substr. MG1655 |
| Characteristics |
growth stage: exponential phase
strain: ML3285
media: LB + 25 ng/µL aTc
|
| Treatment protocol |
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, and 25 ng/mL aTc was added. Cells were grown for 2 hr (OD ~0.3) and then fixed by the addition of 10 mM sodium phosphate [pH 7.6] and 1% formaldehyde (final concentrations). ChIP was then performed as previously reported (Guo et al, 2018).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously reported (Guo et al, 2018). ChIP antibody is Mouse monoclonal anti-FLAG from Sigma (Cat #: F1804).
Libraries were constructed by end repairing DNA with T4 DNA polymerase (NEB), T4 PNK (NEB), and Klenow large fragment (NEB). 3’ overhangs were added with Klenow (3'→5' exo-) (NEB). Y-shaped Illumina adapters were ligated onto the DNA, and libraries were amplified with Kapa HiFi Polymerase (Kapa Biosystems). Libraries were size selected to be 200-500 bp.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| 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.
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.
|
| |
|
| 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) |
| GSE152880 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes [ecChIP] |
| GSE152882 |
High-resolution, genome-wide mapping of positive supercoiling in chromosomes |
|
| Relations |
| BioSample |
SAMN15329699 |
| SRA |
SRX8586153 |
