|
| Status |
Public on Jul 22, 2013 |
| Title |
RGL22 |
| Sample type |
SRA |
| |
|
| Source name |
Genomic DNA
|
| Organism |
Escherichia coli |
| Characteristics |
strain: N7957
relevant genotype: ΔrecG::apra Δtus::cat
growth phase: Exponential
|
| Growth protocol |
Samples from cultures of a strain grown to an A650 of ~1.2 in LB broth were diluted 400-fold in fresh broth and incubated with vigorous aeration until the A650 reached 0.4 at the temperature indicated. Samples from these exponential phase cultures were frozen in liquid nitrogen at this point for subsequent DNA extraction. Incubation of the remaining culture was continued until several hours after the culture had saturated and showed no further increase in the A650. A further sample (stationary phase) was frozen at this point.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the GenElute Bacterial Genomic DNA Kit (Sigma-Aldrich).
Library preparation and sequencing was carried out according to SOLiD instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Description |
MFA wig file generated by taking the ratio between sample RGL22 and RGL29
processed data file: N7957_MFA.wig
|
| Data processing |
Sequence reads were mapped to the E. coli (MG1655) reference genome (Accession number: NC_000913) using BioScope (version 1.3.1).
Sequence reads mapping to a single genomic location were summed in 1 kb bins.
Normalised copy numbers were generated by dividing the sequence read counts from each sample by the counts from a stationary (non-replicating) wild-type sample.
Normalised copy numbers were manually adjusted to give a ratio of ~1 at the origin, oriC.
Genome_build: eschColi_K12
Supplementary_files_format_and_content: wig files of marker frequency analysis (MFA) for indicated comparisons. These are not manually adjusted and therefore reflect the read number obtained for each sample.
|
| |
|
| Submission date |
Nov 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Conrad A Nieduszynski |
| Organization name |
Earlham Institute
|
| Lab |
DNA replication & genome stability
|
| Street address |
Norwich Research Park
|
| City |
Norwich |
| ZIP/Postal code |
NR4 7UZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16232 |
| Series (1) |
| GSE41975 |
Avoiding chromosome pathology when replication forks collide |
|
| Relations |
| SRA |
SRX202294 |
| BioSample |
SAMN01797805 |
