|
| Status |
Public on May 19, 2016 |
| Title |
DL4312G_BR2_3 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial Cell Lysates
|
| Organism |
Escherichia coli |
| Characteristics |
strain: K-12 MG1655
genotype: delta_recG263::KanR lacZ::xxx mhpR::xxx proA::ISceIcs tsx::ISceIcs PBAD-sbcDC lacZ+ cynX::GmR lacIq lacZx-
|
| Treatment protocol |
DNA was isolated from cultures after 1 hour induction of sbcDC expression using the Promega Wizard® Genomic DNA purification kit.
|
| Growth protocol |
Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
To further eliminate potential RNA, 3 units of RiboshredderTM were added per sample. Samples were purified by phenol/chloroform extraction and ethanol precipitation.
Construction of libraries using the Illumina TruSeq DNA Sample Prep kit and DNA sequencing was carried out on an Illumina HiSeq 2000 platform by Edinburgh Genomics
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: DL4312G_BR2_processed.txt
|
| Data processing |
Library strategy: DNA-seq
Paired-end raw datasets were mapped against the reference genomic sequence using BWA sequence aligner (version 0.7.11) and subsequently processed using SAMtools (version 1.2)
Replication profiles of exponentially growing cultures were calculated by normalizing to the number of uniquely mapped sequence reads and then to the normalised reads of a non-replicating stationary-phase wild-type culture.
An in-lab R-script has been used to calculate the enrichment (normalised read depth) in 1 kb non-overlapping windows across the genome.
A non-parametric smoothing method (LOESS, Local regression) has been applied to the data points of the replication profiles for each strain.
Supplementary_files_format_and_content: txt files including count data for the whole genome
|
| |
|
| Submission date |
Jan 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Benura Azeroglu |
| E-mail(s) |
b.azeroglu@ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Lab |
David Leach Lab
|
| Street address |
Alexander Crum Brown Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3FF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL14548 |
| Series (2) |
| GSE77183 |
RecG Directs DNA Synthesis During Double-Strand Break Repair [Chromosomal marker frequency analysis] |
| GSE77184 |
RecG Directs DNA Synthesis During Double-Strand Break Repair |
|
| Relations |
| BioSample |
SAMN04437808 |
| SRA |
SRX1543290 |
