|
| Status |
Public on Jul 18, 2018 |
| Title |
DL2573 stationary phase biological repeat 1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial Cell Lysates
|
| Organism |
Escherichia coli K-12 |
| Characteristics |
background strain: BW27784
strain: DL2573
genotype: BW27784 PBAD-sbcDC lacZ+ cynX::GmR lacIq lacZchi-
|
| 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 |
| |
|
| Data processing |
Library strategy: Marker Frequency Analysis [MFA]
Alignment: reads were aligned to an in house generated draft sequence of strain DL2573 (DL2573_draft_genome_sequence.fasta (available on the series record)) using the Burrows-Wheels Alignment software BWA-MEM and the number of reads mapped to each bp of the genome quantified using SAMtools (mpileup)
Raw Counts: The data from each of the multiple (three or four) sequencing runs was consolidated by merging BAM files using the merge function of SAMtools and the number of reads mapped to each bp of the genome quantified using the mpileup function of SAMtools (with parameters -BQ0 -d10000000). Genomic positions lacking any coverage were given an arbitrary value of 0.1 reads
Normalization: the number of mapped reads for each position in the reference genome was divided by the sum of the number of mapped reads at every position across the genome
Genome_build: DL2573_draft_genome_sequence.fasta (available on the series record)
Supplementary_files_format_and_content: Each CSV file contains a headerless matrix with position on the reference genome in column 1 and the associated raw or normalized read count in column 2. Each matrix has a row for every corresponding genomic position. Values were saved with a maximum precision of 9 significant figures.
|
| |
|
| Submission date |
Dec 12, 2017 |
| 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 |
GPL19529 |
| Series (2) |
| GSE107973 |
RecBCD Coordinates Repair of Two Ends at a DNA Double-Strand Break, Preventing Aberrant Chromosome Amplification [MFA] |
| GSE107974 |
RecBCD Coordinates Repair of Two Ends at a DNA Double-Strand Break, Preventing Aberrant Chromosome Amplification |
|
| Relations |
| BioSample |
SAMN08163669 |
| SRA |
SRX3463419 |
