|
| Status |
Public on Jan 03, 2019 |
| Title |
DL4201 IN biological repeat 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial Cell Lysates
|
| Organism |
Escherichia coli |
| Characteristics |
strain: DL4201
genotype/variation: BW27784 lacZ:XXX mhpR:XXX proA::ISceIcs tsx::ISceIcs PBAD-sbcDC lacZ+ cynX::GmR lacIq lacZX-
treatment: 1% formaldehyde to capture protein DNA interactions for 10 min at 22.5C with and quenched using glycine to a final concentration of 0.5M
|
| Treatment protocol |
Samples denoted as phenol-chloroform based method (samples 1-8) were treated with a series of enzymes.
Samples denoted as IN (sample 9-16) were treated with 1% formaldehyde to capture protein DNA interactions for 10 min at 22.5C with and quenched using glycine to a final concentration of 0.5M
Samples denoted as IN and sonication based method (sample 9-24) underwent a round of sonication to shear the chromatin using a Diagenode Bioruptor at 30 s intervals for 10 min at high amplitude at 5 °C.
|
| 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 |
DNA from samples denoted as phenol-chloroform based method (samples 1-8) was extracted using phenol-chloroform DNA extraction.
DNA from samples denoted as IN (sample 9-24) was isolated using the MinElute PCR purification kit (Qiagen).
Samples for phenol-chloroform based method (sample 1-8) were processed following Illumina's protocol from the Nextera XT library preparation kit, whilst rest of the samples (samples 9-24) were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Alignment: reads were mapped to a bespoke reference sequence (DL4201_in_lab_reference_genome) using the default parameters of software BWA (Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010;26(5):589-595).
Data extraction: Depth of coverage was extracted from each de-duplicated alignment file (in .bam) format using SAMtools software (Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16)).
Normalisation: An in-lab R script was used to normalise (based on the total depth) the library size for individual depth of coverage data.
Genome_build: DL4201_in_lab_reference_genome.fasta (GSE107972)
Supplementary_files_format_and_content: Each of the CSV files contains the coordinates of nucleotides of the reference genome (DL4201_in_lab_reference_genome.fasta (GSE107972)) starting from an arbitrary position at the origin of replication of E. coli and covering the circular genome in column 1 under the header "position". Subsequent eight columns contain the depth of coverage data from individual strains under the headers of the corresponding strain names and biological replicates (A for biological replicate 1 or B for biological replicate 2).
|
| |
|
| Submission date |
Jul 31, 2018 |
| Last update date |
Jan 03, 2019 |
| Contact name |
Benura Azeroglu |
| E-mail(s) |
[email protected]
|
| 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 |
GPL25368 |
| Series (1) |
| GSE117952 |
Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli (MFA profiles) |
|
| Relations |
| Reanalysis of |
GSM3302825 |
| BioSample |
SAMN09745860 |
| SRA |
SRX4493501 |
