|
| Status |
Public on Jul 03, 2015 |
| Title |
Laublab_BglII_HiC_NA1000_IsceI_site_33kb_from_oriC_IsceI_enzyme_induced |
| Sample type |
SRA |
| |
|
| Source name |
C. crecentus_vanillate
|
| Organism |
Caulobacter vibrioides NA1000 |
| Characteristics |
developmental stage: G1-arrested cells
genotype: IsceI site 33kb from oriC and Isce-encoding gene at van locus
restriction enzyme: BglII
|
| Treatment protocol |
Caulobacter cells were depleted of DnaA for 1.5 h before synchronization. Swarmer cells were then released into DnaA depleting conditions (without IPTG) and double-strand breaks were induced for 1 h by the addition of 500 μM vanillate.
|
| Growth protocol |
Caulobacter crescentus were grown as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media) [ug/ml]): chloramphenicol (1/2), kanamycin (5/25), oxytetracycline (1/2), spectinomycin (25/100). Synchronizations were performed on mid-exponential phase cells using Percoll (GE Healthcare) and density gradient centrifugation as described previously in Jones et al., 2001 (PMID: 11283290).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiments were performed using BglII restriction enzyme according to previous publications (Le et al., 2013 PMID: 24158908)
Standard library construction for Illumina Hiseq2000 sequencing platform
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
library strategy: chromosome conformation capture coupled with deep sequencing (Hi-C)
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Caulobacter CB15N (NA1000) independently by Bowtie version 2. All the processing steps afterwards were performed using public-availabe scripts as reported previously in Le et al., 2013 (PMID: 24158908) and in Imakaev et al., 2012 (PMID: 22941365)
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices.
|
| |
|
| Submission date |
Mar 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tung Ba Khanh Le |
| E-mail(s) |
tung.le@jic.ac.uk
|
| Phone |
01603450776
|
| Organization name |
John Innes Centre
|
| Department |
Department of Molecular Microbiology
|
| Lab |
www.tunglelab.org
|
| Street address |
Colney Lane
|
| City |
Norwich |
| State/province |
Norfolk |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18276 |
| Series (1) |
| GSE66811 |
Rapid pairing and subsequent resegregation of distant homologous loci enables double-strand break repair in bacteria |
|
| Relations |
| BioSample |
SAMN03401173 |
| SRA |
SRX952429 |
