|
| Status |
Public on Nov 14, 2021 |
| Title |
Hi-C-rok+rok |
| Sample type |
SRA |
| |
|
| Source name |
168
|
| Organism |
Bacillus subtilis |
| Characteristics |
growth phase: Stationary
growth media: Luria broth
strain: 168
genotype: delta{rok} with rok_wt complementation
|
| Growth protocol |
B. subtilis strains were inoculated from an overnight culture and grown at 37°C in Luria broth (LB) media or Spizizen minimal medium (SMM) prior to sample collection
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total RNA was extracted using PCI followed by ribosomal RNA removal using MICROBExpress™ Bacterial mRNA Enrichment Kit (AM1905). Standard protocol with HindIII digestion was used for Hi-C.
libraries were constructed using the NEBNext® Ultra™ II DNA (NEB#E7103) and Ultra™ II Directional RNA (NEB#E7765) Library Prep kits
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Chromosome conformation capture using Hi-C
|
| Data processing |
RNA-seq and sedimentation assay (DNA-seq) files were then trimmed using Trimmomatic (Galaxy Version 0.36.5) before mapping them to the Bacillus subtilis subsp. subtilis str. 168 reference genome (NC_000964.3) using Bowtie2 (Galaxy version 2.3.4.2). The BAM files were converted to bigwig using the tool bamCoverage (Galaxy version 3.0.2.0)
Paired end reads generated for Hi-C were mapped separately to B. subtilis genome (NCBI Reference Sequence NC_000964.3) using very sensitive local setting mode in Bowtie2. The mapped files were used to build the contact matrix using the tool hicBuildMatrix using a bin size of 10 Kb, HindIII restriction site (AAGCTT) and AGCT as the dangling sequence. The contact matrix (.cool format) was then used for further analysis and visualization
Genome_build: NC_000964.3
Supplementary_files_format_and_content: BigWig, cool matrix file
|
| |
|
| Submission date |
Oct 05, 2020 |
| Last update date |
Nov 14, 2021 |
| Contact name |
Gaurav Dugar |
| E-mail(s) |
g.dugar@uva.nl
|
| Phone |
0630888905
|
| Organization name |
University of Amsterdam
|
| Department |
Bacterial Cell Biology
|
| Street address |
Science Park 904
|
| City |
Amsterdam |
| ZIP/Postal code |
1098 XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL28092 |
| Series (1) |
| GSE144475 |
A chromosomal loop anchor mediates bacterial genome organization |
|
| Relations |
| BioSample |
SAMN16373902 |
| SRA |
SRX9245502 |
