|
Status |
Public on Nov 14, 2021 |
Title |
wt_top |
Sample type |
SRA |
|
|
Source name |
SECO-wt_top
|
Organism |
Bacillus subtilis |
Characteristics |
growth phase: Exponential growth media: Luria broth strain: 168 genotype: wild type
|
Growth protocol |
B. subtilis cultures were grown in LB media and harvested at the given growth phase.
|
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 |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 550 |
|
|
Description |
DNA coverage from top fraction from sedimentation assay
|
Data processing |
Library strategy: SECO-seq SECO-seq and RNA-seqfiles were then trimmed using Trimmomatic (Galaxy Version 0.36.5) before mapping them to the B. 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 |
Jan 29, 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 |
SAMN13940527 |
SRA |
SRX7647504 |