|
| Status |
Public on May 02, 2022 |
| Title |
deletion-3 |
| Sample type |
SRA |
| |
|
| Source name |
whole cells
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
replicate: 3
genotype: delta_ccrZ
|
| Treatment protocol |
Water (vehicle control) for KJW1 and KJW117 or 0.1% xylose (KJW119)
|
| Growth protocol |
OD=0.05 of WT cells were grown at 30C with shaking. Once the culture reached OD=0.2, treatment was administered. Cells were collected once the densities reached OD=0.65-0.9.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction was performed.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
3835-KW-6
|
| Data processing |
Library strategy: DNA-seq
Reads aligned using BWA
Reads with mapping quality < 20 were removed using Samtools
Duplicates were removed & sorted by read-name using SortSam and MarkDuplicates
BAM files converted to BED files
1 kb windows made of PY79 genome using BEDtools
Counts in each window were quantified (annotateBed from BEDtools)
Normalized read counts by total number of reads and log2-transformed
Genome_build: https://www.ncbi.nlm.nih.gov/nuccore/CP006881
Supplementary_files_format_and_content: .txt files containing read counts in 1 kB windows for each sample
|
| |
|
| Submission date |
Jan 19, 2022 |
| Last update date |
May 02, 2022 |
| Contact name |
Lyle A. Simmons |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Michigan
|
| Department |
Molecular, Cellular, & Developmental Biology
|
| Street address |
1105 N. University Ave.
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48105 |
| Country |
USA |
| |
|
| Platform ID |
GPL21373 |
| Series (1) |
| GSE193981 |
Whole genome sequencing of WT, ccrZ deletion, and overexpressed ccrZ in Bacillus subtilis |
|
| Relations |
| BioSample |
SAMN25118360 |
| SRA |
SRX13829642 |
