|
| Status |
Public on Mar 29, 2021 |
| Title |
HU_g1_rep3 [TnseqHU6] |
| Sample type |
SRA |
| |
|
| Source name |
whole cells
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: PY79
treatment: HU7
time: g1
|
| Treatment protocol |
Three samples were treated with vehicle control (water) and three samples were treated with 10 mM HU over three growth periods. Once the cell density reached 1.5, cells were collected for DNA extraction and serially diluted and plated for viable plate counts.
|
| Growth protocol |
Tn-insertion library was grown in LB medium at 30oC supplemented with 100 ng/mL spectinomycin overnight and back diluted into triplicate flasks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extraction was performed.
To ligate barcoded adapters, DNA was digested with MmeI and CIP purified. Adapters were then ligated to the ends and the samples were again purified. Quantitative PCR was performed with a subset of the samples to determine starting volumes for sequencing.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
80751_R1_trim
|
| Data processing |
library strategy: Tn-seq
Trim barcoded adaptors using fastx trimmer
Align reads to PY79 reference using BWA
samtools to generate a fast QC report for quality assessment
removing transposon hits from analysis when transposon falls between two genes in R
when coverage is less than 10 for each sample, remove from analysis
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000497485.1/
Supplementary_files_format_and_content: .csv files containing genes with greatest fitness benefit and defect
|
| |
|
| Submission date |
Mar 24, 2021 |
| Last update date |
Mar 29, 2021 |
| 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 |
GPL19910 |
| Series (2) |
| GSE169564 |
Tn-seq of hydroxyurea treated Bacillus subtilis cells |
| GSE169565 |
RNA-seq,Tn-seq, and whole genome sequencing of hydroxyurea treated Bacillus subtilis cells |
|
| Relations |
| BioSample |
SAMN18474877 |
| SRA |
SRX10437546 |
