|
| Status |
Public on Dec 21, 2022 |
| Title |
HPUra38+2h |
| Sample type |
SRA |
| |
|
| Source name |
JMA222-based transposon insertion library
|
| Organism |
Bacillus subtilis subsp. subtilis |
| Characteristics |
genotype: JMA222 is ICEBs1(0) pheA1 trpC2
treatment: 2 hours after washing out HPUra
|
| Treatment protocol |
HPUra (38 µg/ml) was added to arrest replication, and a duplicate culture was untreated. After 1 h at 37°C, cells from both cultures were harvested by centrifugation, washed, and resuspended in fresh minimal medium. They were allowed to recover for 4 h, and aliquots were harvested every hour during this time.
|
| Growth protocol |
A suspension culture of the transposon insertion library was grown in defined minimal medium at 37°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total DNA was extracted using Qiagen DNeasy Blood and Tissue kit using the protocol for Gram-positive bacteria.
Transposon insertions were prepared for sequencing as described in Johnson, C. M. & Grossman, A. D. Identification of host genes that affect acquisition of an integrative and conjugative element in Bacillus subtilis. Mol Microbiol 93, 1284–1301 (2014).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were trimmed to remove sequence from the transposon
Sequences adjacent to the transposon were mapped to AG174 genome using Bowtie2
Wiggle files were generated from the Bowtie output using in-house R scripts
Assembly: AG174 (GenBank #CP007800.1)
Supplementary files format and content: Wiggle track, variableStep format
Library strategy: Tn-Seq
|
| |
|
| Submission date |
Dec 16, 2022 |
| Last update date |
Dec 23, 2022 |
| Contact name |
Alan Grossman |
| E-mail(s) |
adg@mit.edu
|
| Organization name |
MIT
|
| Department |
Biology
|
| Street address |
31 Ames St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL32956 |
| Series (1) |
| GSE221151 |
Beneficial and detrimental genes in the cellular response to replication arrest |
|
| Relations |
| BioSample |
SAMN32275554 |
| SRA |
SRX18726939 |
