|
| Status |
Public on Jan 01, 2024 |
| Title |
26695 ΔrdxA, pH 5, acidic control |
| Sample type |
SRA |
| |
|
| Source name |
26695/ΔrdxA
|
| Organism |
Helicobacter pylori |
| Characteristics |
cell type: H. pylori 26695 mutant strain
genotype: WT
treatment: acidic pH
|
| Treatment protocol |
Each strain underwent a 72 hour growth in either pH 5 or pH 7 SFBB-cholesterol-vancomycin broth culture conditions. Every 24 hours during this 72 hour growth period, each culture was subcultured by taking 0.2 OD600 units of each culture into 6 mL of fresh media. To collect samples, 4 mL of each culture was harvested by centrifugation at 4,500 rpm, 20°C, for 10 min. The supernatant was decanted, and the pellets were stored at -20°C.
|
| Growth protocol |
H. pylori strains were grown on Trypticase Soy Agar II plates with 5% sheep blood then SFBB-cholesterol-vancomycin broth at 37°C in 5% CO2/ 95% ambient air.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were prepared via genomic DNA extraction using the Bio-Rad genomic DNA extraction kit via the manufacturer’s suggested protocol including the optional RNA elimination step. The extracted DNA was quantified for concentration and purity using a Nanodrop (Thermo Fisher). As an additional quality check, we performed agarose gel electrophoresis to ensure all extracted DNA was above 5kB and had not been fragmented.
SMRT-seq; PacBio SMRTbell libraries were prepared by Azenta Life Sciences
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Sequel |
| |
|
| Description |
1-pH5
|
| Data processing |
Azenta Life Sciences mapped subreads to the H.pylori reference genome GCF_000307795.1, GenBank accession CP003904.1.
Azenta Life Sciences performed Base Modification and Motif Analysis using PacBio SMRTLink v6.0
Assembly: GCF_000307795.1
Supplementary files format and content: comma-delimited file contains motif information for each sample
Supplementary files format and content: gff file contains base modification information for each sample
|
| |
|
| Submission date |
Aug 30, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Mark Forsyth |
| Organization name |
William & Mary
|
| Department |
Biology
|
| Street address |
540 Landrum Dr
|
| City |
Williamsburg |
| State/province |
Virginia |
| ZIP/Postal code |
23185 |
| Country |
USA |
| |
|
| Platform ID |
GPL33724 |
| Series (1) |
| GSE241991 |
The Helicobacter pylori Methylome is Acid-Responsive due to Regulation by the Two-Component System ArsRS and the Type I DNA Methyltransferase HsdM1 (HP0463) |
|
| Relations |
| BioSample |
SAMN37205006 |
| SRA |
SRX21541672 |
