|
| Status |
Public on Mar 06, 2024 |
| Title |
defp replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
strain: 168
cell type: bacterial cell
genotype: defp
|
| Treatment protocol |
Transformed with transposon library
|
| Growth protocol |
LB 37C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysis, ammonium acetate precipitation of proteins, followed by isopropanol precipitation of gDNA
6 µg gDNA was digested with 3 units of MmeI for 2.5 hours at 37 °C, then treated with 6 units of antarctic phosphatase for 1 hour at 37 °C. DNA was then extracted with 300 µl phenol:chloroform:isoamyl alcohol (25:24:1) and precipitated with 50 µL 3M sodium acetate and 500 µL isopropyl alcohol. Dried pellets were dissolved in 27.5 µL 2 mM Tris-HCl pH 8.5. The DNA was ligated with one volume of 200-µM annealed adapters HRH-Tn1 and HRH-Tn2 in 1 mM tris-Cl pH 8.5. The ligated DNA was purified with the Qiagen PCR purification kit and amplified with the primers HRH-Tn3 and HRH-Tn4.
|
| |
|
| Library strategy |
Tn-Seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
∆efp1
|
| Data processing |
Reads were processed with Geneious. 27 bp from the 5' end and 108 base pairs from the 3' end were trimmed to leave only the 16 base pair Tn-insertion site.
Reads were mapped with Geneious
Assembly: NC_000964
Supplementary files format and content: Excel file with tallied reads (RPKMs) of transposon insertions
|
| |
|
| Submission date |
Dec 01, 2023 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Heather Feaga |
| E-mail(s) |
haf54@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
123 Wing Dr
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL23473 |
| Series (1) |
| GSE249203 |
YfmR is a translation factor that prevents ribosome stalling and cell death in the absence of EF-P |
|
| Relations |
| BioSample |
SAMN38579975 |
| SRA |
SRX22714954 |
