|
| Status |
Public on Dec 06, 2022 |
| Title |
Bs168 with 10mM MgCl2 supplement, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
bacillus genetic stock center: 1A866
cell type: bacterial cell
treatment: MgCl2
Stage: OD600 ~ 0.2
|
| Treatment protocol |
Collect cells at exponential stage around OD600 ~0.2
|
| Growth protocol |
168 cells are treaked on LB plate at 37C degree overnight, inoculate single colony in 5mL CH medium with or without 10mM MgCl2 supplement to grow to OD600 ~0.2, and subcultutre into 25mL coresponding CH medium with or without 10mM MgCl2 supplement.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNAprotect Bacteria reagent and RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
Total RNA were prepared for sequencing using TruSeqâ„¢ Stranded Total RNA and Ribo-Zero Gold (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Trimmomatic/0.36-Java-1.8.0_92 to trim reads
use FastQC/0.11.6-Java-1.8.0 to a quality control
use SAMtools/1.6-GCCcore-6.3.0 and HISAT2/2.1.0-intel-2017A-Python-2.7.12 to do mapping and count reads
use Deseq2 R package to do differential expression analysis
Assembly: NC_000964.fasta
Supplementary files format and content: tab-delimited text files include raw read counts for each sample
|
| |
|
| Submission date |
Dec 02, 2022 |
| Last update date |
Dec 07, 2022 |
| Contact name |
Jennifer Herman |
| E-mail(s) |
jkherman@tamu.edu
|
| Organization name |
Texas A&M University
|
| Department |
Biochemistry & Biophysics
|
| Lab |
BCBP 305
|
| Street address |
300 Olsen blvd
|
| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77840 |
| Country |
USA |
| |
|
| Platform ID |
GPL24119 |
| Series (1) |
| GSE219221 |
Magnesium modulates Bacillus subtilis cell division frequency |
|
| Relations |
| BioSample |
SAMN31994338 |
| SRA |
SRX18465589 |
