|
| Status |
Public on Aug 03, 2022 |
| Title |
tmRNA mutant rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10 |
| Characteristics |
cell type: biofilm and planktonic bacteria
strain: tmRNA mutant (TM)
genotype: SsrA-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The growth status of samples in LBMG medium were analyzed and 36 hours was selected. The cells at the selected time point were collected and total RNA was extracted using the Total RNA Kit (OMEGA).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Bacillus subtilis NCIB 3610
|
| Data processing |
Illumina Casava1.7 software used for base-calling.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: CP020102
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 22, 2022 |
| Last update date |
Aug 03, 2022 |
| Contact name |
Shanshan Xu |
| E-mail(s) |
xusslzz@szu.edu.cn
|
| Organization name |
Shenzhen University
|
| Street address |
Xueyuan Avenue, No. 1066
|
| City |
Shenzhen |
| ZIP/Postal code |
518000 |
| Country |
China |
| |
|
| Platform ID |
GPL32075 |
| Series (1) |
| GSE199151 |
Transcriptome sequencing data analysis of Bacillus subtilis NCIB 3610 wild-type strain, tmRNA mutant strain and MB revertant strain |
|
| Relations |
| BioSample |
SAMN26870595 |
| SRA |
SRX14564821 |
