|
| Status |
Public on May 11, 2022 |
| Title |
B. subtilis 168, exponential phase, rep. #2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Bacillus subtilis subsp. subtilis str. 168 |
| Characteristics |
strain: 168 trp-
growth phase: mid-to-late exponential
|
| Growth protocol |
Bacterial cells were grown were grown in LB broth at 37 degrees celsius and 220 rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell were lysed using glassbeads and totRNA was isolated using TRIzol/chloroform
rRNA depletion and cDNA library preparation was performed using Zymo-Seq RiboFree Total RNA-Seq Library Kit (Zymo Research, cat. 3003)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ribo- RNA
|
| Data processing |
Genes deleted in PG10 were removed from the dataset.
Fastq files were mapped to the B. subtilis 168 reference genome using Bowtie (parameters: -a -l 28 -n 2 -m 7 --best --strata).
Counts per gene were calculated using featureCounts and the latest RefSeq annotation (parameters: -t gene -g locus_tag -O -M --fraction).
Differentially expressed genes were identified using DESeq2, selecting genes with an absolute log2(fold-change) ≥ 0.5 and FDR-adjusted p-value < 0.05.
Genome_build: B. subtilis str. 168 (accession: NC_000964.3)
Supplementary_files_format_and_content: BEDGRAPH
|
| |
|
| Submission date |
Mar 23, 2021 |
| Last update date |
May 11, 2022 |
| Contact name |
Anne de Jong |
| E-mail(s) |
anne.de.jong@rug.nl
|
| Phone |
+31 50 363 2047
|
| Organization name |
university of Groningen
|
| Department |
Molecular Genetics
|
| Street address |
Nijenborgh 7
|
| City |
Groningen |
| ZIP/Postal code |
9747 AG |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21796 |
| Series (1) |
| GSE169409 |
Transcriptome analysis of miniBacillus PG10 and its parental strain B. subtilis 168 |
|
| Relations |
| BioSample |
SAMN18437739 |
| SRA |
SRX10417962 |
