|
| Status |
Public on May 12, 2023 |
| Title |
24h_alsS_UB_3 |
| Sample type |
SRA |
| |
|
| Source name |
Biofilm grown for 24 h
|
| Organism |
Bacillus subtilis |
| Characteristics |
strain: NCIB 3610
cell type: Gram-positive bacteria
genotype: {delta}alsS
treatment: Minimally buffered
|
| Treatment protocol |
Biofilms were grown on either MSgg with 100 mM or 1 mM MOPS buffer.
|
| Growth protocol |
Biofilms were grown on MSgg agar for 24 to 36 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Biofilms were harvested into 80% methanol and sonciated, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA libraries for RNA-seq were prepared using Illumina® Stranded TotalRNAPrep, Ligation with Ribo-Zero Plus Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
PT-12
Replicate 3
|
| Data processing |
FastQC
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt
Trimmed reads were aligned to the Bacillus subtilis genome strain 3610 NCBI CP020102.1 and plasmid NCBI CP020103.1 using STAR
Read counts for each gene were calculated using htseq-count (Anders et al, 2015) in conjunction with a gene annotation file for the reference genomes obtained from NCBI
Normalization and differential expression were calculated using DESeq2 that employs the Wald test (Love et al, 2014)
Assembly: Bacillus subtilis genome strain 3610 NCBI CP020102.1 and plasmid NCBI CP020103.1 using STAR
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
May 08, 2023 |
| Last update date |
May 12, 2023 |
| Contact name |
Peter Tran |
| E-mail(s) |
ptran@u.northwestern.edu
|
| Phone |
8133913337
|
| Organization name |
Prindle Lab, Northwestern University
|
| Street address |
impson Querrey Research Bldg 302 E Huron St, Room 11-500
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL29515 |
| Series (1) |
| GSE231939 |
Genome-wide analysis of gene expression by B. subtilis biofilms grown in buffered or minimally buffered conditions, |
|
| Relations |
| BioSample |
SAMN34997918 |
| SRA |
SRX20252071 |
