|
| Status |
Public on Dec 21, 2023 |
| Title |
early stationary butyrate 4 |
| Sample type |
SRA |
| |
|
| Source name |
630
|
| Organism |
Clostridioides difficile |
| Characteristics |
cell line: 630
genotype: WT
treatment: 50 mM butyrate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the appropriate time points, 5mL aliquots of the cultures were diluted 1:1 in chilled 1:1 Ethanol:Acetone to preserve RNA [45]. These samples were then centrifuged for 5 minutes at 3000 x g at room temperature and cell pellets were frozen at -80˚C. Immediately prior to RNA extraction, cell pellets were centrifuged at 4˚C at 3000 x g for 1minute. Residual supernatant was removed from the cell pellets, which were subsequently washed with 5mL nuclease free PBS. Washed pellets were centrifuged at 4˚C at 3000 x g for 1minute, the supernatant was removed, and the resulting pellet was resuspended in 1mL TRIzol and processed using a TRIzol Plus RNA Purification Kit (Thermo) with on-column DNase treatment according to the manufacturer’s instructions. Purified RNA was frozen at -80C and RNA integrity was confirmed via BioAnalyzer (Agilent) prior to proceeding.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Early stationary All Quantified Genes.tsv
1104 Differentially Expressed Genes In E.But vs E.Na.tsv
E_But4
|
| Data processing |
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v3.9.3).
Assembly: GCF_000009205.2
Supplementary files format and content: Differentially Expressed Genes, Quantified Genes
|
| |
|
| Submission date |
Dec 10, 2023 |
| Last update date |
Dec 21, 2023 |
| Contact name |
Daniel Pensinger |
| E-mail(s) |
dpensinger@wisc.edu
|
| Phone |
6086989408
|
| Organization name |
UW-Madison
|
| Department |
Department of Gastroenterology and Department of Medical Microbiology and Immunology
|
| Lab |
Hryckowian
|
| Street address |
1550 Linden Dr., MSB Rm3435
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL32868 |
| Series (1) |
| GSE249810 |
Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile |
|
| Relations |
| BioSample |
SAMN38755238 |
| SRA |
SRX22848149 |
