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Sample GSM7964807 Query DataSets for GSM7964807
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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