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Sample GSM6031790 Query DataSets for GSM6031790
Status Public on Apr 09, 2022
Title Overexpression-reference-biol rep3
Sample type SRA
 
Source name Bacterial
Organism Clostridioides difficile
Characteristics tissue: Bacterial
cell line: UM275
cell type: 630{delta}erm
genotype: Wildtype
treatment: Overexpression (3% xylose, 3h)
Treatment protocol Overexpression: strains were subcultured to OD600=0.05, grown to 0.2, induced with 3% xylose, grown for an additional 3h and fixed.
No xylose: strains were subcultured to OD600=0.03 and grown to 0.7 (~5-6h) and fixed.
Low xylose: strains were subcultured to OD600=0.03, grown to 0.3, back-diluted to 0.1 and induced with 0.1% xylose. They were then grown for an additional 2.5h and fixed.
Growth protocol All cultures were grown in tryptone-yeast exract broth at 37C under anaerobic conditions
Extracted molecule total RNA
Extraction protocol Cultures were fixed by mixing with an equal volume of cells with ice-cold 1:1 ethanol:acetone. Cells were lysed with a FastPrep-24 homogenizer and RNA was extracted with the Qiagen RNeasy kit. All samples had a RIN of 9.4 or higher (Agilent Bioanalyzer).
Illumina Stranded RNA library preparation paired with RiboZero Plus was prepared per manufacturer's specifications.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Description High Output 75cyc 
Data processing Fastq files were trimmed and filtered using a combination of Trimmomatic and FastQC
Alignment, normalization and differential expression were analyzed with SeqMan NGen® Version 17.2. DNASTAR, Madison, WI.
Annotation was imported from NCBI with additional information obtained from proGenomes v2.1.
All subsequent analysis was performed in Excel.
Assembly: AM180355
Supplementary files format and content: Comma separated values (csv) file contains linear rlog reads, log2 fold change and adjusted P-value
 
Submission date Apr 06, 2022
Last update date Apr 09, 2022
Contact name Craig Ellermeier
E-mail(s) craig-ellermeier@uiowa.edu
Organization name University of Iowa
Department Microbiology and Immunology
Lab 200-EMRB
Street address 431 Newton Road
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL32143
Series (1)
GSE200346 Clostridioides difficile WalRK
Relations
BioSample SAMN27393547
SRA SRX14769882

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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