|
| Status |
Public on Apr 09, 2022 |
| Title |
CRISPRi_neg con_no xyl_biol rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial
|
| Organism |
Clostridioides difficile |
| Characteristics |
tissue: Bacterial
cell line: UM554
cell type: 630{delta}erm
genotype: sgRNA-neg
treatment: No xylose
|
| 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) |
|
| Relations |
| BioSample |
SAMN27393544 |
| SRA |
SRX14769885 |
