|
| Status |
Public on Dec 10, 2022 |
| Title |
∆hexRK 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial Culture
|
| Organism |
Clostridioides difficile |
| Characteristics |
cell type: Bacterial Culture
genotype: deltahexRK
treatment: Not applicable
|
| Treatment protocol |
Not applicable
|
| Growth protocol |
Overnight cultures were grown in TY then subcultured 1:100 in 100 mL of TY. Subcultures were grown to OD600 0.7-0.8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA library prep was performed by using Illumina RiboZero Plus librabry preperation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
ProkSeq version 2.0
Adapter trimming and read QC done by FastQC (parameters were automatically detemrined through Prokseq v 2.0 pipeline)
Reads aligned to genome using Bowtie2 (parameters were automatically detemrined through Prokseq v 2.0 pipeline)
Differential expression counts done by FeatureCounts (parameters were automatically detemrined through Prokseq v 2.0 pipeline)
Differential Expression Statisical Analysis done by DESeq2 (parameters were automatically detemrined through Prokseq v 2.0 pipeline)
Assembly: FN545816.1
Supplementary files format and content: text files included DESeq2 analysis output comparing 3 biological replicates of WT R20291 to 3 biological replicates of ∆hexRK
|
| |
|
| Submission date |
Dec 05, 2022 |
| Last update date |
Dec 10, 2022 |
| Contact name |
Anthony Pannullo |
| E-mail(s) |
anthony-pannullo@uiowa.edu
|
| Organization name |
University of Iowa
|
| Street address |
431 Newton Road
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL32868 |
| Series (1) |
| GSE220119 |
HexSDF are Required for Synthesis of a Novel Glycolipid that Mediates Daptomycin and Bacitracin Resistance in C. difficile |
|
| Relations |
| BioSample |
SAMN32046391 |
| SRA |
SRX18497725 |
