|
| Status |
Public on Nov 30, 2020 |
| Title |
CD14+ Bovine Milk Macrophage Challenge with Streptococcus uberis |
| Organism |
Bos taurus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
CD14+ Macrophage were challenged with Wildtype (WT), or S1154-deletion mutant (Del), and sequenced at timepoints zero hours (T0) and twenty-four hours (T24). To generate DEGs T0 and T24 timepoints were compared, a multifactor DESEQ2 run comparing T0 and T24 in both Wildtype and Deletion strains, and a direct comparison of T24 timepoints in Mutant and Deletion were generated.
|
| |
|
| Overall design |
Three replicates of each of: WT T0; WT T24; Del T0; Del T24 were generated using the Quantseq-3' FWD protocol, with the additional of the optional UMI during second strand synthesis. After sequencing across four lanes of a Nextseq 500 high yield run, the data was demulitplexed using BCL2FASTQ with the --no-lane-splitting option enabled. UMIs were used to correct for any PCR amplification errors during alignment using the standard Quantseq-3' FWD-UMI pipeline. For final analysis, (UMI-corrected) read counts were read into R studio and differential expression analysis carried out with DESEQ2. The various plots were generated in graphpad prism or R studio using the enhanced volcano and ggplot2 libraries.
|
| |
|
| Contributor(s) |
Leigh J, Coffey T, Egan S, Archer N |
| Citation(s) |
33260788 |
| Submission date |
Oct 11, 2019 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Nathan Archer |
| E-mail(s) |
nathan.archer1@nottingham.ac.uk
|
| Organization name |
University of Nottingham
|
| Department |
School of Veterinary Medicine and Sciences
|
| Lab |
ARCHER
|
| Street address |
Sutton Bonington
|
| City |
Loughborough |
| State/province |
East Midlands |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platforms (1) |
| GPL23055 |
Illumina NextSeq 500 (Bos taurus) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA577144 |
| SRA |
SRP225254 |
Less...
More...