|
| Status |
Public on May 01, 2017 |
| Title |
P.UF1-2 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria culture
|
| Organism |
Propionibacterium freudenreichii |
| Characteristics |
strain: P. UF1
genotype: wild-type
od600: 2.0
|
| Treatment protocol |
NA
|
| Growth protocol |
The P. UF1 and its genetically modified strains (mutants) were grown at 30°C in MRS medium supplemented with 1% sodium lactate in an anaerobic chamber.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The PowerMicrobiome™ RNA Isolation Kit was used for RNA extraction.
ScriptSeq Complete Gold Kit(Epidemiology) was used for rRNA depletion and cDNA library generation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
wild-type
|
| Data processing |
Standard Illumina demultiplex procedure were done in Basespace (Illumina) after the sequencing
The demultiplexed sequence reads first underwent data preprocessing and quality evaluation including trimming off the low quality ends of reads.
Rockhopper was used to map sequence reads to annotated P. UF1 genome, normalize the counts values by upper quartile normalization and perform differential expression analysis using NB statistical model
Genome_build: P. UF1
Supplementary_files_format_and_content: comma seperated text files include raw counts for all the samples
|
| |
|
| Submission date |
Nov 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Minghao Gong |
| E-mail(s) |
gmhhope@ufl.edu
|
| Phone |
3522831307
|
| Organization name |
University of Florida
|
| Department |
Pathology
|
| Lab |
Morel Laurence's lab
|
| Street address |
1395 Center Drive, D6-18c
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL22641 |
| Series (1) |
| GSE89528 |
Induction of DlaT-Specific Th17 Cell Differentiation by Intestinal P. UF1 Bacterium |
|
| Relations |
| BioSample |
SAMN05981508 |
| SRA |
SRX2327300 |
