|
| Status |
Public on Sep 27, 2021 |
| Title |
Bacteria (GB00112) exposed to cells for 24hr |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria
|
| Organism |
Streptococcus agalactiae |
| Characteristics |
strain: GB00112
exposure: THP-1 24 hour
|
| Treatment protocol |
Cocultured cells were incubated at 37°C in air supplemented with 5% carbon dioxide for 1 to 24h prior to RNA extraction.
|
| Growth protocol |
THP-1 cells were maintained in RPMI 1640 medium without antibiotics and were infected with GB0112 at a multiplicity of infection (MOI) of 10:1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA samples were collected from bacterial culture in liquid medium by adding two volumes of RNAprotect Bacteria Reagent (Qiagen) or from bacteria inside macrophages by washing the cells twice with PBS then adding 1 mL RNAprotect Bacteria Reagent directly to the cells. RNA was extracted using the RNeasy minikit (Qiagen) using enzymatic lysis, Proteinase K digestion, and mechanical disruption. Residual genomic DNA was removed using the Turbo DNA-free kit (Ambion).
Illumina TruSeq Stranded mRNA Library Prep Kit was used. The protocol was modified to skip the oligo-dT bead step and proceeded directly to fragmentation and first strand synthesis
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling was done by Illumina Real Time Analysis (RTA) v1.18.64
The output of RTA was demultiplexed and converted to FastQ files with Illumina Bcl2fastq, v1.8.4
Analysis was carried out on the CLC Genomics workbench using the RNAseq analysis tool by mapping the reads to the GB00112 (AKXO00000000.1) genome
Differential expression analysis was performed using EdgeR using the following comparisons: 1hr vs media alone, 24hr vs media alone, and 1hr vs 24hr. A significant difference in expression was accepted for genes with at least a 2 fold change in expression and P < 0.05
Genome_build: GB00112 genome,AKXO00000000.1
Supplementary_files_format_and_content: xls file containing EdgeR data
|
| |
|
| Submission date |
Sep 23, 2021 |
| Last update date |
Sep 27, 2021 |
| Contact name |
Shannon D Manning |
| E-mail(s) |
[email protected]
|
| Organization name |
Michigan State University
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
1129 Farm Lane
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL23396 |
| Series (1) |
| GSE184709 |
Identification of differentially expressed genes in Streptococcus agalactiae following phagocytic uptake and survival in THP-1 macrophage cells. |
|
| Relations |
| BioSample |
SAMN21583003 |
| SRA |
SRX12322879 |
