|
| Status |
Public on Jul 05, 2019 |
| Title |
Dminus [miRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
Dminus_Bovine alveolar macrophages
|
| Organism |
Bos taurus |
| Characteristics |
animal: Animal 4
condition: Control
timpoint: 24 HPI
cell type: Bovine alveolar macrophages
|
| Treatment protocol |
2 x 10^6 macrophages were seeded in 60 mm tissue culture plates and challenged with M. bovis at an MOI of 10:1 (2 X 107 bacteria per plate) for 24 hours, parallel non-infected controls were prepared simultaneously.
|
| Growth protocol |
Centrifuged cell pellet was resuspended in 15 ml of R10+ media and placed in a 75 cm [2] vented culture flask (CELLSTAR®, Greiner Bio-One Ltd., Stonehouse, UK) and incubated for 24 h at 37 °C, 5% CO2. After incubation, media was removed together with non-adherent cells and adherent cells were washed with 15 ml HBSS pre-warmed to 37 °C (Note: all pre-warmed media and solutions were heated to 37 °C prior to use). Adherent cells were dissociated by adding 10 ml pre-warmed 1× non-enzymatic cell dissociation solution (Sigma–Aldrich Ltd.) to each culture flask and incubating at room temperature for 10 min. Cells were then pelleted (200× g for 5 min at room temperature), resuspended in 10 ml pre-warmed R10+ media and the number of viable cells was counted using a Beckman Coulter® Vi-CELL™ XR Cell Viability Analyzer and reagent kit (Beckman Coulter Inc., High Wycombe, UK).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from infected (n = 4) and control (n = 4) bAM samples using the RNeasy Plus Mini Kit (Qiagen) as previously outlined (10.1095/biolreprod.111.094946). All RNA samples were of excellent quality (RIN >9).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
At each step of data processing, read quality was assessed via fastqc version 0.11.5
Any samples that indicated adapter contamination were trimmed via Cutadapt (version 1.15)
Raw reads were mapped to the bovine reference genome via Bowtie (version 1.2.2).
miRNA detection, identification and quantification was carried out via mirdeep2 (version 0.0.91).
Supplementary_files_format_and_content: Alignment output via mirdeep2 Is in .arf.txt format
|
| |
|
| Submission date |
Jul 06, 2018 |
| Last update date |
Jul 05, 2019 |
| Contact name |
Thomas Hall |
| E-mail(s) |
tjhall1688@gmail.com
|
| Phone |
857168930
|
| Organization name |
UCD
|
| Department |
Vet sciences
|
| Street address |
2, Taney Grove
|
| City |
Dublin |
| State/province |
Select One |
| ZIP/Postal code |
D14 KW14 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL19172 |
| Series (2) |
| GSE116733 |
Initial host response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes [miRNA-seq] |
| GSE116734 |
Initial host response to mycobacterial infection is orchestrated through H3K4 methylation-mediated RNA polymerase II binding at key immune function genes. |
|
| Relations |
| BioSample |
SAMN09623394 |
| SRA |
SRX4348306 |
