|
| Status |
Public on May 08, 2019 |
| Title |
Toxoplasma_Control [5871841143_B] |
| Sample type |
RNA |
| |
|
| Source name |
Toxoplasma_Control
|
| Organism |
Mus musculus |
| Characteristics |
mouse strain: C57BL/6
mouse model: Toxoplasma gondii
condition: Control
infection protocol: Type II avirulent Toxoplasma gondii strain ME-49 cysts were obtained from brains of chronically infected C57BL/6 mice. Cysts preparations were pepsin treated to eliminate potential contamination with host cells and female C57BL/6 mice were inoculated intraperitoneally with an average of 15 cysts in PBS. On day 7 post infection, lung samples were collected from individual mice using uninfected C57BL/6 mice as controls.
tissue: whole blood
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood was collected in Tempus reagent (Life Technologies) at 1:2 ratio. Total RNA was extracted using the PerfectPure RNA Blood Kit (5 PRIME). Globin RNA was depleted from total RNA (1.5–2 µg) using the Mouse GLOBINclear kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
cRNA was prepared from 200 ng globin-reduced blood RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion). Quality was checked using an RNA 6000 Nano kit (Agilent) using a BioAnalyzer 2100 (Agilent). Biotinylated cRNA samples were randomized.
|
| |
|
| Hybridization protocol |
1.5 µg cRNA was then hybridized to Mouse WG-6 v2.0 bead chips (Illumina) according to the manufacturer’s protocols.
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
raw data file: Benaroya.txt
Control samples from Toxoplasma gondii infection model
|
| Data processing |
Microarray data was processed in GeneSpring GX v14.8 (Agilent Technologies). Flags were used to filter out the probe sets that did not result in a ‘present’ call in at least 10% of the samples, with the ‘present’ lower cut-off of 0.99. Signal values were then set to a threshold level of 10, log2 transformed, and per-chip normalised using 75th percentile shift algorithm. Next, per-gene normalisation was applied by dividing each messenger RNA transcript by the median intensity of all the samples. Next, transcripts were filtered to select the most variable probes: those that had a minimum of 1.5-fold expression change compared with the median intensity across all samples, in greater than 10% of all samples.
|
| |
|
| Submission date |
Sep 12, 2018 |
| Last update date |
May 08, 2019 |
| Contact name |
Akul Singhania |
| E-mail(s) |
akul.singhania@crick.ac.uk
|
| Phone |
+442037963319
|
| Organization name |
The Francis Crick Institute
|
| Street address |
1 Midland Road
|
| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17543 |
| Series (2) |
| GSE119848 |
Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases [Microarray_Blood_6] |
| GSE119856 |
Global transcriptional profiling unveils the interferon network in blood and tissues across different diseases |
|
