|
| Status |
Public on Sep 21, 2017 |
| Title |
blood C57BL/6 d21 p.i. mouse 1 |
| Sample type |
RNA |
| |
|
| Source name |
blood C57BL/6 d21 p.i. mouse 1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: whole blood
time point: day 21
infection: Mtb
|
| Treatment protocol |
Aerosol infection with Mtb strain H37Rv and enumeration of bacteria in lung tissue were performed as previously described (Dorhoi et al., 2013)
|
| Growth protocol |
129S2 (129SvPas) mice were bred and kept under specific pathogen-free (SPF) conditions at the Max Planck Institute for Infection Biology in Berlin, Germany. C57BL/6 animals were purchased from Charles Rivers Laboratories. 129S2 and C57BL/6 were matched for age and sex, and co-housed for at least two weeks under specific pathogen-free (SPF) conditions at the Max Planck Institute for Infection Biology in Berlin, Germany before beginning the experiments. At the time of infection, all mice were 9–12 weeks of age.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Blood was drawn from the inferior vena cava of all mice at indicated time points using a 26G needle. 200 µl were directly transferred into 800 µl of TRIzol (Invitrogen). Total RNA extraction of all blood samples was performed according to the manufacturer’s instructions. The RNA yield and A260/280 ratio were measured with a NanoDrop ND 100 spectrometer (NanoDrop Technologies), and RNA integrity was verified using the 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
RNA was labeled with the Low Input Quick Amp Labeling (Agilent Technologies) according to manufacturer’s instructions
|
| |
|
| Hybridization protocol |
Quantity and labeling efficiency were verified before hybridization of the samples to SurePrint G3 Mouse GE 8x60K Microarray (Agilent Technologies, Product Number G4852A, Design ID 028005) according to manufacturer's instruction.
|
| Scan protocol |
Scanning of microarrays was performed with 3μm resolution using a high-resolution laser microarray scanner (Agilent Technologies G2565CA)
|
| Description |
Gene expression after 21 day Mtb infection in C57BL/6 mouse blood
blood B1 d21
|
| Data processing |
Data analysis was performed in R version 3.2.3 (2015-12-10), and a script including all analysis steps is available upon request. The data sets have been analyzed with limma R package for differential expression analysis (Ritchie et al., 2015). The data sets were background corrected using the normexp method and quantile normalized. Limma lmFit function was used to fit linear models which included factors: stimulus type (TB, control) and time point. The p-values were calculated based on the moderated t-statistic and most differentially regulated genes were retrieved with topTable function.
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| |
|
| Submission date |
Nov 01, 2016 |
| Last update date |
Sep 21, 2017 |
| Contact name |
Teresa Domaszewska |
| Organization name |
Max Planck Institute for Infection Biology
|
| Department |
Immunology
|
| Lab |
Kaufmann
|
| Street address |
Virchovweg 12
|
| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
10117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10787 |
| Series (2) |
| GSE89389 |
Novel data integration approaches identify concordant and discordant immune responses between mice and humans [mouse] |
| GSE89392 |
Novel data integration approaches identify concordant and discordant immune responses between mice and humans |
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