|
| Status |
Public on Nov 08, 2018 |
| Title |
TT 740 |
| Sample type |
RNA |
| |
|
| Source name |
Lung collected 48 hours after tail trauma as a control for trauma
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
treatment: TT
|
| Treatment protocol |
When mice reached 22-28 grams (6-8 weeks of age) they received either mild traumatic brain injury or tail trauma. We used tail trauma as our control to determine if any sort of trauma (not necessarily specific to the brain) could provide a response. 48 hours after the respective trauma, the mice were sacrificed and RNA was extracted to analyze via microarray.
|
| Growth protocol |
Female ICR mice were allowed to mature as normal in a temperature/humidity controlled diurnal light room with ad libitum access to water and food.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After RNAlater fixation, a section from each of the two lung samples were placed in 600 μL of buffer RLT (Qiagen, Hilden, Germany) with 6 μL of 14.3 M beta-mercaptoethanol (Sigma) then homogenized using the TissueLyser II at 30 Hz for four minutes. RNA was then extracted from the homogenate using the QiaCube equipped with the RNeasy Plus Mini Kit.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 1.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.
|
| Description |
Gene expression data from Lung collected 48 hours after tail trauma as a control for trauma treated with TT.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene10stmmentrezgcdf R package (version 16.0.0).
|
| |
|
| Submission date |
Sep 21, 2018 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL21783 |
| Series (1) |
| GSE120326 |
Mild traumatic brain injury in mice beneficially alters structural and metabolic protein expression in mouse lung to enhance survival after Pseudomonas aeruginosa infection |
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