|
| Status |
Public on Oct 10, 2015 |
| Title |
CD4ExpC57_2 |
| Sample type |
RNA |
| |
|
| Source name |
CD4 cells from exposed mouse
|
| Organism |
Mus musculus |
| Characteristics |
cell type: CD4 cells
genetic background: C57BL/6
treatment: Expose to Pneumocystis
mouse: C57
|
| Treatment protocol |
C57BL/6 mice (expressing either CD45.1 or CD45.2) exposeure 35 days
|
| Growth protocol |
Healthy C57 black (C57BL/6) mice were obtained from the National Cancer Institute. Mice were housed in microisolator cages and kept in ventilated racks. All animal work was performed under a Clinical Center Animal Care and Use Committee-approved protocol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung CD4 cells and alveolar macrophages were obtained by bronchoalveolar lavage from C57BL/6 mice and were purified using bead for CD4 cells (Miltenyi) and adherence to plastic for 24 hours for alveolar macrophages.Due to the small number of cells recovered, cells from 5 animals were combined in 4 separate pools and each pool was analyzed separately. Because the RNA yield from macrophages was low even after combining cells, RNA was amplified by the Ovation Pico WTA System V2 (NuGen) prior to processing for microarray analysis. cDNA synthesis and amplification used Ambion WT expression kit.
|
| Label |
Biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Data processing |
Data were processed using Partek software. RMA background correction with quantile normalization
MoGene-2_0-st.pgf
MoGene-2_0-st.mps
|
| |
|
| Submission date |
Apr 09, 2015 |
| Last update date |
Oct 10, 2015 |
| Contact name |
Xiaojun Hu |
| Organization name |
SAIC_Frederick, INc
|
| Department |
CSP
|
| Lab |
LIB
|
| Street address |
1050 Boyles St.
|
| City |
Frederick |
| State/province |
MD |
| ZIP/Postal code |
21702 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (2) |
| GSE67717 |
Characterization of chemokine and chemokine receptor expression during Pneumocystis infection in healthy and immunodeficient mice (part 4) |
| GSE67721 |
Characterization of chemokine and chemokine receptor expression during Pneumocystis infection in healthy and immunodeficient mice |
|
