|
| Status |
Public on Oct 10, 2015 |
| Title |
G112_-/-_no |
| Sample type |
RNA |
| |
|
| Source name |
CD40L-KO mice lung, no exposure
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
genetic background: C57BL/6
treatment: no exposure
mouse strain: CD40LKO (-/-)
|
| Treatment protocol |
CD40L-KO -/- mice and, as controls, CD40L +/-, which were littermates of the CD40L-KO mice, were exposed to P. murina infected seeder mice for 5 months.
|
| Growth protocol |
CD40 ligand knock-out (CD40L-KO, strain B6, 129S-Tnfsf5tm1lmx) were subsequently bred at the NIH. 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 tissue was collected and placed in RNAlater (Qiagen) for RNA extraction and in PBS for DNA extraction. Total RNA was isolated using Qiagen Rneasy kit. 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
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.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 |
GPL6096 |
| Series (2) |
| GSE67720 |
Characterization of chemokine and chemokine receptor expression during Pneumocystis infection in healthy and immunodeficient mice (part 2) |
| GSE67721 |
Characterization of chemokine and chemokine receptor expression during Pneumocystis infection in healthy and immunodeficient mice |
|
