|
| Status |
Public on Jan 03, 2015 |
| Title |
ColonicMac_Irgm1_mouse3 |
| Sample type |
RNA |
| |
|
| Source name |
Isolated colonic macrophages
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Irgm1-/-
gender: F
age (weeks): 6
background strain: C57BL/6
|
| Growth protocol |
Mice were housed in an enhanced barrier specific pathogen-free facility, under a strict 12 hour light cycle and fed autoclaved chow diet (PicoLab Rodent Chow 20, Purina Mills). All mice were maintained on a C57BL/6 background
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole tissue or isolated colonic macrophages using the Qiagen RNeasy kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
5ug of RNA was labeled using Kreatech ULS aRNA Fluorescent Cy3/Cy5 labeling kit (Kreatech Diagnostics).
|
| |
|
| Hybridization protocol |
750ng of each labeled aRNA were hybridized to 4x44k Agilent Mouse Whole Genome Microarrays for 18 hours at 65C in Sure-Hyb Hybridization Chambers (Agilent Technologies).
|
| Scan protocol |
Chambers were disassembled in 0.6x SSC 0.005%Triton X-102 wash for 5 minutes at 40C, then dried with HEPA filtered compressed nitrogen and scanned on on the Agilent Technologies DNA Microarray.
|
| Data processing |
Signal normalization was performed using a smoothed windowed piecewise linear regression, trained on log intensities that differed by < 10% rank order between two samples. Local background subtraction was performed for each spot prior to normalization. For each sample, a technical replicate pool was created from the averaged normalized signals of the individual replicate arrays. Within the replicate arrays, a median array was selected as the least distant from the other replicate arrays. All replicate arrays were normalized against the median array prior to calculating the averaged normalized signals of the pool. Probes with technical replicate CV's >= 0.7 were flagged as bad and assigned an intensity value of zero. A final normalization was performed on the averaged Irgm1-/- signals vs. averaged WT signals.
|
| |
|
| Submission date |
Jul 21, 2014 |
| Last update date |
Jan 03, 2015 |
| Contact name |
Lulu Sun |
| Organization name |
Washington University in St. Louis
|
| Department |
Pathology and Immunology
|
| Lab |
Thaddeus S. Stappenbeck
|
| Street address |
4940 Parkview Place, 1020 CSRB-NTA
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE59603 |
Identifying interferon-stimulated genes enriched in multiple tissues of Irgm1-/- mice |
|
