|
| Status |
Public on Jun 28, 2008 |
| Title |
16000508001605_UT 120min vs KDO(EYC060228A32) vs 120min_A02.txt |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RAW264.7 cells
|
| Organism |
Mus musculus |
| Characteristics |
RAW264.7 Cell line treated with KDO for 120 minutes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriPure (Roche) following its protocol. The detailed procedure is available at http://www.signaling-gateway.org/data/ProtocolLinks.html (AfCS Procedure Protocol PP00000009). Duplicate experiments were done for each treatment.
|
| Label |
Cy3
|
| Label protocol |
16 K mouse oligonucleotide arrays were fabricated with 15,631 oligomers of 65-bp or 70-bp long. The oligomers were purchased from Operon and Sigma-Genosys and were inkjet-printed onto glass slides by Agilent Technologies. The list of genes is available through the GEO (Gene Expression Omnibus - http://www.ncbi.nlm.nih.gov/geo) as an accession number GPL254.
|
| |
|
| Channel 2 |
| Source name |
Total RNA from untreated RAW 264.7 cells
|
| Organism |
Mus musculus |
| Characteristics |
RAW264.7 Cell line untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriPure (Roche) following its protocol. The detailed procedure is available at http://www.signaling-gateway.org/data/ProtocolLinks.html (AfCS Procedure Protocol PP00000009). Duplicate experiments were done for each treatment.
|
| Label |
Cy5
|
| Label protocol |
16 K mouse oligonucleotide arrays were fabricated with 15,631 oligomers of 65-bp or 70-bp long. The oligomers were purchased from Operon and Sigma-Genosys and were inkjet-printed onto glass slides by Agilent Technologies. The list of genes is available through the GEO (Gene Expression Omnibus - http://www.ncbi.nlm.nih.gov/geo) as an accession number GPL254.
|
| |
|
| |
| Hybridization protocol |
The hybridization experiment and analysis were performed as previously described 6,31. Cy5-labeled cRNA (RNA of ligand treated cells) and Cy3-labeled cRNA (RNA of time matched controls) were hybridized in the array. Dye-swap labeling was performed for each pair of samples.
|
| Scan protocol |
The arrays were scanned with Agilent Scanner G2505A (Agilent Technologies) and image files were extracted with background subtraction and dye-normalization using Agilent G2566AA Extraction Software version A.6.1.1 (Agilent Technologies).
|
| Description |
RAW 264.7 cells were stimulated with KDO (100 ng/ml), IFN-β (300 pM) and/or 8-Br 100 μM. These ligands were applied individually or in combination with KDO for 60 min and 120 min.
|
| Data processing |
=IF((COUNTIF(C2,"=0")+COUNTIF(D2,"=0")=0),(C2-D2)/2,0)
|
| |
|
| Submission date |
May 14, 2008 |
| Last update date |
Jun 27, 2008 |
| Contact name |
Sangdun Choi |
| E-mail(s) |
schoi@its.caltech.edu
|
| Phone |
626-395-8732
|
| URL |
http://www.signaling-gateway.org
|
| Organization name |
California Institute of Technology
|
| Department |
Biology
|
| Lab |
Alliance for Cellular Signaling Molecular Biology Laboratory
|
| Street address |
1200 E. California Blvd
|
| City |
Pasadena |
| State/province |
CA |
| ZIP/Postal code |
91125 |
| Country |
USA |
| |
|
| Platform ID |
GPL254 |
| Series (1) |
| GSE11449 |
RAW264.7 cells were treated with KDO, IFN beta and 8Br |
|
