|
| Status |
Public on Mar 22, 2012 |
| Title |
Effect of LPS on global gene expression in human skin fibroblasts |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
To examine responses induced by TLR4 activation at the genome-wide level, confluent fibroblasts in serum-free media were incubated with or without LPS for 6 h, and RNA was isolated using RNeasy mini kits (Qiagen, Valencia, CA). The integrity of RNA was ascertained using Agilent Bioanalyzer (Santa Clara, CA), cDNA was labeled using an Ambion labeling kit (Ambion), and hybridized to Illumina human HT-12 version 4 Expression Microarray Chips (Illumina, San Diego, CA) as described. Raw signal intensities for each probe were obtained using Illumina Beadstudio data analysis software and imported to the Bioconductor lumi package for data transformation and normalization. Probes with all samples absent (near or below background levels) were filtered. To control for multiple testing and reduce the false positive rate (FDR), stringent statistical criteria were used to identify differentially expressed genes with raw p < 0.01 and FDR adjusted p value < 0.05.
|
| |
|
| Overall design |
Confluent human skin fibroblasts in serum-free media were incubated with or without LPS for 6 h, and RNA was isolated using RNeasy mini kits (Qiagen, Valencia, CA).
|
| |
|
| Contributor(s) |
Bhattacharyya S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Mar 21, 2012 |
| Last update date |
Aug 13, 2018 |
| Contact name |
Swati Bhattacharyya |
| E-mail(s) |
s-bhattacharyya@northwestern.edu
|
| Phone |
312 503 0565
|
| Organization name |
Northwestern University
|
| Department |
Medicine
|
| Lab |
Rheumatology
|
| Street address |
240 E Huron st, McGAW, M230
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
|
| Samples (6)
|
|
| Relations |
| BioProject |
PRJNA153589 |
Less...
More...