|
| Status |
Public on Jul 01, 2008 |
| Title |
BDCA-4 biologic rep2 |
| Sample type |
RNA |
| |
|
| Source name |
BDCA-4 cells from peripheral blood leukapharesis samples after MACS and FACS purification
|
| Organism |
Homo sapiens |
| Characteristics |
unstimulated plasmacytoid DCs
|
| Treatment protocol |
Cells were magnetically isolated from peripheral blood leukopharesis samples and then sorted by FACS and stored on ice prior to total RNA extraction for gene array studies
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted via the Quiagen RNAEasy method (Qiagen, Valencia, CA)
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The RNA was hybridized to the gene chip using the method established by Affymetrix and run on the Affymetrix system (Affymetrix, Santa Clara, CA)
|
| Scan protocol |
Affymetrix scanner at the Dartmouth Genomics and Microarray laboratory was used to scan the hybridized gene chips
|
| Description |
Gene Expression Data from BDCA-4 cells from donor 2
|
| Data processing |
Affymetrix image and data files were directly imported in GeneTraffic Uno Microarray Data Management and Analysis Software Version 3.2, Iobion Informatics LLC, La Jolla, CA. Data was normalized by transforming with Robust Multichip Analysis (RMA). Fold change values were generated by comparing BDCA-4 chips to CD14 chips from the same donor. The dataset was filtered to remove genes without at least one instance of expression change that was greater than or less than an absolute fold change value of 3 across 4 separate gene arrays (one array per four separate BDCA-4 cell isolations). The resulting genes were analyzed using Significance Analysis of Microarrays (SAM) to determine reproducibility across replicates as well as identify significant expression changes between cell types. Using a two-class paired test with a significance cutoff of 0.001%, 1232 genes were identified that were significantly up or down-regulated when compared to CD14 cells. Subsets of differentially expressed genes were further analyzed using Onto-Express to identify significantly represented ontology groups.
|
| |
|
| Submission date |
Jun 30, 2008 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Stephen Henry Wrzesinski |
| E-mail(s) |
swrzesinski@sphcs.org
|
| Phone |
518-525-6418
|
| Fax |
518-525-5016
|
| Organization name |
St. Peter's Cancer Care Center
|
| Department |
Medical Oncology
|
| Street address |
317 S. Manning Blvd
|
| City |
Albany |
| State/province |
NY |
| ZIP/Postal code |
12022 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE11943 |
Human Dendritic Cell Subtype Gene Arrays |
|
| Relations |
| Reanalyzed by |
GSE86363 |
