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Sample GSM301726 Query DataSets for GSM301726
Status Public on Jul 01, 2008
Title BDCA-4 biologic rep4
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 4
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

Data table header descriptions
ID_REF
VALUE RMA signal
ABS_CALL MAS5 detection
DETECTION P-VALUE MAS5 detection P-value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
1007_s_at 31 P 0.013091824
1053_at 24 P 0.043967802
117_at 24 M 0.054470435
121_at 87 P 0.014936572
1255_g_at 9 A 0.52061963
1294_at 172 P 0.000388206
1316_at 16 P 0.008689182
1320_at 10 A 0.7959779
1405_i_at 7 A 0.9679803
1431_at 7 A 0.7325374
1438_at 25 A 0.5819307
1487_at 39 A 0.089405015
1494_f_at 14 A 0.32083008
1598_g_at 1380 P 0.000218889
160020_at 62 P 0.017000513
1729_at 190 P 0.000804598
1773_at 16 A 0.37818444
177_at 15 A 0.2674626
179_at 122 A 0.43836087
1861_at 22 A 0.107262634

Total number of rows: 22283

Table truncated, full table size 562 Kbytes.




Supplementary file Size Download File type/resource
GSM301726.CEL.gz 1.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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