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Sample GSM251632 Query DataSets for GSM251632
Status Public on Oct 21, 2008
Title Mature_dendritic_cells_PGE2_sample_1
Sample type RNA
 
Source name Mature dendritic cells, treated with PGE2
Organism Homo sapiens
Characteristics Inhibitory mature monocyte-derived human dendritic cells, treated with PGE2.
Treatment protocol After harvesting (day 7 of culture) immature DC were treated with anti-CD40 mAb and TNFalpha with addition of prostaglandin E2 (PGE2) and consequently incubated for three days to obtain mature DC treated with PGE2 (PGE2-DC).
Growth protocol Circulating CD14+ monocytes were positively enriched from PBMC, obtained from buffy coats of healthy donors using CD14 MicroBeads (cell purity > 95%). Immature monocyte-derived dendritic cells (immDC) were generated from the CD14+ monocytes in a serum-free medium (CellGro) supplemented with 2mM glutamine, 500 U/ml IL-4 and 800 U/ml GM-CSF for seven days (cytokines were replenished on day 3 and 5).
Extracted molecule total RNA
Extraction protocol Mature monocyte-derived PGE2-treated DC were harvested on day 10, lyzed in TRIzol and stored at –80° until further processing. RNA was extracted from cell lyzates with chloroform/isopropanol method, and was clean-uped in silica columns (Qiagen). The quality of the isolated RNA was determined by measuring the A260 / 280 ratio and the integrity of the ribosomal 28s and 18s bands were determined by agarose-gel electrophoresis.
Label Biotin.
Label protocol Synthesis of biotin labeled cRNA was performed with BioArray HighYield RNA TranscriptLabeling Kit (ENZO) following standard procedures.
 
Hybridization protocol Hybridization and washing was performed following standard procedures for Affymetrix HG-U133A arrays (www.affymetrix.com) on a GeneChip Fluidic station 400, using the EukGe-WS2v4 protocol.
Scan protocol Scanning was performed twice with filter set at 570 nm on an Agilent gene array scanner (Affymetrix).
Description Sufficient amount of high quality RNA was isolated and PGE2-DC transcriptome was assessed using the HG-U133A Affymetrix microarray.
Data processing MAS5.0 (Affymetrix) was used for raw data measurement and quality control. dChip 2006 was used for data normalization, quality control and data analysis.
 
Submission date Dec 18, 2007
Last update date Sep 01, 2016
Contact name Joachim Schultze
E-mail(s) j.schultze@uni-bonn.de
Organization name LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)
Department Genomics and Immunoregulation
Street address Carl-Troll-Strasse 31
City Bonn
State/province NRW
ZIP/Postal code 53115
Country Germany
 
Platform ID GPL96
Series (1)
GSE9946 Comparison of stimulatory and inhibitory dendritic cell subsets reveals new role of DC in granulomatous infection
Relations
Reanalyzed by GSE86363

Data table header descriptions
ID_REF
VALUE signal intensity after normalization with dChip

Data table
ID_REF VALUE
1007_s_at 484.3
1053_at 187.2
117_at 151.8
121_at 606.2
1255_g_at 17.3
1294_at 333.4
1316_at 361.4
1320_at 148.2
1405_i_at 161.1
1431_at 124.7
1438_at 135.9
1487_at 224.6
1494_f_at 183.3
1598_g_at 526.0
160020_at 1292.0
1729_at 494.2
177_at 184.4
1773_at 103.1
179_at 670.5
1861_at 48.7

Total number of rows: 22283

Table truncated, full table size 358 Kbytes.




Supplementary file Size Download File type/resource
GSM251632.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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