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Sample GSM377454 Query DataSets for GSM377454
Status Public on Mar 05, 2009
Title BMDCs_NPs_24h_2
Sample type RNA
 
Source name bone marrow derived dendritic cells
Organism Mus musculus
Characteristics gender: female
age: 6 - 8 weeks
Treatment protocol Immature DCs (1 × 10^6 cells/ml) were incubated with either 300 µg/ml γ-PGA NPsA. The cultures were incubated for 6, 12 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.
Growth protocol Femurs and tibias were removed from mice and purified from the surrounding muscle tissues. Both ends of the bones were cut with scissors, and the marrow was flushed with PBS using a syringe with a 26-gauge needle. The suspension was passed through a 50-mm cell strainer. Bone marrow cells (2.5 × 10^6 cells/10 ml) were suspended in RPMI 1640 medium supplemented with 10 % heat-inactivated fetal bovine serum, 100 U/ml penicillin G, 100 µg/ml streptomycin, 2-mercaptoethanol, and 20 ng/ml recombinant GM-CSF (PeproTech) and placed into a Petri dish (InaOptica). Fresh culture medium was added to the dish on day 3. On day 7, non-adherent or loosely adherent cells were harvested and used as immature DCs.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the cells with RNeasy (Qiagen). The quality of the total RNA was examined by 2100 Bioanalyzer (Agilent).
Label Cy3
Label protocol RNA (500 ng) was converted to cDNA with Molony murine leukemia virus RT and T7 promoter primer. The cDNA was transcribed and amplified with T7 RNA polymerase to produce the cRNA labeled with cyanine 3. The cyanine 3-labeled cRNA was purified with RNeasy and examined for its concentration and labeling quality by a spectrophotometer.
 
Hybridization protocol The cRNA was fragmented and hybridized to Agilent whole mouse genome oligonucleotide microarray (4 × 44K slide format) at 37 ºC for 17 hours.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides
Description Gene expression after 24hr in gamma-PGA-NPs-treated mouse bone marrow derived dendritic cells
Data processing The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Mar 03, 2009
Last update date Mar 04, 2009
Contact name Takayuki Hamasaki
E-mail(s) t-hamask@m2.kufm.kagoshima-u.ac.jp
Phone +81-99-275-5931
Organization name Kagoshima University
Department Graduate School of Medical and Dental Sciences
Lab Center for Chronic Viral Diseass
Street address 8-35-1 Sakuragaoka
City Kagoshima
State/province Kagoshima
ZIP/Postal code 890-9544
Country Japan
 
Platform ID GPL7202
Series (1)
GSE15089 Time-course of gene expression in BMDCs stimulated with gamma-PGA nanoparticles

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_51_P454913 0.22622353
A_52_P311491 0.71602714
A_51_P323531 1.1335835
A_51_P183025 0.8923933
A_52_P179250 0.5998234
A_52_P370935 0.65529877
A_52_P30065 0.9577254
A_51_P415029 1.1012827
A_51_P117881 0.910522
A_52_P731333 0.6649084
A_51_P105709 0.77912617
A_51_P517672 6.8242993
A_51_P517182 0.3779544
A_51_P310196 0.9312263
A_51_P438924 1.45433
A_51_P126643 3.2726588
A_52_P368214 1.663662
A_52_P5905 0.80989254
A_51_P126647 1.2314663
A_52_P537887 0.7614547

Total number of rows: 41262

Table truncated, full table size 931 Kbytes.




Supplementary file Size Download File type/resource
GSM377454.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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