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Sample GSM190131 Query DataSets for GSM190131
Status Public on Dec 13, 2007
Title pDC medium 1h, biological rep1
Sample type RNA
 
Source name pDC cultured in medium for 1h
Organism Mus musculus
Characteristics pDC isolated from spleen of Flt-3L-treated DPEGFPxRag1-/- mice
Treatment protocol pDC were sorted from spleens of Flt-3L-treated DPExRag1-/- mice and cultured at 1x106/ml for 1h in complete media (RPMI supplemented with 10% heat-inactivated FBS (Valley Biomedical, Inc.), Penicillin/Streptomycin (Invitrogen), 10mM HEPES (Invitrogen), 2mM L-Glutamine (Invitrogen), 10mM pyruvate (Invitrogen), 50µM 2-mercaptoethanol (Sigma).
Growth protocol DPEGFPxRag1-/- were injected 12-14 days prior to sort with 2x10^6 B16F10-Flt-3L cells, which leads to expansion of immature pDCs in spleens of mice
Extracted molecule total RNA
Extraction protocol isolation of total RNA was performed using the Rneasy Micro Kit according to manufacturer's instructions (Qiagen)
Label biotin
Label protocol 5ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporates the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP using the Enzo High-Yield amplification kit.
 
Hybridization protocol The cRNA products were fragmented to 200 nucleotides or less, heated at 99oC for 5 min and hybridized for 16 h at 45oC to GeneChip microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
Scan protocol The GeneChip 3000 scanner was used to collect fluorescence signal after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.
Description Gene expression data from plasmacytoid dendritic cells at baseline (medium 1h)
Data processing Data were processed using Affymetrix GCOS v1.4 software and probe intensity files (.cel files) were further analyzed using the GeneSpring v7.0 software (Silicon Genetics). GCRMA algorithm was used to summerize and normalize data.
 
Submission date May 17, 2007
Last update date Aug 28, 2018
Contact name Amaya I Wolf
E-mail(s) aiwolf@wistar.org
Organization name Wistar Institute
Street address 3601 Spruce street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL1261
Series (1)
GSE7831 Expression data from immature pDC and pDC activated with CpG 1826 and influenza virus PR8
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE GCRMA (not log-transformed)

Data table
ID_REF VALUE
1415670_at 735.3349
1415671_at 1188.1044
1415672_at 1907.0845
1415673_at 211.20113
1415674_a_at 436.05872
1415675_at 270.84424
1415676_a_at 1658.362
1415677_at 129.40802
1415678_at 435.76752
1415679_at 1830.8944
1415680_at 499.9805
1415681_at 431.116
1415682_at 97.11842
1415683_at 2171.2612
1415684_at 278.89557
1415685_at 162.66672
1415686_at 642.0642
1415687_a_at 14235.983
1415688_at 838.9171
1415689_s_at 123.576355

Total number of rows: 45101

Table truncated, full table size 925 Kbytes.




Supplementary file Size Download File type/resource
GSM190131.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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