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Sample GSM85336 Query DataSets for GSM85336
Status Public on Jan 11, 2006
Title IKDC-2_U74B
Sample type RNA
 
Source name Mouse Spleen interferon producing killer-dendritic cells (IKDCs)
Organism Mus musculus
Characteristics BALB/c, female, 6-8 weeks old, spleen, FACS-sorted IKDC, untreated samples (Ex vivo)
Extracted molecule total RNA
Extraction protocol Rwe isolated total RNA using the Trizol Reagent (Invitrogen) then purified using the RNeasy Mini Kit (Qiagen). RNA from spleen cDCs, PDCs and IKDCs were processed using the two-round RNA amplification protocol described by Affymetrix (Affymetrix GeneChip Expression Manual Small Sample_2) (http://www.affymetrix.com/support/technical/technotes/smallv2_technote.pdf).
Label biotinylation then SA-PE as readout
Label protocol We label anti-sense cRNA using BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc).
 
Hybridization protocol hybridized 10 μg of total fragmented cRNA to the Affymetrix murine genome GeneChip array U74 set for 16 h at 45 oC with constant rotation (60 rpm).
Scan protocol Fluorescence was detected using the Affymetrix- GS3000 GeneArray Scanner
Description image analysis of each GeneChip was done through the GeneChip Operating System software from Affymetrix (GCOS1.1.1), using the standard default settings. We used global scaling for comparisons between different chips, scaling all probe sets to a user defined target intensity (TGT) of 150. To ascertain the quality control of the total RNA from each sample, we used the Agilent Bioanalyzer Lab on a Chip technology, and confirmed the rRNA ratios and clean run patterns of each sample. Likewise, this technology is used to confirm the quality of the RNA in the form of cRNA and fragmented cRNA. To assess QC of the hybridization, GeneChip image, and comparison between chips, we confirmed the following parameters: scaling factor values within comparable range; low background values (between 20 and 100); high percentage of present calls (between 25 and 50); consistent 3’/5’ ratios of Gapdh as representation of housekeeping genes, and presence or absence of Bio B and C as internal spike controls.
Data processing MAS5.0
 
Submission date Nov 28, 2005
Last update date Jan 11, 2006
Contact name Drew Pardoll
E-mail(s) dmpardol@jhmi.edu
Phone 410 955-1500
Fax 410 955-1500
Organization name Drew Pardoll
Street address orleans st
City baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL82
Series (1)
GSE3691 Gene profiling analysis of mouse splenic DC subpopulations

Data table header descriptions
ID_REF
VALUE Absolute Fluorescence Value; transformated using MAS5
ABS_CALL Detection level

Data table
ID_REF VALUE ABS_CALL
AFFX-YEL024w/RIP1_at 83 A
AFFX-YEL021w/URA3_at 62.3 A
AFFX-YEL018w/_at 7.6 A
AFFX-YEL002c/WBP1_at 24 A
AFFX-TrpnX-M_at 4.7 A
AFFX-TrpnX-5_at 69.7 A
AFFX-TrpnX-3_at 22.8 A
AFFX-TransRecMur/X57349_M_at 4.3 A
AFFX-TransRecMur/X57349_5_at 76.4 A
AFFX-TransRecMur/X57349_3_at 65.8 A
AFFX-ThrX-M_at 10.8 A
AFFX-ThrX-5_at 8.2 A
AFFX-ThrX-3_at 12.7 A
AFFX-PyruCarbMur/L09192_MB_at 28.3 A
AFFX-PyruCarbMur/L09192_MA_at 49.3 A
AFFX-PyruCarbMur/L09192_5_at 71.8 A
AFFX-PyruCarbMur/L09192_3_at 145.2 A
AFFX-PheX-M_at 5.8 A
AFFX-PheX-5_at 3.8 A
AFFX-PheX-3_at 19.1 A

Total number of rows: 12477

Table truncated, full table size 213 Kbytes.




Supplementary data files not provided

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