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Sample GSM1057800 Query DataSets for GSM1057800
Status Public on Sep 30, 2013
Title CD86 positive DCs LLC rep1
Sample type RNA
Source name Axillary lymph nodes, LLC, replicate1
Organism Mus musculus
Characteristics strain: C57/BL6N
gender: female
tissue: Tumor draining lymph nodes
cell type: CD86 positive DCs
treatment: LLC
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol .
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray 4x44K v2 (Probe Name version) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression after 2days in LLC cell injected-mouse tumor draining lymph nodes
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Dec 27, 2012
Last update date Sep 30, 2013
Contact name kenzaburo tani
Organization name Kyushu University
Department Medical Institute of Bioregulation
Lab Department of Molecular Genetics
Street address 3-1-1 Maidashi
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
Platform ID GPL11202
Series (1)
GSE43169 Gene expression profiling of mature dendritic cells from mice s. c. treated with GM-CSF-gene transduced LLC cells (LLC/SeV/GM) or control cells (LLC, LLC/SeV/GFP)

Data table header descriptions
VALUE quantile normalized signal (non-log scaled)

Data table
ID_REF VALUE Detection
A_51_P100034 3719.337 P
A_51_P100174 598.8052161 P
A_51_P100208 2.687156667 A
A_51_P100289 1115.1659 P
A_51_P100298 13.62284478 P
A_51_P100309 2.698816302 A
A_51_P100327 1272.856032 P
A_51_P100347 56.28604333 P
A_51_P100519 2.531197667 A
A_51_P100537 11.02531337 P
A_51_P100573 436.8978721 P
A_51_P100624 2.436217 A
A_51_P100625 5.239539843 A
A_51_P100768 12.50067333 A
A_51_P100776 133.3735928 P
A_51_P100787 1420.015367 P
A_51_P100828 957.3158489 P
A_51_P100852 488.9496899 P
A_51_P100991 36.59314667 P
A_51_P100997 37.63974907 P

Total number of rows: 39429

Table truncated, full table size 1024 Kbytes.

Supplementary file Size Download File type/resource
GSM1057800_US22502696_252665510128_S01_GE1-v5_95_Feb07_1_1.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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