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Sample GSM880641 Query DataSets for GSM880641
Status Public on Apr 03, 2012
Title LPS-StimB_+fl_rep2
Sample type RNA
Source name LPS-StimB_+fl_rep2
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: spleen
cell type: B cell
genotype/variation: Ebf1+/flRERTCre (heterozygote control)
tamoxifen-citrate treatment: yes
lps stimulation: yes
Treatment protocol Ebf1 fl/fl-RERT-Cre mice and heterozygote control animals were treated with 3mg Tamoxifen-Citrate on four consecutive days and were sacrificed for analysis on the tenth day after the start of the experiment. B220+AA4.1- and B220+AA4.1-CD21lo splenic B cells were sorted from Tamoxifen-treated Ebf1+/flRERTCre and Ebf1fl/flRERTCre mice in triplicates, and total RNA was extracted.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from sorted mouse splenic B cells using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Quick Amp Labeling Kit (One-Colo)r and RNA Spike-In Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug 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 Human Genome Oligo Microarrays (G4112A) 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 4x44k 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 conditional deletion of Ebf1 following LPS-stimulation
Sample name: p2051LPS
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Feb 24, 2012
Last update date Apr 03, 2012
Contact name Soeren Boller
Phone 0049(0)7615108755
Organization name Max Planck Institute of Immunobiology and Epigenetics
Department Cellular & Molecular Immunology
Lab Grosschedl lab
Street address Stuebeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
Platform ID GPL7202
Series (1)
GSE36061 Microarray analysis to identify genes that are differentially expressed in resting and in LPS-activated splenic B cells of Ebf1+/fl-RERTCre and Ebf1fl/fl-RERTCre mice

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_51_P100021 2.92819
A_51_P100034 50996.19000
A_51_P100052 2.72838
A_51_P100063 22.86596
A_51_P100084 25.94601
A_51_P100099 661.12115
A_51_P100155 10254.08800
A_51_P100174 376.14005
A_51_P100181 470.66765
A_51_P100218 2.36196
A_51_P100227 6783.77950
A_51_P100238 2.54521
A_51_P100246 3533.90700
A_51_P100289 3572.03700
A_51_P100298 11.76472
A_51_P100309 2.86767
A_51_P100327 3061.30800
A_51_P100347 2.91695
A_51_P100379 12.69566
A_51_P100428 3.18929

Total number of rows: 41250

Table truncated, full table size 893 Kbytes.

Supplementary file Size Download File type/resource
GSM880641_US45103052_251486815586_S01_GE1-v5_95_Feb07_1_4.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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