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Sample GSM999799 Query DataSets for GSM999799
Status Public on Sep 13, 2012
Title IRF4-control_Th17_cells_42hr_rep3
Sample type RNA
 
Channel 1
Source name IRF4-control_Th17_cells_42hr
Organism Mus musculus
Characteristics strain background: C57BL/6J
genotype/variation: IRF4 +/-
tissue: spleen
cell type: Naïve CD4+, CD62L hi, CD25 - T cells
differentiation condition: Th17
timepoint: 42 hrs
Growth protocol Naïve T- cells isolated from spleen were cultured on a-CD3 coated plates with 2.5 mg/ml a-CD28, 20 ng/ml IL-6, 20 ng/ml IL-23, 1 ng/ml hTGFb, 10 mg/ml a-IL4 and 10 mg/ml a-IFNg for 42 hrs
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol and including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.
Label Cy5
Label protocol Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).
 
Channel 2
Source name Stratagene's Universal Mouse Reference RNA (UMRR) cat # 740100
Organism Mus musculus
Characteristics sample type: Reference: pooled RNA from 11 tissues
Growth protocol Naïve T- cells isolated from spleen were cultured on a-CD3 coated plates with 2.5 mg/ml a-CD28, 20 ng/ml IL-6, 20 ng/ml IL-23, 1 ng/ml hTGFb, 10 mg/ml a-IL4 and 10 mg/ml a-IFNg for 42 hrs
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Qiagen RNeasy kit following manufacturer's protocol and including on-column DNase-digestion. RNA was quantified using UV-spec Nanodrop and then profiled on Agilent Bioanalyzer.
Label Cy3
Label protocol Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).
 
 
Hybridization protocol Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.
Scan protocol Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.
Description IRF4+-/- rep3
Data processing The matrix data table was created by first log transforming the raw data and then filtering out all probes that showed a standard deviation of <0.25 across all samples as well as probes that do not have an associated entrez id. Agilent Feature Extraction software version 10.7 was used for background subtraction and LOWESS normalization.
The normalized data was then analyzed further using Partek Genomic Suite Version 6.6 by performing a 1-way ANOVA test between the IRF4 KO vs IRF4 Het samples. Data for the probes which showed a > 2-fold change (up or down) with a p-value <0.05 is presented in the 'Analyzed_data.txt' file (available on Series records). It is presented in ascending order of differential expression (Fold-Change) between the IRF4 KO vs IRF4 Het samples. The probeset ID, Gene Symbol, p-value of differential expression and Fold-Change between the IRF4 KO and IRF4 Het samples are indicated. Negative fold changes indicate down-regulation in IRF4 KO samples and positive fold changes indicate up-regulation.
 
Submission date Sep 10, 2012
Last update date Sep 13, 2012
Contact name Smita Agrawal
Organization name Genentech Inc.
Department Immunology
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platform ID GPL7202
Series (2)
GSE40483 A genomic regulatory element that directs assembly and function of immunespecific AP-1-IRF complexes
GSE40726 Transcriptional profiling of IRF4 -/- vs IRF4 +/- T-cells under Th17 polarizing conditions

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (Cy5/Cy3) representing test/reference

Data table
ID_REF VALUE
A_51_P195244 -1.65529
A_52_P221804 -0.580516
A_52_P155692 0.2551
A_51_P293015 -0.540947
A_51_P446510 -0.701632
A_52_P109232 0
A_52_P235102 -2.19959
A_51_P279712 -0.895771
A_51_P258098 -1.08963
A_52_P573543 0.320176
A_52_P339054 0.812323
A_52_P514306 0.802888
A_51_P384148 -3.06386
A_51_P391836 0.858056
A_51_P117015 1.81567
A_51_P162098 1.65875
A_52_P55732 -0.726309
A_51_P209118 -1.39967
A_51_P504735 0.722762
A_52_P511821 0.407297

Total number of rows: 22749

Table truncated, full table size 482 Kbytes.




Supplementary file Size Download File type/resource
GSM999799_Th17_IRF4_het3.txt.gz 4.3 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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