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Sample GSM870394 Query DataSets for GSM870394
Status Public on Feb 04, 2012
Title C-Ig_day3_mouse2
Sample type RNA
 
Source name naive CD4+ T cells, control, day 3
Organism Mus musculus
Characteristics strain: C57BL6/NCrl
tissue: inguinal, axillary and brachial lymph nodes and spleen
cell type: naive CD4+ T cells
stimulus: control Ig
timepoint: day 3
mouse: 2
Treatment protocol Mouse CD62L+CD44-CD25-DX5-CD4+ T cells were stimulated with plate-bound anti-CD3e (10ug/ml), soluble anti-CD28 (1ug/ml) in the presence of plate-bound Delta4-Ig or control Ig (each at 5ug/ml).
Growth protocol Cells were grown in IMDM with 10% FCS, 2mM GlutaMAX (Invitrogen), 100 U/ml penicillin (Invitrogen), 100 μg/ml streptomycin (Invitrogen) and 50μM β-Mercaptoethanol.
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol followed by purification with RNeasy columns.
Label biotin
Label protocol Total RNA samples were amplified and biotinylated using the Ambion Illumina TotalPrep RNA Amplification Kit.
 
Hybridization protocol Whole Genome Expression with IntelliHyb Seal.
Scan protocol Standard Illumina scanning protocol using the Illumina HiScan.
Description 5773678088_E
Data processing Array data were extracted using Illumina's GenomeStudio software. Normalization and statistical analyses were carried out using Bioconductor packages in the statistical software package R. We performed normexp-by-control background correction, quantile normalization and log2 transformation on the Illumina sample and control probe profiles using the limma package. Probes that were not expressed (detection p-value < 0.05) on any of the arrays were filtered out. The arrayQualityMetrics package was used to ensure that the microarray data was of good quality. The normalized intensities of technical replicate arrays were averaged. Differential expression between the DLL4-Fc activated and control-Ig samples was assessed via a paired moderated t-test using the limma package.
 
Submission date Feb 03, 2012
Last update date Feb 04, 2012
Contact name Derk Amsen
E-mail(s) D.Amsen@amc.nl
Phone 0031205664977
Organization name AMC
Street address Meibergdreef 9
City Amsterdam
ZIP/Postal code 1105AZ
Country Netherlands
 
Platform ID GPL6885
Series (1)
GSE35547 Notch controls the magnitude of CD4+ T cell responses by promoting cellular longevity

Data table header descriptions
ID_REF
VALUE Log2 normalized signal intensity
Detection Pval 5773678088_E

Data table
ID_REF VALUE Detection Pval 5773678088_E
ILMN_2896528 11.01024072 0
ILMN_2721178 7.593548187 0
ILMN_3033922 7.685880868 0
ILMN_3092673 10.71561411 0
ILMN_2816356 5.626000098 0.03634085
ILMN_2808939 11.24463184 0
ILMN_2634564 9.570872827 0
ILMN_2737647 4.873263418 0.4335839
ILMN_2734484 8.732581605 0
ILMN_2952292 6.115877475 0.005012531
ILMN_2699078 4.478768245 0.9962406
ILMN_1213681 8.544579958 0
ILMN_2735413 4.719493315 0.6954888
ILMN_2735415 4.781947345 0.566416
ILMN_2891688 10.72941264 0
ILMN_2637698 10.33217333 0
ILMN_2674228 8.785585946 0
ILMN_2601546 5.328225482 0.09774436
ILMN_1230831 5.32359158 0.0989975
ILMN_2848071 5.325321636 0.0989975

Total number of rows: 25697

Table truncated, full table size 813 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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