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Sample GSM1012121 Query DataSets for GSM1012121
Status Public on Nov 09, 2012
Title CD4 T cells, WT, biological rep1
Sample type RNA
 
Source name CD4+ T cells from spleen and lymph nodes
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: WT
cell type: CD4+ T cells [activated]
Treatment protocol CD4 T cells were activated upon culture in the presence of 1ug/mL CD3 and CD28 antibodies in 20U/mL IL-2 for 3 days at 37oC, 5% CO2.
Growth protocol CD4 T cells were isolated using CD4 dynabeads (Invitrogen) according to the manufacture's instructions.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
 
Hybridization protocol Performed according to the manufacturer's instructions.
Scan protocol Performed according to the manufacturer's instructions.
Description Gene expression data from WT activated CD4 T cell
Data processing Data was normalized with robust multi-array analysis (RMA) normalization using the 'affy' Bioconductor package in R. Gene level expression was summarized from mean probe set level intensities using Mouse430A 2 Annotations, Release 31. log2(gene expression change) was calculated using the WT expression level as reference. All log gene expression changes were centered with mean log2(expression change) and normalized to have unit variance. This normalization resulted in a simple Z-transformation of log2(gene expression change).
 
Submission date Oct 01, 2012
Last update date Nov 09, 2012
Contact name Aly Azeem Khan
Organization name University of Chicago
Street address 6045 S. Kenwood Ave.
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL8321
Series (2)
GSE41241 Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting [mRNA expression data]
GSE41288 Transcriptome-wide miR-155 binding map reveals widespread non-canonical microRNA targeting

Data table header descriptions
ID_REF
VALUE RMA calculated signal intensity

Data table
ID_REF VALUE
1415670_at 9.489981191
1415671_at 9.829017844
1415672_at 11.34818115
1415673_at 10.30547332
1415674_a_at 10.00102521
1415675_at 9.087693598
1415676_a_at 11.5143244
1415677_at 9.041311917
1415678_at 9.338956694
1415679_at 11.1427638
1415680_at 9.921597718
1415681_at 9.86631352
1415682_at 8.6382785
1415683_at 11.14213885
1415684_at 8.138119744
1415685_at 9.087713802
1415686_at 8.569693907
1415687_a_at 9.72032267
1415688_at 9.853431003
1415689_s_at 8.951891539

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM1012121_GL_wt_091019_Mouse430A_2.CEL.gz 2.0 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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