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Sample GSM1012120 Query DataSets for GSM1012120
Status Public on Nov 09, 2012
Title CD4 T cells, 155KO, biological rep3
Sample type RNA
 
Source name CD4+ T cells from spleen and lymph nodes
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: miR-155 KO
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 155KO 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 9.365361755
1415671_at 10.28217453
1415672_at 11.37368078
1415673_at 9.132545886
1415674_a_at 10.10317134
1415675_at 9.015492995
1415676_a_at 10.70533968
1415677_at 10.24278408
1415678_at 9.53215656
1415679_at 11.62683572
1415680_at 9.622075739
1415681_at 10.03135425
1415682_at 8.060566857
1415683_at 10.87679734
1415684_at 7.962323461
1415685_at 8.79743788
1415686_at 8.525730335
1415687_a_at 10.50236178
1415688_at 9.716401118
1415689_s_at 9.154210682

Total number of rows: 22690

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM1012120_GL_mir155KO_091210_Mouse430A_2.CEL.gz 1.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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