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Sample GSM340384 Query DataSets for GSM340384
Status Public on Sep 22, 2009
Title m1_Tnaive
Sample type RNA
 
Source name Sorted CD4+ T cells, naïve
Organism Mus musculus
Characteristics Strain: C57BL/6
Gender: male
Age: 15 weeks
Tissue: pooled spleen and lymph nodes
Treatment protocol Sorted lymphocytes.
Growth protocol Primary cells.
Extracted molecule total RNA
Extraction protocol Total RNA was purified with the RNEasy mini kit (Qiagen) with on-column DNAse treatment according to manufacturer's instructions. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto).
Label Cy3
Label protocol RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturer’s protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE).
 
Hybridization protocol Equal amounts of Cy3-labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol (Agilent).
Scan protocol Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent).
Description Amplified total RNA was hybridized to Agilent 4X44k arrays.
Sample 6
Data processing This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003). This procedure was carried out using the Bioconductor package limma (http://www.bioconductor.org). No background subtraction was performed.
 
Submission date Nov 06, 2008
Last update date Sep 22, 2009
Contact name Mark Klinger
E-mail(s) mark.klinger@ucsf.edu
Phone 415-502-5432
Organization name University of California, San Francisco
Department Microbiology and Immunology
Lab Nigel Killeen
Street address 513 Parnassus Avenue, Box0414
City San Francisco
State/province CA
ZIP/Postal code 94122
Country USA
 
Platform ID GPL7202
Series (1)
GSE13502 Gene expression analysis of Ox40-cre/ROSA-YFP CD4+ T cell subsets

Data table header descriptions
ID_REF
VALUE Normalized log2-transformed signal intensities

Data table
ID_REF VALUE
A_52_P616356 5.46
A_52_P580582 6.95
A_52_P403405 6.02
A_52_P819156 5.71
A_51_P331831 13.62
A_51_P430630 5.53
A_52_P502357 5.41
A_52_P299964 8.60
A_51_P356389 6.42
A_52_P684402 8.75
A_51_P414208 5.56
A_51_P280918 8.39
A_52_P613688 10.35
A_52_P258194 6.15
A_52_P229271 7.88
A_52_P214630 5.46
A_52_P579519 6.47
A_52_P979997 5.53
A_52_P453864 5.49
A_52_P655842 5.82

Total number of rows: 41174

Table truncated, full table size 732 Kbytes.




Supplementary file Size Download File type/resource
GSM340384.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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