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Sample GSM1036854 Query DataSets for GSM1036854
Status Public on Dec 10, 2012
Title THPOK+CD8a-_2_TR
Sample type RNA
 
Source name TR CD4 T-cell sIEL
Organism Mus musculus
Characteristics strain: B6-ThPOK-GFP reporter
age: 10-12 weeks
tissue: small intestine
cell type: CD4 intraepithelial T lymphocytes
cell sub-type: THPOK+CD8a-
Extracted molecule total RNA
Extraction protocol RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp nano kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description replicate 2
Illumina.SingleColor.MouseRef-8_V2_0_R2_11278551_A
Data processing Gene SpringGX software version 11.5.1 was used to do percentile shift normalization. 1.Transforms the signal values to the log base 2. 2.Arranges the log transformed signal values in increasing order. 3.Computes the rank of the required percentile (Pth percentile)The data were normalised using quantile normalisation with IlluminaGUI in R
 
Submission date Nov 14, 2012
Last update date Jan 31, 2013
Contact name Bernardo Reis
E-mail(s) breis@rockefeller.edu
Organization name Rockefeller University
Street address 1234 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL6885
Series (1)
GSE42277 Transcriptional Reprogramming of Mature CD4 T helper Cells generates distinct MHC class II restricted Cytotoxic T Lymphocytes

Data table header descriptions
ID_REF
VALUE log2 percentile shift normalized signal intensity

Data table
ID_REF VALUE
ILMN_2607609 -0.009809017
ILMN_1238674 -0.22180843
ILMN_3062534 -0.005406857
ILMN_3140158 -0.08188248
ILMN_2674533 0
ILMN_2680307 -0.11471176
ILMN_2935307 0.25689745
ILMN_1215893 -0.021347046
ILMN_2910106 0.122496605
ILMN_2732092 -0.17839146
ILMN_2603725 -0.35243893
ILMN_2664884 -0.27204037
ILMN_3003575 0
ILMN_1229397 0
ILMN_1225873 0.06786108
ILMN_2899591 -0.13542843
ILMN_2658355 -0.034413338
ILMN_2682763 0
ILMN_2521511 -0.022103786
ILMN_2691286 0

Total number of rows: 25697

Table truncated, full table size 536 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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