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Sample GSM356607 Query DataSets for GSM356607
Status Public on May 11, 2009
Title Treg_culture_CD4+CD25-RA-_rep1
Sample type RNA
 
Source name Treg expansion culture
Organism Homo sapiens
Characteristics Treg culture CD4+CD25-RA-
Treatment protocol Treg and Tconv cell FACS sorting and expansion culture was performed as previously described by Hoffmann et al. 2004 (Blood. Aug 1;104(3):895-903). Cell-culture was performed according to Hoffmann et al. 2006 (Blood. Dec 15;108(13):4260-7).
Growth protocol Treg and Tconv cell isolation and expansion culture was performed as previously described by Hoffmann et al. 2004 (Blood. Aug 1;104(3):895-903). Cell-culture was performed according to Hoffmann et al. 2006 (Blood. Dec 15;108(13):4260-7).
Extracted molecule total RNA
Extraction protocol Total cellular RNA of the different cell types was isolated using the RNeasy Kit (Qiagen). RNA concentration was measured with a ND-1000 Spectrophotometer (NanoDrop, Thermo Fisher Scientific) and quality was controlled on agarose gels or using the Agilent Bioanalyzer.
Label Cy3
Label protocol Labeling and hybridization were performed using the Agilent Gene Expression system according to the manufacturer’s instructions. In brief, 200 ng to 1000 ng of high-quality RNA were amplified and Cyanine 3-CTP labeled with the One Color Low RNA Input Linear Amplification Kit (Agilent). Labeling efficiency was controlled using the NanoDrop spectrophotometer.
 
Hybridization protocol Samples were hybridized using a stringent protocol according to the manufacture's instruction. 1.65 µg labeled cRNA was supplemented with 11 µl Agilent 10x blocking agent, 2.2 µl Agilent 25x fragmentation buffer and nuclease-free water up to 55 µl final volumen. The sample was incubated at 60°C for 30 minutes, supplemented with 55 µl 2x hybridisation buffer and 100 µl of the mix was hybridisized for 16h at 65°C using an SureHyb chamber and an Agilent hybridization oven. Arrays were disassembled and washed for 1 minute in Agilent gene Expression (GE) wash buffer 1 followed by washing 1 minute in prewarmed (37°C) GE wash buffer 2.
Scan protocol Images were scanned immediately after washing using a DNA microarray scanner (Agilent) at 5 µm resolution.
Description gender: male
Data processing Data was processed using Feature Extraction Software (Agilent) and further analyzed using GeneSpring GX software version 7.
 
Submission date Dec 30, 2008
Last update date May 11, 2009
Contact name Christian Schmidl
E-mail(s) christian.schmidl@klinik.uni-regensburg.de
Organization name Rengensburg Center for Interventional Immunology
Lab Schmidl Lab
Street address Franz-Josef-Strauss-Allee 11
City Regensburg
ZIP/Postal code 93053
Country Germany
 
Platform ID GPL6480
Series (2)
GSE14232 Transcriptome analysis of freshly sorted and expanded regulatory and conventional T cells
GSE14281 Regulatory and conventional T-cells

Data table header descriptions
ID_REF
VALUE normalized log2 values: standard agilent feature extraction protocol 'GE1-v5_95_Feb07', polynomial datafit with a multiplicative detrendDegree of 4.

Data table
ID_REF VALUE
A_23_P100001 0.51067364
A_23_P100011 0.007852472
A_23_P100022 -1.3197739
A_23_P100056 -1.5249652
A_23_P100074 0.6332772
A_23_P100092 0.40797552
A_23_P100103 0.18816625
A_23_P100111 0.005783348
A_23_P100127 3.7980459
A_23_P100133 0.26241648
A_23_P100141 -0.36270517
A_23_P100156 0.5595323
A_23_P100177 -1.3344002
A_23_P100189 -1.3704965
A_23_P100196 0.44250238
A_23_P100203 0.42777792
A_23_P100220 -0.29800165
A_23_P100240 -1.6313378
A_23_P10025 0.20591731
A_23_P100263 -0.7423225

Total number of rows: 41046

Table truncated, full table size 947 Kbytes.




Supplementary file Size Download File type/resource
GSM356607.txt.gz 7.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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