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Sample GSM723863 Query DataSets for GSM723863
Status Public on Nov 23, 2012
Title Human_Teff_repeated_T200min
Sample type RNA
 
Source name human peripheral blood of healthy donor
Organism Homo sapiens
Characteristics cell type: sorted human Teff cells (CD4+CD25-) stimulated by anti-CD3/anti-CD28 Dynal beads/IL2
Treatment protocol Human Tregs or Teffs were mixed with anti-CD3/anti-CD28-coated Dynabeads (Invitrogen) at a ratio of 1:1 and with 100 U/ml of IL2 (Proleukin, Novartis) and were distributed with 4x106 cells into 1.5 ml microtubes (Eppendorf) for each time point. Before the cells were cultured at 37°C, they were first stored at 4°C to allow cells and beads to settle properly. Samples were taken every 20 min during the first six hours following stimulation, except for TeffGARP and TeffGFP cells, which were measured at time points 0, 100 and 360 min. The cells were centrifuged, and the cell pellets were lysed in RLT buffer (Qiagen) and immediately stored at -70°C.
Growth protocol taken from donors, sorted, expanded ex vivo and stimulated
Extracted molecule total RNA
Extraction protocol RNeasy
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Affymetrix GCS 3000.
Description transcriptomic data to construct a dynamic functional network of human regulatory T cell genes
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.
 
Submission date May 13, 2011
Last update date Sep 01, 2016
Contact name Feng Q. Hefeng
E-mail(s) feng.hefeng@lih.lu
Organization name Luxembourg Institute of Health
Department Department of Infection and Immunity
Street address 29, rue Henri Koch
City Esch-sur-Alzette
ZIP/Postal code 4354
Country Luxembourg
 
Platform ID GPL570
Series (1)
GSE11292 High-time-resolution dynamic analysis of human regulatory T cell (Treg) / CD4+ T-effector cell (Teff) activation
Relations
Reanalyzed by GSE86362

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 314.277 P 0.000296708
AFFX-BioB-M_at 521.692 P 4.42873e-05
AFFX-BioB-3_at 292.742 P 5.16732e-05
AFFX-BioC-5_at 868.489 P 5.16732e-05
AFFX-BioC-3_at 1390.31 P 4.42873e-05
AFFX-BioDn-5_at 2734.31 P 4.42873e-05
AFFX-BioDn-3_at 4291.46 P 5.16732e-05
AFFX-CreX-5_at 13299.6 P 5.16732e-05
AFFX-CreX-3_at 13608.2 P 4.42873e-05
AFFX-DapX-5_at 1.46927 A 0.876428
AFFX-DapX-M_at 7.16462 A 0.659339
AFFX-DapX-3_at 3.2607 A 0.737173
AFFX-LysX-5_at 8.21337 A 0.425962
AFFX-LysX-M_at 2.36907 A 0.455413
AFFX-LysX-3_at 24.9386 P 0.0336653
AFFX-PheX-5_at 1.80542 A 0.916408
AFFX-PheX-M_at 0.944355 A 0.987453
AFFX-PheX-3_at 22.7983 A 0.455409
AFFX-ThrX-5_at 3.9079 A 0.686277
AFFX-ThrX-M_at 12.3383 A 0.262827

Total number of rows: 54675

Table truncated, full table size 1626 Kbytes.




Supplementary file Size Download File type/resource
GSM723863.CEL.gz 4.8 Mb (ftp)(http) CEL
GSM723863.CHP.gz 301.7 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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