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Sample GSM723852 Query DataSets for GSM723852
Status Public on Nov 23, 2012
Title Human_Teff_T360min
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.he@lih.lu
Organization name Luxembourg Institute of Health
Department 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 553.64 P 6.02111e-05
AFFX-BioB-M_at 880.974 P 4.42873e-05
AFFX-BioB-3_at 606.85 P 0.000146581
AFFX-BioC-5_at 1463.76 P 8.14279e-05
AFFX-BioC-3_at 2144.91 P 4.42873e-05
AFFX-BioDn-5_at 3620.22 P 5.16732e-05
AFFX-BioDn-3_at 4787.54 P 4.42873e-05
AFFX-CreX-5_at 21278.6 P 4.42873e-05
AFFX-CreX-3_at 21204.4 P 4.42873e-05
AFFX-DapX-5_at 2.26845 A 0.574038
AFFX-DapX-M_at 28.6138 A 0.262827
AFFX-DapX-3_at 4.42053 A 0.712274
AFFX-LysX-5_at 4.33767 A 0.699394
AFFX-LysX-M_at 18.0579 A 0.631562
AFFX-LysX-3_at 3.77451 A 0.645547
AFFX-PheX-5_at 4.39735 A 0.737173
AFFX-PheX-M_at 6.01761 A 0.559354
AFFX-PheX-3_at 34.135 A 0.354453
AFFX-ThrX-5_at 23.4505 A 0.227636
AFFX-ThrX-M_at 9.08895 A 0.544587

Total number of rows: 54675

Table truncated, full table size 1614 Kbytes.




Supplementary file Size Download File type/resource
GSM723852.CEL.gz 4.8 Mb (ftp)(http) CEL
GSM723852.CHP.gz 302.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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