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Sample GSM433809 Query DataSets for GSM433809
Status Public on Jul 29, 2009
Title CD8+ T-cells_healty control_donor3
Sample type RNA
 
Source name CD8+ T-cells purified with immunomagnetic beads from the pheripheral blood lymphocytes of the healthy control C3
Organism Homo sapiens
Characteristics tissue: peripheral blood
cell type: CD8+ T-cells
treatment type: normal donor
Treatment protocol Mononuclear cells from peripheral blood were isolated by density gradient centrifugation on Ficoll-Hypaque (Nycomed Pharma A/S). Thereafter, the CD4 and CD8 T-cell subsets were purified with positive selection by immunomagnetic technique using anti-CD4 and anti-CD8 antibody-coated microbeads (Miltenyi Biotec). Two steps of purification were performed to increase the purity to greater than 98%-99%. RNA was directly extracted from cell pellets.
Growth protocol Heparinized blood samples were obtained from patients with ADA-SCID and age-matched healthy controls after parents of patients gave informed consent following standard ethical procedures and with the approval of the Institutional Ethical Committee and immediately processed for mononuclear cell purification.
Extracted molecule total RNA
Extraction protocol RNA was isolated from 1x10^6 cells using Eurozol reagent (Euroclone S.p.A., Italy) according to the manufacturer's instructions. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration, purity, and integrity of RNA samples using Agilent 2100 Bioanalyzer.
Label biotin
Label protocol The one-cycle target labeling assay was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). Briefly, biotin-labeled target synthesis was performed, starting from 5 µg of total cellular RNA, according to the protocol supplied by the manufacturer (Affymetrix, Santa Clara, CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration, quality and to optimize the cRNA fragmentation.
 
Hybridization protocol Affymetrix Human HG-U133A GeneChip array hybridization and staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara,CA). The fragmented cRNA were hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip scanner 3000 enabled for High-Resolution Scanning.
Description Gene expression data from CD8+ T-cells isolated from healty control
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Data analysis was performed using GeneSpring® GX 7.3.1 version (Agilent Technologies).
 
Submission date Jul 27, 2009
Last update date Sep 01, 2016
Contact name Alessandro Aiuti
E-mail(s) a.aiuti@hsr.it
Phone +39-02-26434435
Fax +39-02-26434668
Organization name San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET)
Street address via olgettina 58
City Milan
ZIP/Postal code 20132
Country Italy
 
Platform ID GPL96
Series (1)
GSE17354 Gene expression profiling of CD4+ and CD8+ T-cells from gene therapy treated ADA patients and from healthy controls
Relations
Reanalyzed by GSE86363

Data table header descriptions
ID_REF
VALUE MAS5 normalized signal intensity
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 595.299 P 0.000753643
AFFX-BioB-M_at 906.019 P 5.16732e-05
AFFX-BioB-3_at 470.557 P 4.42873e-05
AFFX-BioC-5_at 1676.48 P 6.02111e-05
AFFX-BioC-3_at 1750.92 P 4.42873e-05
AFFX-BioDn-5_at 3243.6 P 4.42873e-05
AFFX-BioDn-3_at 9776.41 P 5.16732e-05
AFFX-CreX-5_at 11549.1 P 4.42873e-05
AFFX-CreX-3_at 21049.7 P 5.16732e-05
AFFX-DapX-5_at 23.7222 A 0.262827
AFFX-DapX-M_at 44.6011 A 0.354453
AFFX-DapX-3_at 5.09218 A 0.916408
AFFX-LysX-5_at 1.61993 A 0.945787
AFFX-LysX-M_at 42.629 A 0.631562
AFFX-LysX-3_at 37.1173 A 0.195266
AFFX-PheX-5_at 4.91675 A 0.963431
AFFX-PheX-M_at 7.63863 A 0.852061
AFFX-PheX-3_at 57.4769 A 0.368438
AFFX-ThrX-5_at 11.5802 A 0.910522
AFFX-ThrX-M_at 43.6633 A 0.250796

Total number of rows: 22283

Table truncated, full table size 666 Kbytes.




Supplementary file Size Download File type/resource
GSM433809.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM433809.CHP.gz 204.0 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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