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Sample GSM160855 Query DataSets for GSM160855
Status Public on Oct 01, 2007
Title Unstimulated Circulating CD4+ T cells AGM_unstim_2
Sample type RNA
 
Source name unstimulated circulating CD4+ T cells
Organism Chlorocebus sabaeus
Characteristics African Green Monkey cells (chlorocebus sabaeus from Senegal).
Cells : CD4+ cells isolated from Peripheral Blood Mononuclear Cells (PBMC) consists of >95% of CD4+ T lymphocytes (CD3+ CD4+ cells).
Treatment protocol PBMC were isolated by Ficoll-Hypaque (Pharmacia Biotech) density gradient centrifugation. The CD4+ cell subset was further isolated using the MACS magnetic labeling system (Miltenyi Biotec, Cologne, Germany) according to instructions of the manufacturer.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from 3 to 10 x 10^6 cells by using the RNeasy® Mini extraction Kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions.
Label Chemiluminescence / DIG-UTP
Label protocol Digoxigenin-UTP labeled cRNA was generated and amplified from 0.8µg of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v2.0 according to the manufacturer’s protocol.
 
Hybridization protocol 15µg of the labeled cRNA were hybridized to the ABI Human Whole Genome Arrays v2.0 Array using the Applied Biosystems Chemiluminescence Detection Kit accordingly to the protocol.
Scan protocol Array processing, chemiluminescence detection, image acquisition, and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer following manufacturer’s protocol.
Description A pool of total RNA was prepared from enriched blood unstimulated CD4+ T lymphocytes isolated from 4 AGM. A unique sample was obtained and then divided to generate 4 aliquots used to hybridized 4 ABI microarrays with 4 distinct RNA input quantities.
Data processing Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software.
 
Submission date Feb 07, 2007
Last update date Aug 23, 2007
Contact name Beatrice JACQUELIN
E-mail(s) beajac@pasteur.fr
Organization name Institut Pasteur
Department Virologie
Lab Regulations des Infections Retrovirales
Street address 25 rue du Docteur Roux
City Paris cedex 15
ZIP/Postal code 75724
Country France
 
Platform ID GPL2986
Series (1)
GSE6982 Long Oligonucleotide Microarrays for African Green Monkey Gene Expression Profile Analysis

Data table header descriptions
ID_REF
VALUE Normalized signal
SIGNAL_RAW raw signal intensity
STDEV Estimated measurement uncertainty of Signal
S2N Signal to Noise ratio is equal to SIGNAL_RAW/STDEV
CV Coefficient of Variation of signal intensity based on error model built in the ABI image analysis software
FLAG quality flag of spot: a numeric code identifies conditions for each feature, less than 5000 is good

Data table
ID_REF VALUE SIGNAL_RAW STDEV S2N CV FLAG
100002 209.62 215648.91 1626.80 132.56 0.04 0
100003 0.12 136.49 136.49 -2.53 0.40 1
100027 0.12 142.74 142.74 -0.56 1.77 1
100036 0.27 307.61 307.61 0.22 4.49 1
100037 23.64 24317.21 1398.21 17.39 0.07 0
100039 14.51 16731.98 291.22 57.45 0.04 0
100044 0.21 239.81 239.81 -1.31 0.76 1
100045 0.26 265.99 265.99 0.92 1.09 1
100051 0.76 880.76 263.78 3.34 0.30 0
100052 0.14 145.24 145.24 0.70 1.44 1
100057 4.66 5368.11 308.46 17.40 0.07 0
100058 55.30 56888.48 613.65 92.71 0.04 0
100060 0.93 957.50 363.75 2.63 0.38 0
100062 1.78 1826.98 404.41 4.52 0.22 0
100064 0.23 235.35 198.62 1.18 0.84 0
100079 22.30 25715.06 447.46 57.47 0.04 0
100089 5.26 6062.81 394.12 15.38 0.07 0
100093 0.38 388.99 187.00 2.08 0.48 0
100095 1.18 1356.80 1356.80 -0.04 22.95 1
100100 14.98 17277.89 222.48 77.66 0.03 0

Total number of rows: 32878

Table truncated, full table size 1276 Kbytes.




Supplementary file Size Download File type/resource
GSM160855.txt.gz 3.3 Mb (ftp)(http) TXT

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