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Sample GSM152481 Query DataSets for GSM152481
Status Public on Dec 29, 2007
Title E59 00h_rep2
Sample type RNA
 
Channel 1
Source name T cells, 0 hour
Organism Homo sapiens
Characteristics primary T cells, donor 1
Biomaterial provider All Cells, Berkeley, CA
Treatment protocol No treatment
Growth protocol Grown in AIM V with 2% Human AB Serum, 37degC, 5% CO2
Extracted molecule total RNA
Extraction protocol Agilent RNA isolation mini-kit
Label Cy3
Label protocol Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)
 
Channel 2
Source name Human Thymus Total RNA
Organism Homo sapiens
Characteristics Human Thymus Total RNA
Biomaterial provider Ambion
Extracted molecule total RNA
Extraction protocol Extraction performed by the manufacturer
Label Cy5
Label protocol Agilent Low RNA Input Fluorescent Linear Amplification kit (v2.0) (reverse transcription with oligo-dT primers, in vitro transcription with direct incorporation of fluorescently labeled CTP analogs)
 
 
Hybridization protocol Followed Agilent 60-mer oligo microarray processing protocol v 4.1, using SSC wash protocol and forced nitrogen drying
Scan protocol Scanned using Agilent Microarray Scanner (G2565BA) at 10um resolution
Description primary T cell response to oxidative stress under the context of T-cell activaiton
Data processing Agilent Feature Extraction software (v.7.2) was used to assess spot quality and extract feature intensity statistics; duplicate spots were averaged; background-subtracted data were normalized using SNNLERM (Yang et al., PNAS 2003; 100:1122-1127)
 
Submission date Dec 21, 2006
Last update date Jan 03, 2007
Contact name Eleftherios Terry Papoutsakis
E-mail(s) papoutsakis@dbi.udel.edu
Organization name University of Delaware
Department Chemical Engineering
Street address 15 Innovation Way
City Newark
State/province DE
ZIP/Postal code 19711
Country USA
 
Platform ID GPL887
Series (1)
GSE6607 Temporal expression profile of primary T cell culture and T cell response to Oxidative stress

Data table header descriptions
ID_REF
VALUE Normalized natural log (Sample/Control).
CH1_MEDIAN_INT Channel 1 median intensity
CH1_MEDIAN_BKG Channel 1 median background intensity
CH1_BKG_STD_DEV Channel 1 background intensity standard deviation
CH2_MEDIAN_INT Channel 2 median intensity
CH2_MEDIAN_BKG Channel 2 median background intensity
CH2_BKG_STD_DEV Channel 2 background intensity standard deviation
CONF_DIFF_EXPR Confidence of differential expression (per method of Yang et al., PNAS 2003; 100:1122-1127 [0,1]

Data table
ID_REF VALUE CH1_MEDIAN_INT CH1_MEDIAN_BKG CH1_BKG_STD_DEV CH2_MEDIAN_INT CH2_MEDIAN_BKG CH2_BKG_STD_DEV CONF_DIFF_EXPR
1 NULL 1150 43 4.16 205 62 9.02 NULL
2 NULL 42 44 4.45 61 61 8.50 NULL
3 -0.3216 51 44 4.25 91 62 8.41 0.8509
4 0.4757 3689 44 4.46 6101 61 8.46 0.5874
5 -0.1819 114 44 4.34 326 61 8.56 0.2370
6 NULL 48 44 4.18 69 61 8.34 NULL
7 NULL 951 44 4.06 95 61 8.60 NULL
8 -0.4059 162 44 4.40 622 62 8.26 0.6254
9 NULL 111 44 4.27 283 63 8.63 NULL
10 -0.4814 47 45 4.53 97 61 8.27 0.9692
11 -0.4322 55 45 4.49 95 61 8.34 0.9475
12 -1.0459 59 44 4.71 166 60 8.12 0.9542
13 -0.4403 54 44 4.31 94 61 8.08 0.9518
14 NULL 988 45 4.07 95 61 8.52 NULL
15 -0.2644 400 46 4.28 1405 61 7.85 0.3329
16 -0.1291 75 45 4.45 160 61 8.02 0.2148
17 NULL 49 45 4.74 71 61 7.79 NULL
18 -0.3368 111 44 4.61 356 61 7.79 0.4235
20 NULL 55 46 4.41 71 62 8.29 NULL
21 NULL 1313 46 4.53 100 59 7.80 NULL

Total number of rows: 22153

Table truncated, full table size 932 Kbytes.




Supplementary file Size Download File type/resource
GSM152481.txt.gz 5.5 Mb (ftp)(http) TXT

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