GEO help: Mouse over screen elements for information.
Status
Public on Nov 13, 2006
Title
Cdc25a_expt_pair1_rep2
Sample type
RNA
Channel 1 Source name
MMTV-cdc25a;MMTV-neu #1868
Organism
Mus musculus Characteristics
Strain: FVB/N , Gender: female , Age: 26 weeks, Tissue: mammary, Tumor Stage: T1 (<1cm, early stage)
Biomaterial provider
H. Kiyokawa
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
FvBn-MMTV-neu #5
Organism
Mus musculus Characteristics
Strain: FVB/N , Gender: female , Age: 26 weeks, Tissue: mammary, Tumor Stage: T1 (<1cm, early stage)
Biomaterial provider
H. Kiyokawa
Extracted molecule
total RNA
Extraction protocol
Agilent RNA isolation mini-kit
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
None
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
Jan 28, 2006
Last update date
Nov 14, 2006
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
GPL2872 Series (1)
GSE4114 Gene expression changes resulting from cdc25a over-expression
Data table header descriptions ID_REF VALUE Normalized natural log (Ch2/Ch1). Replicate spots on array representing same 60mer were averaged prior to normalization.
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 (Ch1 vs Ch2, 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
671
33
4.09
298
59
7.84
NULL
2
NULL
65
35
4.23
65
60
8.26
NULL
3
NULL
212
34
3.94
468
60
8.28
NULL
4
NULL
66
35
4.15
67
60
7.70
NULL
5
NULL
112
34
4.35
195
61
8.53
NULL
6
NULL
76
35
3.89
99
61
7.76
NULL
7
NULL
580
34
3.89
93
60
8.57
NULL
8
NULL
65
35
3.71
78
59
8.52
NULL
9
NULL
72
35
4.06
86
60
8.42
NULL
10
NULL
255
35
4.06
556
59
8.33
NULL
11
NULL
85
35
4.02
111
61
9.40
NULL
12
NULL
72
35
3.79
79
60
9.06
NULL
13
NULL
75
35
3.91
88
59
8.80
NULL
14
NULL
660
34
3.98
100
60
8.62
NULL
15
NULL
66
35
4.07
66
60
9.55
NULL
16
NULL
91
35
4.25
125
60
9.24
NULL
17
NULL
493
34
3.89
870
61
8.56
NULL
18
NULL
111
34
4.26
204
60
8.34
NULL
19
NULL
70
35
4.17
70
60
8.10
NULL
20
NULL
478
34
4.41
1362
60
8.28
NULL
43790 1820 Kbytes .Supplementary file Size Download File type/resource GSM94016.txt.gz
11.1 Mb
(ftp) (http) TXT
