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Status
Public on Jul 14, 2006
Title
CSB wt-rescued replicate 3 U133A
Sample type
RNA
Source name
human Cockayne syndrome skin fibroblasts
Organism
Homo sapiens Characteristics
Patient: CS1AN
Extracted molecule
polyA RNA
Extraction protocol
Stable lines of hTERT-immortalized, CSB wt-rescued fibroblasts were grown to 60-80% confluence, and total RNA collected in RNeasy spin columns (Qiagen). Samples were enriched for PolyA RNA using Oligotex (Qiagen).
Label
biotin
Label protocol
Approximately 2 microg of polyA RNA was processed to produce biotinylated cRNA targets.
Hybridization protocol
standard Affymetrix procedures
Scan protocol
standard Affymetrix procedures
Description
Cockayne syndrome (CSB) fibroblasts rescued with expression of wt CSB cDNA
Data processing
Affymetrix Microarray Suite version 5.0, values scaled to Target Signal of 800
Submission date
Oct 03, 2005
Last update date
Jul 14, 2006
Contact name
John C Newman
E-mail(s)
[email protected] Organization name
University of Washington
Department
Biochemistry
Lab
Alan Weiner
Street address
1959 NE Pacific St.
City
Seattle
State/province
WA
ZIP/Postal code
98195
Country
USA
Platform ID
GPL96 Series (1)
GSE3407 Cockayne syndrome (CSB) fibroblasts
Data table header descriptions ID_REF VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call
Data table ID_REF VALUE ABS_CALL DETECTION P-VALUE AFFX-BioB-5_at
667.5
P
0.004484
AFFX-BioB-M_at
969.1
P
5.2e-05
AFFX-BioB-3_at
398.9
P
0.000127
AFFX-BioC-5_at
1321
P
0.000195
AFFX-BioC-3_at
942.5
P
0.000195
AFFX-BioDn-5_at
1450.1
P
9.5e-05
AFFX-BioDn-3_at
9086.7
P
0.000297
AFFX-CreX-5_at
14111.4
P
4.4e-05
AFFX-CreX-3_at
20351.7
P
4.4e-05
AFFX-DapX-5_at
8.2
A
0.425962
AFFX-DapX-M_at
36.4
A
0.440646
AFFX-DapX-3_at
11.5
A
0.868639
AFFX-LysX-5_at
6.1
A
0.834139
AFFX-LysX-M_at
163.2
A
0.354453
AFFX-LysX-3_at
10.6
A
0.51489
AFFX-PheX-5_at
5
A
0.963431
AFFX-PheX-M_at
2.7
A
0.953518
AFFX-PheX-3_at
52.3
A
0.544587
AFFX-ThrX-5_at
17.9
A
0.574038
AFFX-ThrX-M_at
26.4
A
0.5
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