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Sample GSM76889

Query DataSets for GSM76889

Status

Public on Jul 14, 2006

Title

CSB mut-rescued replicate 2 U133B

Sample type

RNA

Source name

human Cockayne syndrome skin fibroblasts

Organism

Homo sapiens

Characteristics

Patient: CS1AN
Primary cell line: GM00739B

Extracted molecule

polyA RNA

Extraction protocol

Stable lines of hTERT-immortalized, CSB mut-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 ATPase mutant (K538R) 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

ZIP/Postal code

98195

Country

USA

Platform ID

GPL97

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	2864.6	P	0.000581
AFFX-BioB-M_at	5378.9	P	4.4e-05
AFFX-BioB-3_at	3046.4	P	5.2e-05
AFFX-BioC-5_at	7206.8	P	6e-05
AFFX-BioC-3_at	5420.8	P	6e-05
AFFX-BioDn-5_at	8130.2	P	4.4e-05
AFFX-BioDn-3_at	36077.2	P	7e-05
AFFX-CreX-5_at	81333	P	4.4e-05
AFFX-CreX-3_at	97634.4	P	4.4e-05
AFFX-DapX-5_at	98.2	A	0.250796
AFFX-DapX-M_at	168.7	A	0.313723
AFFX-DapX-3_at	23.4	A	0.921998
AFFX-LysX-5_at	42.5	A	0.772364
AFFX-LysX-M_at	254.6	A	0.48511
AFFX-LysX-3_at	66.4	A	0.544587
AFFX-PheX-5_at	16.7	A	0.949771
AFFX-PheX-M_at	28	A	0.834139
AFFX-PheX-3_at	231.1	A	0.340661
AFFX-ThrX-5_at	62.7	A	0.749204
AFFX-ThrX-M_at	64.6	A	0.574038

Total number of rows: 22644

Table truncated, full table size 596 Kbytes.

Supplementary file	Size	Download	File type/resource
GSM76889.CEL.gz	3.3 Mb	(ftp)(http)	CEL