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Sample GSM141678 Query DataSets for GSM141678
Status Public on Nov 07, 2006
Title mouse brain antisense U74B
Sample type RNA
Source name total mouse brain
Organism Mus musculus
Characteristics Strain 129SvJ
Male, age 5 weeks
Treatment protocol The brain was dissected, rinsed in ice cold PBS and directly used for RNA extraction with TRIzol (Invitrogen).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the GeneChip? Scanner 3000 (Affymetrix).
Description Antisense transcripts: Reversely annotated probesets identified using the mask provided by Affymetrix to distinguish beween reverse and forward probe sets.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Submission date Oct 23, 2006
Last update date Nov 06, 2006
Contact name Andreas Werner
Phone +44 191 222 6990
Organization name Newcastle University
Department Cell and Molecular Biosciences
Street address Framlington Place
City Newcastle
ZIP/Postal code NE2 4HH
Country United Kingdom
Platform ID GPL33
Series (1)
GSE6106 Sense-antisense transcript comparison in mouse brain and kidney

Data table header descriptions
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
105966_at 40.7 A 0.138765
105968_at 46.4 A 0.138765
105969_f_at 16.3 A 0.861235
105970_at 7.5 A 0.892699
105971_at 88.4 A 0.089405
105973_at 12 A 0.795978
105974_at 105.6 A 0.107301
105976_at 93.8 A 0.234557
105979_at 3.9 A 0.990015
105980_at 128.5 A 0.127645
105982_at 43.4 A 0.732537
105983_at 40.8 A 0.697453
105984_f_at 169.9 A 0.204022
105985_at 6.2 A 0.660544
105986_at 65.3 A 0.52062
105987_at 218.1 A 0.162935
105988_at 9.2 A 0.951005
105989_at 19.7 A 0.795978
105990_at 391.3 A 0.162935
105992_at 365.6 A 0.089405

Total number of rows: 3041

Table truncated, full table size 78 Kbytes.

Supplementary file Size Download File type/resource
GSM141678.CEL.gz 1.7 Mb (ftp)(http) CEL

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