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Sample GSM109558 Query DataSets for GSM109558
Status Public on Jul 28, 2006
Title liver, normal, U74C
Sample type RNA
 
Source name newborn liver, normal
Organism Mus musculus
Characteristics Strain: T65H translocation mouse (Beechey et al., Mammalian Genome 8(4):236-240, 1997) without uniparental duplications (normal)
Age: newborn
Tissue: liver
Biomaterial provider Colin Beechey, Mammalian Genetics Unit, Harwell, Oxfordshire, UK
Treatment protocol Tissues were snap frozen in liquid nitrogen, permanently stored at -80C, and put on dry ice during transport.
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues in guanidine isothiocyanate by centrifugation through caesium chloride.
Label Biotin
Label protocol Caesium chloride isolated total RNA was quantified on an Agilent Bioanalyser and 5 to 7µg were used to prepare biotin-labeled cRNA target, as prescribed in the Affymetrix expression manual (Affymetrix, 2004). The biotinylated cRNA target was purified using cRNA Cleanup spin columns (Affymetrix), fragmented with 5x fragmentation buffer (Affymetrix), and quantified prior to hybridization on an Agilent Bioanalyser.
 
Hybridization protocol 0.15µg of labeled probe was hybridised to the array, washed and stained on the Affymetrix fluidics station 450. Standard protocol.
Scan protocol The Affymetrix Scanner 3000 system was used. Standard protocol.
Description Tissue-specific comparison of gene expression levels in T65H translocation mice, either with or without uniparental duplications of Chrs 7 & 11. Identification of highly differentially expressed transcripts. See T65H series record.
Data processing MAS5/GCOS: TGT=500, otherwise default values.
 
Submission date May 19, 2006
Last update date Jul 28, 2006
Contact name Reiner Schulz
E-mail(s) reiner.schulz@kcl.ac.uk
Organization name King's College London
Department Medical & Molecular Genetics
Lab Epigenetics
Street address 8th floor Guy's Tower
City London
ZIP/Postal code SE1 9RT
Country United Kingdom
 
Platform ID GPL83
Series (1)
GSE4870 Expression data from T65H translocation mice

Data table header descriptions
ID_REF Affymetrix probe set identifier
VALUE MAS5/GCOS-calculated signal intensity
ABS_CALL MAS5/GCOS detection call (default P-value thresholds)
DETECTION P-VALUE MAS5/GCOS-calculated P-value

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
128520_at 10622 A 0.066865
128523_at 35.3 A 0.892699
128529_at 372.1 A 0.358668
128550_at 149.1 A 0.849473
128554_at 107.7 A 0.732537
128577_s_at 400 A 0.218983
128578_r_at 3406.3 P 0.000219
128579_r_at 552.8 A 0.07383
128580_at 212.9 A 0.715253
128582_at 259.4 A 0.204022
128583_at 221.2 A 0.418069
128590_at 377.3 A 0.418069
128624_at 139.6 A 0.458816
128643_r_at 242.6 A 0.910595
128644_at 324.3 A 0.204022
128645_at 363.7 A 0.64131
128646_at 298.2 A 0.378184
128647_at 644.4 A 0.250724
128651_at 1480.2 A 0.302547
128652_at 264.4 A 0.204022

Total number of rows: 11934

Table truncated, full table size 316 Kbytes.




Supplementary file Size Download File type/resource
GSM109558.CEL.gz 2.5 Mb (ftp)(http) CEL
GSM109558.EXP.gz 508 b (ftp)(http) EXP

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