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Sample GSM340922 Query DataSets for GSM340922
Status Public on Mar 12, 2010
Title XmO3-K
Sample type RNA
 
Source name Kidney
Organism Mus musculus
Characteristics tissue: Kidney
gender: female
age: 12 weeks old
genetic background: random bred MF1, one single progenitor X chromosome background
genotype/variation: 39,XmO from 40,XX x 40,XPafY*
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from homogenized tissues using Trizol reagent and purified using a column based centrifugation method (Qiagen) according to the manufacturer’s instructions.
Label biotin
Label protocol Biotin-16 UTP of in vitro transcribed RNA. Used Illumina RNA amplification kit (Cat # 1755 Ambion US)
 
Hybridization protocol 1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 16 hours at 58 degrees celsius. 1500ng of cRNA from each sample was hybridized to each of the six microarrays on the platform for 15 hours at 55 degrees celsius. The microarrays were washed and then stained with streptavidin conjugated to Cy3 fluorescent dye. The staining procedure relies on the affinity of streptavidin to biotin which is incorporated into the UTP residues of the hybridised cRNA sample. Arrays were then washed again and air dried.
Scan protocol Microarrays were scanned under 532nm laser illumination using a confocal type image system (BeadArray Reader, Illumina California USA).
Description 39,XmO from 40,XX x 40,XPafY*
Data processing The values for each bead in the array were imported into the Illumina software BeadStudio for preliminary quality checks, summarized according to bead type and then exported into R. Normalization across all arrays was performed on a log scale using the quantile normalization method implemented in the Lumi normalization package from the bioconductor repository (www.bioconductor.org).
 
Submission date Nov 07, 2008
Last update date Aug 04, 2010
Contact name Alexandra M. Lopes
E-mail(s) alopes@ipatimup.pt
Organization name IPATIMUP
Lab Population Genetics
Street address R. Dr. Roberto Frias s/n
City Porto
ZIP/Postal code 4200-465
Country Portugal
 
Platform ID GPL6105
Series (1)
GSE13520 Expression profiles of (40,XX) and (39,XO) females

Data table header descriptions
ID_REF
VALUE log2 normalised intensity signal

Data table
ID_REF VALUE
ILMN_1239746 7.09
ILMN_2660056 7.01
ILMN_2771738 7.05
ILMN_1258125 8.20
ILMN_1253348 13.41
ILMN_1260047 7.93
ILMN_1254104 8.74
ILMN_2677728 10.91
ILMN_2612635 11.71
ILMN_1250192 6.97
ILMN_3163078 7.10
ILMN_2635507 9.54
ILMN_1259739 8.47
ILMN_1223907 10.27
ILMN_2699805 11.14
ILMN_1253035 8.15
ILMN_1221859 11.79
ILMN_1241465
ILMN_2680066 10.71
ILMN_2606835 7.01

Total number of rows: 28885

Table truncated, full table size 489 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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