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Sample GSM958331 Query DataSets for GSM958331
Status Public on Mar 31, 2013
Title Du-het
Sample type RNA
Source name Dullard-heterozygous
Organism Mus musculus
Characteristics tissue: whole embryo
strain: C57BL/6
genotype/variation: Dullard-heterozygous
developmental stage: E7.5
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using RNeasy Plus Micro RNA extraction kits (Qiagen, Hilden, Germany) from the embryos. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.nomic DNA Enzymatic Labeling Kit (Agilent) according to the manufacturer's instructions.
Hybridization protocol 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44K v2 Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT is set to 100%).
Description whole embryo
Data processing The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Jul 10, 2012
Last update date Mar 31, 2013
Contact name Satomi S Tanaka
Organization name Kumamoto University
Department Institute of Molecular Embryology and Genetics
Lab Department of Kidney Development
Street address 2-2-1 Honjo
City Kumamoto
State/province Kumamoto
ZIP/Postal code 860-0811
Country Japan
Platform ID GPL10333
Series (1)
GSE39224 Agilent microarray analysis between a Dullard-heterozygous and a Dullard-homozygous E7.5 embryo

Data table header descriptions
VALUE Normalized signal intensity

Data table
12 117.2
13 91.6
14 727.9
15 2005.6
16 2320.4
17 4256.4
18 8.8
19 8.8
20 24.1
21 8.7
22 157.9
23 85243.2
24 1668.1
25 1935.0
26 8.6
27 11969.1
28 608.5
30 3366.2
31 6384.6
32 8.5

Total number of rows: 43020

Table truncated, full table size 486 Kbytes.

Supplementary file Size Download File type/resource
GSM958331_AR0839_01raw.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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