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Sample GSM1336908 Query DataSets for GSM1336908
Status Public on Nov 07, 2014
Title parthenogenetic_diploid_ESC_2
Sample type RNA
Source name parthenogenetic_diploid_ESC_line2
Organism Mus musculus
Characteristics cell type: embryonic stem cells
gender: female
Extracted molecule total RNA
Extraction protocol RNA was prepared using Trizol and RNaeasy Purification kit following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. After fragmentation reaction, 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Genome Oligo Microarrays 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 using one color scan setting for 4x44k array slides.
Description gene expression parthenogenetic diploid ESCs
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Submission date Feb 27, 2014
Last update date Nov 07, 2014
Contact name Saori Takahashi
Phone +81-3-5803-4864
Organization name Tokyo Medical and Dental University
Department Epigenetics
Lab Epigenetics
Street address 1-5-45 Yushima Bunkyo-ku, Tokyo
City Tokyo
ZIP/Postal code 113-8510
Country Japan
Platform ID GPL11202
Series (2)
GSE55444 G2/M transition for stabilizing mouse haploid ESCs: Gene Expression
GSE55446 G2/M transition for stabilizing mouse haploid ESCs

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_51_P100174 462.4818
A_51_P100298 136.35
A_51_P100309 4.517349
A_51_P100327 16.77362
A_51_P100537 8.903692
A_51_P100573 141.3714
A_51_P100625 4.599954
A_51_P100776 13.10365
A_51_P100787 1546.19
A_51_P100828 1717.906
A_51_P100852 42.72655
A_51_P100997 31.95592
A_51_P101006 76.415
A_51_P101075 1051.162
A_51_P101196 2161.121
A_51_P101228 61.91819
A_51_P101375 10.79031
A_51_P101460 64.90153
A_51_P101660 67.52753
A_51_P102122 19.6142

Total number of rows: 39429

Table truncated, full table size 865 Kbytes.

Supplementary file Size Download File type/resource
GSM1336908_US45102915_252665512113_S01_GE1_1100_Jul11_1_4.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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