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Sample GSM1336905 Query DataSets for GSM1336905
Status Public on Nov 07, 2014
Title parthenogenetic_haploid_ESC_1
Sample type RNA
 
Source name parthenogenetic_haploid_ESC_line1
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 haploid 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
E-mail(s) saori.takahashi@riken.jp
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
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_51_P100174 540.2832
A_51_P100298 101.7725
A_51_P100309 4.503098
A_51_P100327 19.50016
A_51_P100537 7.309317
A_51_P100573 111.7315
A_51_P100625 4.928096
A_51_P100776 13.4617
A_51_P100787 1665.042
A_51_P100828 1708.397
A_51_P100852 39.79601
A_51_P100997 37.21714
A_51_P101006 108.2922
A_51_P101075 1263.615
A_51_P101196 2031.098
A_51_P101228 48.19039
A_51_P101375 15.94701
A_51_P101460 51.34572
A_51_P101660 81.21917
A_51_P102122 12.72103

Total number of rows: 39429

Table truncated, full table size 865 Kbytes.




Supplementary file Size Download File type/resource
GSM1336905_US45102915_252665512113_S01_GE1_1100_Jul11_1_1.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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