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Sample GSM991396 Query DataSets for GSM991396
Status Public on Feb 23, 2014
Title 3_RNA from posterior half of wild-type embryo
Sample type RNA
Source name embryo_wild-type
Organism Mus musculus
Characteristics genotype/variation: wild-type
developmental stage: E9.5
tissue: posterior half of embryo
Treatment protocol Embryos were collected at E9.5 and posterior half of embryos were frozen immediately at -80°C.
Growth protocol Jmjd3+/- mice were intercrossed and embryos were collected at E9.5 according to the time after mating and the somite number.
Extracted molecule total RNA
Extraction protocol After genotyping, total RNAs were extracted using RNeasy mini RNA purification kit (QIAGEN, Valencia, CA). RNA was quantified 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 0.4 ug RNA using the Low RNA Input Fluorescent Linear Amplification 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-1000 Spectrophotometer.
Hybridization protocol 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug 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 Whole Genome Microarray 4x44K (G4122F) 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 by raise it slowly from buffer 2.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green. Scan mode is eXtended Dynamic range Scan mode and PMT is set to 10% and 100%).
Description Gene Expression of posterior half of wild-type embryo
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20100617) to obtain background subtracted and spatially detrended Processed Signal intensities. These data were analyzed further with the GeneSpring GX11.5 software (Agilent Technologies). Normalization was performed as follows: 1, intensity-dependent Lowess normalization; 2, data transformation, with measurements less than 0.01 set to 0.01; 3, per-chip normalization, in which the 75th percentile method was used to normalize each array; 4, per-gene normalization, in which the data were normalized to control samples (wild-type).
Submission date Aug 23, 2012
Last update date Feb 23, 2014
Contact name Takumi Nishiuchi
Organization name Kanazawa University
Street address 13-1 Takaramachi
City Kanazawa
ZIP/Postal code 920-0934
Country Japan
Platform ID GPL7202
Series (1)
GSE40332 Gene expression profiles in wild-type and Jmjd3-/- embryos

Data table header descriptions
VALUE normalized signal

Data table
GE_BrightCorner 0.048434258
DarkCorner -1.6732111
A_52_P616356 0.043925285
A_52_P580582 -0.0662868
A_52_P403405 0.09723377
A_52_P819156 0.044067383
A_51_P331831 -0.028573513
A_51_P430630 0.04398775
A_52_P502357 0.043895245
A_52_P299964 0.043815136
A_51_P356389 0.043732166
A_52_P684402 -0.11748028
A_51_P414208 0.043427467
A_51_P280918 -0.019506454
A_52_P613688 -0.0660007
A_52_P258194 -0.11796427
A_52_P229271 0.1450262
A_52_P214630 -0.04193163
A_52_P579519 -0.093147755
A_52_P979997 0.042312622

Total number of rows: 41252

Table truncated, full table size 995 Kbytes.

Supplementary file Size Download File type/resource
GSM991396_US22502564_251486829627_S01_GE1_107_Sep09_1_2.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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