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Sample GSM1162177 Query DataSets for GSM1162177
Status Public on Aug 13, 2014
Title tg_0909
Sample type RNA
Source name tg_E12.5 pooled fore- and hindlimb tissue
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: SHOX transgene
tissue: pooled fore- and hindlimb tissue
age: E12.5
Treatment protocol Tissue was stored at -80°C until RNA preparation
Growth protocol murine embryonic fore- and hindlimb tissue was dissected at stage E12.5
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the RNeasy Kit (Qiagen) according to the manufacturer's instructions, following homogenization using a PT1300 D polytron (Kinematica). DNA was hydrolyzed using the RNAse-free DNAse Kit (Qiagen). Samples from embryonic limbs (E12.5) of the same genotype (wildtype and SHOX transgene) were pooled.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
Hybridization protocol Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
Scan protocol Affymetrix GeneArray Scanner3000
Description Gene expression data from murine SHOX-transgenic pooled fore- and hindlimbs at stage E12.5
Data processing The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of mouse430_2 -type from Affymetrix. A Custom CDF Version 13 with entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization.
Submission date Jun 13, 2013
Last update date Aug 13, 2014
Contact name Carsten Sticht
Organization name University Heidelberg
Department ZMF
Street address Theodor-Kutzer-Ufer
City Mannheim
ZIP/Postal code 68169
Country Germany
Platform ID GPL14661
Series (1)
GSE47902 Expression profiles of wildtype and SHOX transgenic embryonic mouse limbs

Data table header descriptions
VALUE Quantile normalized intensity

Data table
100009600_at 7.15058594
100012_at 5.9329723
100017_at 7.81756037
100019_at 8.83333333
100034251_at 7.01500355
100036521_at 8.41690341
100037258_at 8.72167969
100037278_at 7.55726207
100038570_at 6.89333767
100038635_at 6.21182528
100038680_at 6.5218099
100038887_at 13.0198396
100038959_at 7.83062066
100039026_at 7.71899414
100039027_at 5.98657227
100039094_at 7.0921875
100039235_at 7.37089844
100039282_at 5.99189453
100039284_at 8.37686435
100039307_at 6.95837402

Total number of rows: 16556

Table truncated, full table size 327 Kbytes.

Supplementary file Size Download File type/resource
GSM1162177_Rappold_010909_E12.5-Tg_Mou430_2.CEL.gz 6.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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