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Sample GSM1162180 Query DataSets for GSM1162180
Status Public on Aug 13, 2014
Title tg_0309
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 7.18818359
100012_at 5.99604936
100017_at 8.1550071
100019_at 9.0546875
100034251_at 7.23819247
100036521_at 8.16379616
100037258_at 8.28232422
100037278_at 7.77228338
100038570_at 6.87076823
100038635_at 6.19389205
100038680_at 6.73925781
100038887_at 12.8056127
100038959_at 8.15299479
100039026_at 7.54443359
100039027_at 5.95874023
100039094_at 7.31123047
100039235_at 7.41660156
100039282_at 6.02792969
100039284_at 8.61603338
100039307_at 6.97229004

Total number of rows: 16556

Table truncated, full table size 327 Kbytes.

Supplementary file Size Download File type/resource
GSM1162180_Rappold_130309_8_E12.5-Tg-SHOX-limb_Mou430_2.CEL.gz 6.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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