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Sample GSM677536 Query DataSets for GSM677536
Status Public on Jun 01, 2012
Title ES21
Sample type RNA
 
Source name mouse ES EB
Organism Mus musculus
Characteristics tissue: embyonic Body cell 21
strain: C57BL/6
Extracted molecule total RNA
Extraction protocol RNA was isolated with the miRNeasy Mini Kit (Qiagen), according to the manufacturers instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturers instructions.
Label biotin
Label protocol Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at NIH.
Scan protocol Array scanning was performed according to the manufacturer's instruction (Affymetrix)
Description RMA expression value derived from Expression Console software; extended-exon analysis
Data processing Raw data were processed with the Expression console (Affymetrix) for background correction and normalization log2 transformation. Data analysis and statistical evaluations were performed with customized R codes (version 2.10.1, http://www.r-project.org/).
 
Submission date Feb 17, 2011
Last update date Jul 19, 2013
Contact name chunjiang he
Organization name university of chicago
Street address 900 east 57th st
City chicago
State/province il
ZIP/Postal code 60637
Country USA
 
Platform ID GPL6193
Series (1)
GSE27397 26 mouse ES EB samples affymetrix exon array (affymetrix exon array)

Data table header descriptions
ID_REF
VALUE Quantification
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
4304922 2.01178 0.701044
4304925 7.75283 1.7253e-06
4304927 2.77566 0.619778
4304928 12.4684 4.68706e-09
4304929 11.3694 3.49201e-06
4304930 2.7662 0.396089
4304937 2.26324 0.409591
4304938 6.11969 0.000107519
4304941 5.31077 0.0821854
4304943 7.93128 1.63199e-05
4304945 10.0286 4.55766e-09
4304949 7.92797 0.00926747
4304956 6.27118 0.00173348
4304961 3.08048 0.100449
4304967 6.21683 0.032835
4304969 12.1017 4.6259e-09
4304970 4.13883 0.0339334
4304971 4.72558 0.00345863
4304972 6.4021 4.23126e-08
4304973 9.70428 8.44285e-09

Total number of rows: 631748

Table truncated, full table size 16203 Kbytes.




Supplementary file Size Download File type/resource
GSM677536.chp.gz 6.0 Mb (ftp)(http) CHP
GSM677536_PL26.CEL.gz 22.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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