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Sample GSM677518 Query DataSets for GSM677518
Status Public on Jun 01, 2012
Title ES3
Sample type RNA
 
Source name mouse ES EB
Organism Mus musculus
Characteristics tissue: embyonic Body cell 3
strain: 129S2/SvPas
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 5.09174 0.000308129
4304925 8.31108 1.37482e-07
4304927 3.65891 0.197813
4304928 12.1415 4.68706e-09
4304929 10.7636 1.97197e-06
4304930 2.70609 0.132723
4304937 2.52511 0.271122
4304938 7.86527 9.06944e-08
4304941 4.59125 0.0507021
4304943 9.22423 1.63199e-05
4304945 9.78401 4.55766e-09
4304949 8.42626 0.000979451
4304956 6.74488 0.000271511
4304961 2.91881 0.101735
4304967 6.05243 0.0226214
4304969 6.47748 8.93038e-05
4304970 4.9049 0.000632789
4304971 5.2051 0.000738264
4304972 7.28611 8.61042e-09
4304973 10.2074 4.54456e-09

Total number of rows: 631748

Table truncated, full table size 16328 Kbytes.




Supplementary file Size Download File type/resource
GSM677518.chp.gz 6.0 Mb (ftp)(http) CHP
GSM677518_PL4.CEL.gz 22.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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