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Sample GSM298268 Query DataSets for GSM298268
Status Public on Jun 18, 2008
Title E11.5_heterozygous_embryo#3
Sample type RNA
 
Source name Ott1 knockdown, heterozygous embryo #3
Organism Mus musculus
Characteristics The mouse ES cell line XK135 (obtained from BayGenomics; funded by the National Heart, Lung, and Blood Institute, http://baygenomics.ucsf.edu), harbours a LacZ-neo fusion cassette inserted into the first coding exon of Ott1, 20 nt upstream the initiator codon, generating a low-expression Ott1XK135 allele. After injection into C57BL/6 blastocysts, the chimeric mice were bred for germline transmission. Genomic DNA from tail snips or yolk sacs was used for PCR genotyping. Ott1 alleles were detected by using primers, which span the XK135 insertion site.
Treatment protocol Dissected embryos, snap-frozen in liquid nitrogen
Extracted molecule total RNA
Extraction protocol Total RNA was extracted and purified using RiboPure RNA isolation (Ambion).
Total RNA samples were quantitated by UV spectrophotometry (OD260/280).
Quality of Total RNA was assessed using an Agilent Bioanalyzer.
Label biotin
Label protocol First and second strand cDNA was prepared from the total RNA samples using standard CodeLink protocol.
Biotinylated cRNA target was prepared from the DNA template and verified on the Bioanalyzer.
cRNA was fragmented to uniform size and verified on the Bioanalyzer.
 
Hybridization protocol CodeLink Bioarrays were hybridized with the cRNA target and stained with Cy5-streptavidin.
Scan protocol Slides were washed and then scanned on an Axon GenePix 4000B scanner.
Description Mice harboring a low expression Ott1 allele were mated and embryos at day E11.5 were dissected and genotyped.
Data processing Data were analyzed for quality with CodeLink software package, and transcripts of which the values were missing in at least one mictoarray were removed from the dataset, and raw intensity values less than 0.01 were set to 0.01.

Normalization Method: Median-Normalization;
Computation Method for Median: Spot Based;
Threshold Trim Percentage: 20;
Raw TrimMean Negative Control: 13.82897093;
Normalized TrimMean Negative Control: 0.238254448;
Median 58.04286575
 
Submission date Jun 13, 2008
Last update date Jun 17, 2008
Contact name Andrei S Zolotukhin
E-mail(s) zolotukh@ncifcrf.gov
Organization name NCI-Frederick
Street address P.O. Box B
City Frederick
State/province MD
ZIP/Postal code 21702
Country USA
 
Platform ID GPL2897
Series (1)
GSE11785 Control of gene expression by Ott1/RBM15 protein

Data table header descriptions
ID_REF
VALUE Median-normalized intensity
SIGNAL_RAW Raw intensity

Data table
ID_REF VALUE SIGNAL_RAW
1002 19.99658009 1160.658813
1003 0.326763558 18.96629333
1004 0.84693836 49.15872955
1005 1.477356414 85.75
1006 0.19749127 11.46295929
1010 1.651589827 95.86300659
1012 0.541204156 31.41304016
1013 0.460443957 26.72548676
1017 0.141019648 8.185184479
1018 0.451287689 26.19403076
1019 0.363126791 21.07691956
1020 0.331376459 19.23403931
1024 0.196406593 11.40000153
1026 1.901611827 110.375
1027 0.314610102 18.26087189
1030 0.443569289 25.74603271
1031 -0.027438241 -1.592594147
1034 0.963152067 55.90410614
1039 1.18877659 69
1040 0.084475928 4.903224945

Total number of rows: 35587

Table truncated, full table size 1048 Kbytes.




Supplementary file Size Download File type/resource
GSM298268.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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