NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM298265 Query DataSets for GSM298265
Status Public on Jun 18, 2008
Title E11.5_homozygous_embryo#2
Sample type RNA
 
Source name Ott1 knockdown, homozygous embryo #2
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: 16.95388803;
Normalized TrimMean Negative Control: 0.273318201;
Median: 62.02985382
 
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 21.97216488 1362.930176
1003 0.434931246 26.97872162
1004 0.812414234 50.39393616
1005 1.568599586 97.30000305
1006 0.033724943 2.091953278
1010 1.20794374 74.92857361
1012 0.555326278 34.44680786
1013 0.159370224 9.88571167
1017 0.245849362 15.25
1018 0.208911715 12.95876312
1019 0.203844545 12.64444733
1020 0.679396417 42.14286041
1024 0.060088358 3.727272034
1026 1.63630887 101.5
1027 0.520622229 32.29412079
1030 0.578142071 35.86206818
1031 0.085296168 5.290908813
1034 0.902543142 55.98461914
1039 0.928528529 57.59648895
1040 0.217039997 13.46295929

Total number of rows: 35587

Table truncated, full table size 1048 Kbytes.




Supplementary file Size Download File type/resource
GSM298265.txt.gz 1.4 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap