NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM286817 Query DataSets for GSM286817
Status Public on May 06, 2008
Title NCCs at E13.5, biological rep1
Sample type RNA
 
Source name NCCs at E13.5 in dorsal root ganglion
Organism Mus musculus
Characteristics CD1 embryo of litter
Extracted molecule total RNA
Extraction protocol Arcturus PicoPure RNA extraction kit was used for total RNA extraction according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MOUSE GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the GeneChip® laser confocal fluorescence scanner.
Description Gene expression data from embryos at E13.5.
Data processing The data were analyzed with Affymetrix Microarray Suite Software.
CEL files obtained by GeneChip Operating Software (GCOS, Affymetrix) were analyzed with the program dChip: a statistical method for model-based expression analysis (Li and Wong, 2001: "Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection." Proc Natl Acad Sci USA. 98, 31–36). After normalization, measures of the expression levels of each gene in each experiment were calculated using the perfect match/mismatch model described in Li and Wong, 2001: "Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application." Genome Biol. 2, 0032.1–0032.11
In parallel, CEL files obtained by GeneChip Operating Software (GCOS, Affymetrix) were analyzed with the program SAM. Data were normalized according to the GeneChip robust multiarray average (GCRMA) algorithm of the R/Bioconductor 1.4 package (http://www.bioconductor.org). Statistically significant expression changes were determined using permutation tests SAM (http://www-stat.stanford.edu/~tibs/SAM/). Genes regulated at least two fold between conditions were considered. The ∆ value was set to return a median false significant number = 0. The q values were 0 for the different gene lists created. Annotations were obtained through the Database for Annotation, Visualization, and Integrated Discovery (DAVID; http://david.niaid.nih.gov/david/beta/index.htm).
 
Submission date May 06, 2008
Last update date Aug 28, 2018
Contact name Domenico Albino
E-mail(s) domenico.albino@istge.it
Phone +39-010-5737463
Organization name National Institute for Cancer Research (IST)
Street address L.go R. Benzi, 10
City genoa
ZIP/Postal code 16132
Country Italy
 
Platform ID GPL1261
Series (1)
GSE11356 Expression data from early and adult stages of mouse development
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE dChip-calculated signal intensities
ABS_CALL Present, Absent, or Marginal according to dChip
VALUE_GCRMA GCRMA-calculated signal intensities
ABS_CALL_GCRMA Present, Absent, or Marginal according to GCRMA
DETECTION P-VALUE_GCRMA Detection p-value according to GCRMA

Data table
ID_REF VALUE ABS_CALL VALUE_GCRMA ABS_CALL_GCRMA DETECTION P-VALUE_GCRMA
AFFX-BioB-5_at 147.646 P 99.04 P 0.000581
AFFX-BioB-M_at 142.641 P 135.05 P 0.000169
AFFX-BioB-3_at 138.626 P 83.5 P 0.000044
AFFX-BioC-5_at 328.114 P 265.88 P 0.000127
AFFX-BioC-3_at 368.948 P 250.13 P 0.000044
AFFX-BioDn-5_at 911.087 P 11521.9 P 0.000044
AFFX-BioDn-3_at 1753.613 P 22676.1 P 0.000052
AFFX-CreX-5_at 6302.013 P 65457.4 P 0.000052
AFFX-CreX-3_at 6092.682 P 69087.7 P 0.000044
AFFX-DapX-5_at 15.967 A 3.88 A 0.16584
AFFX-DapX-M_at 2.361 A 0.58 A 0.52976
AFFX-DapX-3_at 13.505 A 3.25 A 0.60308
AFFX-LysX-5_at 2.408 A 0.25 A 0.60308
AFFX-LysX-M_at 8.192 A 3.71 A 0.41138
AFFX-LysX-3_at 2.858 A 1.05 A 0.262827
AFFX-PheX-5_at 5.093 A 1.3 A 0.574038
AFFX-PheX-M_at 1.094 A 1.63 A 0.686277
AFFX-PheX-3_at 16.7 A 1.42 A 0.58862
AFFX-ThrX-5_at 8.571 A 0.67 A 0.843268
AFFX-ThrX-M_at 13.909 A 0.34 A 0.60308

Total number of rows: 45101

Table truncated, full table size 1598 Kbytes.




Supplementary file Size Download File type/resource
GSM286817.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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