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Sample GSM286814 Query DataSets for GSM286814
Status Public on May 06, 2008
Title NCCs at E8.5, biological rep1
Sample type RNA
 
Source name NCCs at E8.5 during neural tube closure
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 E8.5.
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 458.738 P 49.67 P 0.000509
AFFX-BioB-M_at 491.833 P 66.92 P 0.000052
AFFX-BioB-3_at 463.653 P 48.09 P 0.000052
AFFX-BioC-5_at 1016.172 P 146.96 P 0.00007
AFFX-BioC-3_at 1137.316 P 179.13 P 0.000044
AFFX-BioDn-5_at 2103.077 P 284.33 P 0.000044
AFFX-BioDn-3_at 3169.944 P 15207.8 P 0.000052
AFFX-CreX-5_at 7276.744 P 33946.8 P 0.000052
AFFX-CreX-3_at 7061.491 P 39655.9 P 0.000044
AFFX-DapX-5_at 17.589 P 2.46 P 0.042962
AFFX-DapX-M_at 7.075 A 2.75 A 0.089478
AFFX-DapX-3_at 19.499 A 1.5 A 0.559354
AFFX-LysX-5_at 4.977 A 0.67 A 0.455413
AFFX-LysX-M_at 7.584 A 2.17 A 0.51489
AFFX-LysX-3_at 4.283 A 1.42 A 0.239063
AFFX-PheX-5_at 6.158 A 0.21 A 0.891021
AFFX-PheX-M_at 3.358 A 0.21 A 0.897835
AFFX-PheX-3_at 20.302 A 2.67 A 0.48511
AFFX-ThrX-5_at 7.771 A 2.13 A 0.58862
AFFX-ThrX-M_at 17.566 A 2.79 A 0.165861

Total number of rows: 45101

Table truncated, full table size 1598 Kbytes.




Supplementary file Size Download File type/resource
GSM286814.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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