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Sample GSM1230334 Query DataSets for GSM1230334
Status Public on Sep 11, 2014
Title Head_knockout_male_replicate1
Sample type RNA
Source name Head_knockout_male
Organism Mus musculus
Characteristics gestational age: E14.5
strain: C57BL/6N ,C57BL/6J
tissue: Head
genotype: Peg3 knockout
gender: male
Treatment protocol A litter of 14.5-dpc fetuses were harvested from a timed mating between a male heterozygote (-m/+) and wild-type female littermate. Three tissues were obtained from each fetus: embryo head, placenta and amnionic sac. The DNA from amnionic sac was used for determining the genotype and gender of each fetus.
Extracted molecule total RNA
Extraction protocol Trizol isolated total RNA from each sample was treated with DNAse I and later purified with columns to remove any genomic contaminations (Qiagen, RNeasy Mini-kit).
Label biotin
Label protocol 400ng total RNA was labeled with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina system
Hybridization protocol 750ng labeled RNA was hybridized to MouseRef-8 v2 BeadChip arrays (Illumina) according to manufacturer’s protocol.
Scan protocol Chips were scanned using Illumina iScan system with default settings
Description Two different types of heterozygotes were prepared for breeding experiment: male and female heterozygotes carrying the paternally (+/-p) and maternally (-m/+) transmitted targeted allele. These 4 heterozygotes were bred with their littermates: for Breeding 1, female wild-type littermates x male heterozygotes (+/-P); Breeding 2, female heterozygotes (+/-P) x male wild-type littermates; Breeding 3, female wild-type littermates x male heterozygotes (-m/+); for Breeding 4, female heterozygotes (-m/+) x male wild-type littermates.
Data processing Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6. Raw data were background-subtracted and normalized using the quantile normalization method (lumi software package). Normalized data were filtered for genes with significant expression levels compared to negative control beads. Selection for differentially expressed genes was performed on the basis of arbitrary thresholds for fold changes plus statistical significance according to the Illumina t-test error model (limma software). Pathway analyses were also performed with the EGAN (Explorative Gene Association Networks) package using up- and down-regulated gene sets.
Matrix normalized contains quantile normalized and background subtracted signal exported from GenomeStudio. Matrix non-normalized contains background subtracted non-normalized data exported from GenomeStudio
Submission date Sep 12, 2013
Last update date Sep 11, 2014
Contact name Joomyeong Kim
Phone 225-578-7692
Organization name Louisiana State University
Department Biological Sciences
Street address 202 Life Sciences
City Baton Rouge
State/province LA
ZIP/Postal code 70803
Country USA
Platform ID GPL6885
Series (1)
GSE50818 Peg3 mutational effects on reproduction and placenta-specific gene families

Data table header descriptions
VALUE quantile normalized signal
H2KM.Detection Pval

Data table
ID_REF VALUE H2KM.Detection Pval
ILMN_2896528 3618.319 0
ILMN_2721178 468.7989 0
ILMN_3033922 728.1101 0
ILMN_3092673 5625.532 0
ILMN_2816356 16.32795 0.02882206
ILMN_2808939 701.8729 0
ILMN_2634564 536.058 0
ILMN_2737647 8.14457 0.1265664
ILMN_2734484 772.0894 0
ILMN_2952292 102.0585 0
ILMN_2699078 1.493082 0.3408521
ILMN_1213681 196.7062 0
ILMN_2735413 2.106609 0.3032582
ILMN_2735415 7.00109 0.1566416
ILMN_2891688 1015.398 0
ILMN_2637698 1878.036 0
ILMN_2674228 315.5625 0
ILMN_2601546 2.232423 0.2944862
ILMN_1230831 -6.607922 0.7543859
ILMN_2848071 11.11701 0.07393484

Total number of rows: 25697

Table truncated, full table size 718 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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