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Sample GSM1230335 Query DataSets for GSM1230335
Status Public on Sep 11, 2014
Title Head_knockout_female_replicate1
Sample type RNA
 
Source name Head_knockout_female
Organism Mus musculus
Characteristics gestational age: E14.5
strain: C57BL/6N ,C57BL/6J
tissue: Head
genotype: Peg3 knockout
gender: female
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
E-mail(s) jkim@lsu.edu
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
ID_REF
VALUE quantile normalized signal
H3KF.Detection Pval

Data table
ID_REF VALUE H3KF.Detection Pval
ILMN_2896528 3004.229 0
ILMN_2721178 438.1199 0
ILMN_3033922 617.7759 0
ILMN_3092673 5702.093 0
ILMN_2816356 34.22572 0
ILMN_2808939 654.3806 0
ILMN_2634564 477.5953 0
ILMN_2737647 -12.98101 0.9536341
ILMN_2734484 749.7001 0
ILMN_2952292 77.48139 0
ILMN_2699078 -1.367878 0.508772
ILMN_1213681 216.8868 0
ILMN_2735413 -8.477481 0.8571429
ILMN_2735415 3.786112 0.2481203
ILMN_2891688 858.231 0
ILMN_2637698 1886.211 0
ILMN_2674228 325.0603 0
ILMN_2601546 2.999207 0.2857143
ILMN_1230831 -6.173332 0.7518797
ILMN_2848071 2.854828 0.2907268

Total number of rows: 25697

Table truncated, full table size 711 Kbytes.




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

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