GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1094434 Query DataSets for GSM1094434
Status Public on Jul 03, 2013
Title MommeD1 Female Rep1
Sample type RNA
Source name E9.5 embryos
Organism Mus musculus
Characteristics strain: FVB/n
gender: female
developmental stage: E9.5
genotype: MommeD1
ChIP: chip1
Extracted molecule total RNA
Extraction protocol RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control (RIN>8) was performed with Agilent Bioanalyser.
Label biotin
Label protocol biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit from Applied Biosystems
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description replicate 1
Data processing Data was processed using R2.11.1, beadarray 1.16.0. Differential expression was analysed with limma using design matrix design=cbind(M.WT=c(1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0), M.MD=c(0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0), F.WT=c(0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0), F.MD=c(0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1), Array2=c(0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1))
Submission date Mar 07, 2013
Last update date Jul 03, 2013
Contact name Matthew J Wakefield
Organization name Walter and Eliza Hall Institute
Department Bioinformatics
Street address 1G Royal Parade
City Parkville
State/province VIC
ZIP/Postal code 3050
Country Australia
Platform ID GPL6885
Series (1)
GSE44958 Smchd1 regulates autosomal genes subject to monoallelic expression

Data table header descriptions
VALUE quantile normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 11.55993947 1
ILMN_2721178 9.301744573 1
ILMN_3033922 9.027376769 1
ILMN_3092673 10.69857582 1
ILMN_2816356 6.912678591 0.99624
ILMN_2808939 9.808374005 1
ILMN_2634564 9.665768297 1
ILMN_2737647 6.159817563 0.85965
ILMN_2734484 8.415451707 1
ILMN_2952292 7.460737757 1
ILMN_2699078 5.743077394 0.27444
ILMN_1213681 8.190709513 1
ILMN_2735413 6.182442913 0.87845
ILMN_2735415 6.071644739 0.7807
ILMN_2891688 9.990225047 1
ILMN_2637698 9.317000201 1
ILMN_2674228 9.289449498 1
ILMN_2601546 6.340267111 0.93609
ILMN_1230831 6.027891267 0.73684
ILMN_2848071 6.378030229 0.95113

Total number of rows: 25697

Table truncated, full table size 768 Kbytes.

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

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