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Sample GSM524442 Query DataSets for GSM524442
Status Public on Mar 25, 2010
Title NPd14_3 biological rep3
Sample type RNA
 
Source name Endometrial biopsy collected at day 14 of the oestrous ccycle from hiefers resulted in no pregnancy after embryo transfer
Organism Bos taurus
Characteristics day of the oestrous cycle: 14
pregnancy: no
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from three pools of each endometrial sample (CDd7, CDd14, NPd7 or NPd14 ) using RNeasy mini kit (Qiagen).
RNA amplification was perfomed using MEGAscript® T7 Kit (Ambion, Inc., Austin, TX, USA) according to GeneChip® expression analysis technical manual (P/N 702232)
Label biotin
Label protocol The cRNA was biotin labeled using the GeneChip® IVT Labeling Kit (Affymetrix, Inc., Santa Clara, CA, USA) according to GeneChip® expression analysis technical manual (P/N 702232)
 
Hybridization protocol The biotin-labeled cRNA was fragmented. Following this, a hybridization cocktail consisting of fragmented and labeled cRNA, control oligonucleotide B2 (3nM), 20X eukaryotic hybridization controls (bioB, bioC, bioD, cre), 2X hybridization mix, DMSO and RNAse free water were mixed to a final volume of 200 µl and heated to 99°C for 5 followed by warming at 45°C for 5 min. The samples were then hybridized to GeneChip® Bovine Genome Array for 16 h at 45°C in hybridization oven. For each sample of CDd7, CDd14, NPd7 or NPd14, three biotin labeled cRNA hybridizations were performed.
Scan protocol The arrays were washed and stained using Fluidics Station 450/250 and scanned using the GeneChip® scanner 3000 integrated with Affymetrix® Microarray Suite software as recommended in GeneChip® expression wash, stain and scan user manual (P/N 702731).
Data processing The microarray data normalization and background correction was performed using guanine cytosine robust multi-array analysis (gcrma) . The quality of the arrays after hybridization was evaluated by assessing the absent and present calls of the control probesets. Differentially expressed genes were generated using linear models for microarray data analysis (LIMMA). For this, we used R software, (www.r-project.org) and bioconductor packages (www.bioconductor.org).
 
Submission date Mar 19, 2010
Last update date Mar 24, 2010
Contact name Dessie Salilew-Wondim
E-mail(s) dsalilew@uni-bonn.de
Organization name University of Bonn
Department Animal breeding and husbandry group
Street address Endenicher Allee 15
City Bonn
State/province NRW
ZIP/Postal code D-53115
Country Germany
 
Platform ID GPL2112
Series (2)
GSE20974 Bovine pre-transfer endometrium and embryo transcriptome fingerprints as predictors of pregnancy success after embryo transfer (endometrial study)
GSE21049 Bovine pre-transfer endometrium and embryo transcriptome fingerprints as predictors of pregnancy success after embryo transfer

Data table header descriptions
ID_REF
VALUE GCRMA signal intensity

Data table
ID_REF VALUE
Bt.639.1.S1_at 3.56244799
Bt.17967.1.A1_at 1.82493825
Bt.1522.1.A1_at 5.23384006
Bt.12755.1.S1_a_at 1.979563706
Bt.17394.2.S1_at 1.906478773
Bt.22274.1.S1_at 4.229143145
Bt.15758.1.S1_at 1.800731451
Bt.5934.1.S1_at 4.550739798
Bt.16068.1.A1_at 3.44814453
Bt.13265.2.S1_at 2.240865542
Bt.29725.1.S1_at 2.744271538
Bt.9699.1.S1_at 1.652274276
Bt.20951.1.A1_at 2.179721681
Bt.21852.1.S1_at 4.498935353
Bt.26343.1.S1_at 2.41093811
Bt.25546.1.A1_at 2.076312275
Bt.14220.1.S1_at 2.600471541
Bt.28022.1.A1_s_at 7.876770207
Bt.16101.1.S1_s_at 3.778843535
Bt.20534.1.S1_at 2.686196634

Total number of rows: 24128

Table truncated, full table size 676 Kbytes.




Supplementary file Size Download File type/resource
GSM524442.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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