GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1136286 Query DataSets for GSM1136286
Status Public on Jun 02, 2014
Title Inter-implantation decidua sample mice 3
Sample type RNA
Source name Day 6.5 post-coitum murine uterus
Organism Mus musculus
Characteristics strain: B6CBA F1/J
tissue: inter-implantation decidua
Extracted molecule total RNA
Extraction protocol To ensure that total RNA was recovered we performed RNA extraction using the Arcturus PicoPure RNA Isolation Kit (Life Technologies S.A. Madrid, Spain). RNA extracted was quantified using a NanoDrop (Thermo Fisher Scientific Inc, MA, USA) spectrophotometer and the RNA quality was evaluated using the total eukariote Pico RNA LabChip in the BioAnalyzer 2100, (Agilent Technologies Inc, DE, USA)
Label Cy3-CTP
Label protocol Total RNA was obtained from uterine and trophoblast tissues and analyzed as previously described [17]. Briefly, total RNA was extracted using Trizol reagent (Life Technologies, Paisley, UK) and treated with DNase I (Promega, Southampton, UK) for 30 min at 37°C and then reextracted with Trizol. RNA quality was assessed with an A2100 bioanalyzer (Agilent Technologies, Santa Clara, CA). Only those samples with a RNA integrity number (RIN)7.5 were included for microarray analysis. One microgram of each RNA sample were labeled and hybridized to the One-Color Agilent Whole Mouse Genome Microarray 44K. For each group, 3 samples were analyzed in duplicate.
Hybridization protocol 1.65 ug of cRNA was used to be fragmented in presence of blocking agent and fragmentation buffer for 30º at 60ºC and cooled. Then sample was mixed with hybridization buffer.
Scan protocol Microarrays slides were washed and scanned in Genepix Personal 4100A Scanner and scanned in Genepix Pro Software with a spot resolution of 5um in the green channel.
Description each sample was previous tested for total RNA quality using total pico RNA Labchip in an agilent bioanalyzer and with RIN above 9.0
Data processing Median intensity value of each spot data was log2 transformed and normalized using R software and libraries from bioconductor database. Next, replicated probes were merged by mean using GEPAS.
Submission date May 08, 2013
Last update date Jun 02, 2014
Contact name Juan M Moreno-Moya
Organization name FIVI
Street address Catedrático Agustín Escardino
City Valencia
ZIP/Postal code 46980
Country Spain
Platform ID GPL10333
Series (1)
GSE46732 Transcriptomic of early embryonic invasion at implantation sites in a murine model.

Data table header descriptions
VALUE Normalized signal intensity

Data table
1 10.2131
2 5.5811
3 5.4032
4 5.5161
5 5.6109
6 5.6781
7 5.4808
8 5.7391
9 6.1152
10 5.3294
11 5.8974
12 6.8083
13 5.6109
14 10.6463
15 5.6402
16 9.3906
17 13.9556
18 5.8032
19 5.8344
20 10.2104

Total number of rows: 45220

Table truncated, full table size 567 Kbytes.

Supplementary file Size Download File type/resource
GSM1136286_ID3.gpr.gz 4.1 Mb (ftp)(http) GPR
Processed data included within Sample table

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