NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE8375 Query DataSets for GSE8375
Status Public on Aug 01, 2007
Title Gene expression profile in labouring and non-labouring human placenta near term
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Sample and RNA preparation:
The series is composed of seventeen hybridizations for analysis of differentially expressed genes in placenta tissues from women after vaginal delivery (labouring) and after elective caesarean section (non-labouring). Total RNA extraction was performed by using the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science).
Labeling and hybridization:
Total RNA was reverse transcribed and labeled with Cy3-attached dendrimer using the Genisphere 3DNA HS kit (Genisphere) as described in the manufacturer’s protocol. Hybridizations were carried out with a TECAN HS4800 instrument using the foramamide-based hybridization buffer from Genisphere containing 5% dextran sulphate and 0.5 microgram COT1 DNA/microgram RNA at 37°C for 23 hours. 3DNA dendrimer hybridizations were carried out in formamide-based hybridization buffer alone. Post-hybridization washes were carried out at room temperature with 2xSSC for 1 min, 0.2% SDS/2xSSC for 1 min and finally with0.2xSSC for 30 sec.
Scanning, image analysis and data processing:
The microarrays were scanned on an AXON 4000B scanner and images were quantified using GenePix pro 6.0 software. The background estimates were calculated using the morphological opening method. Spots that displayed a signal-to-noise ratio of less than 3 or that were significantly saturated (more than 20 % saturation among foreground pixels) were filtered out. The median was used as the averaging measure of the foreground pixels. After quality control, genes that were present in less than 50 % of the arrays were filtered out. Normalization was carried out using lowess normalization Sample labelling was balanced across the groups, presumably attenuating any dye-effect. For the purpose of finding differentially expressed genes empirical Bayes analysis, using the LIMMA package was applied. The data were analysed using a two-component linear model. The prior guess of the number of D.E genes was set to 0.01. Multiple testing was accounted for by estimating the false discovery rate. We applied the Benjamini-Hochberg procedure, as well as Storeys less conservative Q-value procedure was applied. In none of the cases were any genes significant at a reasonable (15-20% FDR) level. In summary, a 2.5-fold change in expression of any gene that was present on ≥ 8 arrays was considered significant, if the difference in fluorescence intensity between two groups reached a p-value of < 0.01.


Keywords: Tissue samples of placenta from women after vaginal delivery (labouring) and after elective caesarean section (non-labouring)
 
Overall design Samples from the placenta of 17 women who had elective sectio(non-labouring) were hybridised together on the same array with placenta samples from women who had vaginal delivery (labouring). This resulted in 17 direct comparisons on 17 arrays.

To reduce the dye-bias, every second array had a reversed labeling orientation.

 
Contributor(s) Sitras V, Paulssen RH, Grønaas HS, Vårtun A, Acharya G
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jul 04, 2007
Last update date Mar 17, 2012
Contact name Ruth Hracky Paulssen
E-mail(s) ruthp@fagmed.uit.no
Phone +47 77645480
Fax +47 77644650
URL http://www.unn.no/labforum
Organization name Universitetet i Tromsø
Department Institute of Clinical Medicine
Lab Molecular Medical Research
Street address MH-Bygget Breivika
City Tromsø
ZIP/Postal code N-9037
Country Norway
 
Platforms (1)
GPL4790 NMC Human 35k oligo array v2.1
Samples (17)
GSM207427 Near term replicate 1
GSM207428 Near term replicate 2
GSM207429 Near term replicate 3
Relations
BioProject PRJNA101409

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE8375_RAW.tar 64.4 Mb (http)(custom) TAR (of GPR)
Processed data included within Sample table

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