Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 6
Release date: Oct 31 2007
Last update date: Aug 28 2018
Access: Public
Diseases: Deficiency Diseases, Ovarian Neoplasms
Genes: NOBOX, ASTL, JAG1, FETUB, RSPO2, POU5F1, SALL4, DMRT1
Dataset link Microarray Analyses of Newborn Mouse Ovaries Lacking Nobox

Experimental Protocol


Newborn ovaries were pooled separately from wild type and Nobox -/- animals and total RNA isolated using RNeasy mini kit (Qiagen, CA). Newborn ovaries were collected within 12 hours of delivery. Animal experimentation was approved by the Institutional Animal Care and Use Committee of Baylor College of Medicine. Three independently pooled RNA samples from wild type and Nobox -/- newborn ovaries were used to generate biotinylated cRNA. Biotinylated cRNA was hybridized to GeneChip Mouse Expression Set 430 2.0 (Affymetrix, Inc.). Since three independent experiments were performed from three independent pools of wild type and Nobox -/- RNA, signal intensities for particular genes were averaged between the three chips and ratio of the wild type over knockout signal calculated. Signal less than 100 was considered background. The raw data in the Affymetrix CEL files were normalized by the RMA method (robust multi-array analysis) [15, 16]. Then the null hypothesis was tested that there is no significant changes in gene expression between the treatment pairs. This was done by LIMMA [17] and the pooled local error (LPE) method [18]. The raw pvalues were adjusted by the Benjamini-Hochberg method for the false discovery rate of 5% [19]. We used DAVID database [20] to aid in functional annotation of genes affected by Nobox deficiency

Repositories


GEO

GSE7775

ArrayExpress

E-GEOD-7775

BioProject

PRJNA109019

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Contact


Aleksandar Rajkovic