E-GEOD-4248 - Transcription profiling of mouse thymocytes from ild type or RORg-/- animals

Submitted on 15 February 2006, released on 12 June 2008, last updated on 3 May 2014
Mus musculus
Samples (4)
Array (1)
Protocols (2)
Microarray analysis was performed in order to identify changes in gene expression in thymocytes isolated from RORg-/- mice in comparison to those of wild type mice. Experiment Overall Design: Microarray analyses were carried out by the NIEHS Microarray Group (NMG). Gene expression analysis was conducted using Agilent Mouse arrays (Agilent Technologies, Palo Alto, CA) representing about 20,000 genes. For each condition, equal amounts of total RNA from thymocytes of three individual wild type or RORg-/- mice were pooled and amplified. Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 1 mg of total RNA, Cy3- or Cy5-labeled cRNA was synthesized according to manufacturer’s protocol. For each comparison, 750 ng of each Cy3- and Cy5-labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 h in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Slides were washed as indicated in this protocol and then scanned with an Agilent Scanner. Data was obtained with the Agilent Feature Extraction software (v7.1) using defaults for all parameters.
Experiment types
transcription profiling by array, unknown experiment type
NABP1, a novel RORgamma-regulated gene encoding a single-stranded nucleic-acid-binding protein. Hong Soon Kang, Ju Youn Beak, Yong-Sik Kim, Robert M Petrovich, Jennifer B Collins, Sherry F Grissom, Anton M Jetten. Biochem J 397(1):89-99 (2006)
Investigation descriptionE-GEOD-4248.idf.txt
Sample and data relationshipE-GEOD-4248.sdrf.txt
Processed data (1)E-GEOD-4248.processed.1.zip
Array designA-AGIL-8.adf.txt