A survey of gene expression in 17 mouse tissues with biological replication

Description

A tissue survey was performed examining gene expression profiles across 17 mouse tissues. The unique feature of this tissue survey is that 5 biological (mouse) replicates were profiled individually, as opposed to hybridizing a pool of their RNA samples to microarrays.

Gene expression was measured on 8-weeks old males from the C57/BL/6J strain, fed a standard 6% fat chow diet with ad libitum access to food and water. Five animals were sampled for liver, heart, lung, kidney, adrenals, muscle, testes, gonadal fat, and brown fat. A second set of five mice were sampled for pancreas, brain, duodenum, jejunum, ileum, colon, stomach, and spleen. One adrenal sample did not pass quality control so the sample size is consequently four for that tissue. Due to highly degraded RNA samples from pancreas, these extractions were repeated in a third set of five animals. All animals, however, where sex and age matched, and were handled by the same protocol. Kidney samples were hybridized in duplicate to use extra available hybridization spots on the BeadChips. For detailed protocols see Verdugo et al. (in prep).

References

A survey of gene expression in 17 mouse tissues with biological replication
Verdugo RA, Paigen BJ, Churchill GA.
Manuscript in preparation.

Datasets

Custom Genome Browser Tracks

The files below may be used to display gene expression from the tissue survey in a genome context. You can download these files to your desktop and upload them to the UCSC Genome browser or you can directly provide the url to these links. The mm9 assembly version should be used. To use these custom tracks, follow the instructions under "Loading a Custom Track into the Genome Browser" in UCSC Genome Browser Help . Note: You do not need to uncompress these files. Paste in their URLs or upload them as they are.

  • Probe locations: Use this track to show the location of probes on the mm9 genome. Use this Track Description file to see a description page when you click on a probe. The "outside link" will direct you to an expression report hosted in our server.
  • Expression values: This track allows you to see heatmaps of gene expression in genome context. Use this Track Description file to see a description page when you click on a probe. This will show a color palette for expression values. The "outside link" will direct you to an expression report hosted in our server.
  • RIDGEs: This track contains Regions of IncreaseD Gene Expression (RIDGEs) predicted by dynamic programing in each tissue separatly. Use this Track Description file to see a description page when you click on a probe. The track will show each tissue in different color.

Online database

This web interface allows you to search for expression profiles by probe annotations, such as location on the genome, EntrezGene id, gene official symbol, and mRNA accession number. You can also filter the list by tests results to find, for instance, genes that are differentially expression between tissues with FDR < 0.01. You can export query results in a variety of formats. You can see online plots of gene expression across tissues.

bioGPS Plugin

This tissue survey will also be available as a plugin in bioGPS. Look for the CGDTissueSurvey plugin and add it to your layout.

GEO entry

This dataset will be made available as soon as the manuscript is published.