INIA Hypothalamus Affy MoGene 1.0 ST (Nov10)

Accession number: GN281

Summary:

These hypothalamic gene expression data were generated by Khyobeni Mozhui, Lu Lu, and Robert W. Williams and colleagues with funding support from NIAAA. The data set includes samples from 50 strains, including 46 BXDs, both parental strains, and reciprocal F1 hybrids. Expression data were generated using the Affymetrix Mouse Gene 1.0 ST exon-style microarray (multiple probes in all known exons) by Lorne Rose in the UTHSC Molecular Resources Center (MRC), Memphis TN. The table below provides a summary of cases, sex, and age. Hypothalamic tissue was dissected by K. Mozhui (description to follow) with special attention to time of day (every sample has time stamp). RNA was extracted by K. Mozhui. All other processing steps by the UTHSC MRC by L. Rose. Data were processed by Arthur Centeno.

Data released initially Nov 25, 2010, updated March 7, 2011 by A. Centeno and K. Mozhui to add two additional arrays. Data appear to be error-free in terms of sex and strain assignments shown in the table below.

Dissection protocol:

1. Animals were sacrificed by quick cervical dislocation and brains were removed and stored in RNAlater (www.ambion.com) for 2 to 3 days
2. Brain was placed with ventral side up and a partial cut was made with a blade at -2.5 from Bregma (just a little rostral from the pontine fibres when viewed from the ventral side)
3. The brain was then place in a coronal matrix and a 2 mm section was made rostral to the first cut
4. The 2mm Section was placed on a clean glass slide and hypothalamus was sliced out and placed in a tube on dry ice.
5. To dissect out the BLA, the temporal lobes were detached by placing a scalple in the lateral ventricles and teasing it apart. The cortical amygdala was removed and the BLA was then sliced out and placed in a tube on dry ice.
6. Tissues from two mice of the same strain and sex were pooled. The only exceptions to this are the BLA samples for strains BXD5, BXD13, BXD16, BXD19, BXD25, BXD38, BXD51, and BXD61 (tissue from only one animal).

RNA isolation
Total RNA was purified using the RNAeasy micro kit on the QIAcube system (www.qiagen.com). RNA purity and concentration was checked using 260/280 nm absorbance ratio and RNA integrity was analyzed using the Agilent Bioanalyzer 2100 (Agilent Technologies).

This preliminary data set is associated with 430 eQTLs with LOD scores above 10. Peak LRS is 146 for Trait ID 10513604 (Hdhd3).

About the strains used to generate this set of data

Animals and Tissue Used to Generate This Set of Data:

Sample Processing:

Experimental Design and Batch Structure:

Data Source Acknowledgements: