UTHSC BXD Hippocampus MBD-Seq RPKM Log2 (Aug24)

Summary

The dataset was generated from male and female mice from 11 BXD recombinant inbred strains to examine the methylome that will reveal the genetic basis for individual susceptibility and difference in the chronic basis of the Gulf War Illness (GWI).

There are two groups of animals in this study. Control mice (CTL) received normal handling and housing for the study period. At 60 days of age, the animals in the treatment group (DD+DFP) were placed on drinking water containing 20 mg of corticosterone for 7 days (CORT). On the 7th day, the animals were injected i.p. with 4mg/kg diisopropyl fluorophosphate (DFP). From Week 3, the animals receive  CORT at alternative week in Week 3, Week 5, Week 7, Week 9, and Week 11 for 5 times. In Week 12-41 no treatment was applied. In Week 42 final CORT was applied to the animals, and in Week 43 Euthanized and prepared tissues (hippocampus) for DNA extraction, MBD enrichment, and MBD-seq analysis. 

Experiment design

Male and female mice from 11 BXD strains aged 60-80 days of age were the subjects for this study. All subjects received corticosterone in their drinking water (20mg% w/v) for seven days.  On the eighth day, the animals received 4.0 mg kg-1 i.p. diisopropylfluorophosphate (DFP), a sarin surrogate. Over the next 300 days and on alternate weeks, the animals received corticosterone as above in their drinking water. This was done to maintain the neuroinflammatory effect of the original DFP treatment. One week following the last corticosterone treatment, the mice were euthanized and the medial prefrontal cortex harvested. The DNA was extracted from the tissues and prepared for MBD-seq to identify genome-wide methylation and RNA was extracted for analysis.

About cases

About data processing

MBD-seq: This stands for Methyl-binding domain sequencing. This uses a methyl-binding protein to enrich for fragments of DNA that have methylated CpGs. This is very similar to ChIP-seq. Instead of single CpG resolution, the quantification is based on how many sequenced reads maps to a particular region of the mouse genome. Number of sequenced reads were counted at every 150 bp non-overlapping window. The data on Genenetwork are the 150 bp regions that (1) contained CpGs, and (2) had sufficient number of reads mapping to it (counts per million of > 0.5 in at least 5 libraries).
Standardizing microarray and MBD-seq: Since each probe ID on the microarray platform has a known location, you can get the corresponding 150 bp from the MBD-seq data. But the data types are quite different: MBD-seq is methylation level of a regions that has CpGs; microarray is methylation level of a CpG.