HQF BXD Striatum Illumina Mouse-6.1 November 2007 Rank Invariant Data Set modify this page

INFO file to be provided by Rob Williams and Lu Lu. This data set that is still being error-checked and annotated. Data quality appear to be excellent. There do not appear to be any errors in strain assignment of the BXD lines. Conventional inbred strain (the Mouse Diversity Panel) have not been error checked for genotype.

Illumina Mouse-6.1 array (second generation of the Illumina Mouse 6 platform)

This Rank Invariant Illumina data set yields 1567 probes associated with LOD values of great than 10 using data from 54 BXD strains. This is the second large data set Dr. Lu and colleagues have generated and the first to use the slightly modified Illumina array (6.1) and to use the new slide holder for processing. This data set is of high quality. Our first Illumina array data set (LXS hippocampus May07 Rank Invariant using the first generation Mouse-6 array) yielded 1183 probes with LOD>10 using 75 LXS strains.

Figure 1: Sex balance illustrated by the expression of Xist (Illumina probe 104280446). Strains represented by a single male sample have low expression (BXD44, 65, 66, 69, 70, 85, 86, 87, 89, 90, and 97). Strains represents by one or more female samples have high expression (KK, BXD43, 68, 77, and 100). All other strains are represented by one male and one female sample. Note that the Xist signal intensity in females of the wild strains (PWK, PWD, MOLF, CAST and WSB) is lower than in standard mouse strains.

Useful links

  1. A movie of the dissection of the brain, including the striatum, by Dr. Glenn Rosen.

Notes for Dr. Lu on the RNA cleanup (Jan 22, 2008)

We purify RNA by using Na4OAc before running arrays. Here is the detailed method:

Final RNA purification protocol

  1. Add 1/10th volume of 3M Na4OAc , PH5.2. If the sample was eluted with 100 µl nuclease-free Water as suggested, this will be 10 µl of 3M Na4OAc.
  2. Add 2.5 volumes of 100% ethanol (250 µl if the RNA was eluted in100 µl). Mix well and incubate at –20°C for 2hrs.
  3. Centrifuge at speed of 1,3000 rpm for 20 min at 4°C,Carefully remove and discard the supernatant.
  4. Wash the pellet with 800 µl 75% cold ethanol, centrifuge at speed of 8600 rpm for 5 min, and remove the 75% ethanol. Wash again.
  5. To remove the last traces of ethanol, quickly respin the tube, and aspirate any residual fluid.
  6. Air dry the pellet.
  7. Resuspend pellet in nuclease-free water.