in Jake Lusis Lab at UCLA.
General information and background for BXD and BXH UCLA Cartilage data sets:
- BXD UCLA data sets
- BXH UCLA data sets
All mice were maintained on a 12 h light–12 h dark cycle and fed ad libitum.
Mice were killed at XX weeks, and tissues, including the cartilage were immediately collected and flash-frozen in liquid nitrogen.
All procedures of housing and treatment of animals were performed in accordance with Institutional Animal Care and Use Committee regulations (UCLA).
Array design and preparation of labeled cDNA and hybridizations to microarrays for the mouse tissue samples. RNA preparation and array hybridizations were performed at UCLA using Illumina Mouse 6 version 1.1 arrays.
Mouse cartilage was homogenized, and total RNA was extracted using Trizol (Invitrogen) according to manufacturer's protocol. ADD MORE.
Arrays were quantified using Illumina Rank Invariant protocol and normalized to a mean of 8 units and a SEM of all probes to 2.0 units (a modified Z score).
Data entered by Evan Williams (July 24, 2008).
These unapproved notes by RWW, Sept 4, 2008.
Notes from Evan Williams on this version 2 data set: I uploaded JJ's new 'corrected' dataset into GN. I didn't take a look at anything to make sure it was more right than before (I actually am not really sure what the problem was) but hopefully it's better this time. It contains all 46k probes, but I think I reimported the v1 to contain all 46k probes too, so I don't actually know what the differences are.
-Evan
Begin forwarded message:
From: egw4693
Date: September 20, 2008 12:03:38 AM CDT
To: jaijam suwanwela
Subject: v2 now in GeneNetwork
Hey JJ,
I uploaded the (hopefully) corrected data set into GeneNetwork. I put it on a test site for you to look over and make sure everything is OK before it goes into GeneNetwork.
www.genenetwork.org , look under either BXD or BXH and select Cartilage mRNA, then select the "V2" combined.
