UCLA BXD and BXH Cartilage Illumina WG-6 v2 **

Accession number: GN208

Summary:

Associated Publication: Jaijam Suwanwela, Aldons J. Lusis, and colleagues, 2011. PDF version 20954177

Description from the paper by Suwanwela and colleagues: "The recombinant inbred strains that have been proven to have significant differences in bone traits and that were available from the Jackson Laboratories (Bar Harbor, ME, USA) were used. Those strains were C3H/HeJ, C57BL/6J, DBA/2J, B6Cc3-1/KccJ, BXH2/ TyJ, BXH4/TyJ, BXH6/TyJ, BXH7/TyJ, BXH8/TyJ, BXH9/TyJ, BXH14/ TyJ, BXH19/TyJ, BXH22/KccJ, BXD1/TyJ, BXD2/TyJ, BXD6/TyJ, BXD 12/TyJ, BXD16/TyJ, BXD 19/TyJ, BXD21/TyJ, BXD 24a/TyJ, BXD27/ TyJ BXD 28/TyJ, BXD 32/TyJ, BXD 39/TyJ, BXD 40/TyJ, and BXD 42/ TyJ recombinant inbred (RI) strains. All mouse protocols were performed according to the guidelines of the American Association for Accreditation of Laboratory Animal Care (AAALAC). Cartilage from the rib cage of 1- to 2-day-old male mice was dissected to remove bone and any adherent noncartilage tissue for microarray analysis. The cartilage was digested in 0.3% bacterial collagenase (Invitrogen, Carlsbad, CA, USA) for 10 hours, and the cells were collected by centrifugation. RNA was isolated and purified using the Rneasy kit (Qiagen, Valencia, CA, USA). It then was quantified and assessed for purity using a NanoDrop spectrophotometer (Rockland, DE, USA). RNA integrity was verified with a BioAnalyzer 2100 (Agilent, Santa Clara, CA, USA). Given the small amount of RNA we could isolate from the rib cages, we had to pool the RNA from three mice from the same strain. All 27 strains were applied separately to the Illumina arrays."

"llumina Mouse-6 V1 BeadChip mouse whole-genome expres- sion arrays (Illumina, Inc., San Diego, CA, USA) were used in this study. Of the 27 RNA samples from 27 strains, 3 were hybridized twice and were used as technical replicates. A total of 200 ng of DNA-free, quality-checked RNA was amplified using the Ambion Illumina RNA amplification kit with biotin UTP (Enzo, Farming- dale, NY, USA) labeling. The Ambion Illumina RNA amplification kit uses T7 oligo(dT) primers to generate single-stranded cDNA, followed by a second-strand synthesis to generate double- stranded cDNA, which then is column-purified. In vitro transcription was done to synthesize biotin-labeled cRNA using T7 RNA polymerase. The cRNA then was column-purified. The cRNA then was checked for size and yield using the Molecular Probes Quant-iT RiboGreen assay (Invitrogen). A total of 1.5 mg of cRNA was hybridized to each array using standard Illumina protocols with streptavidin-Cy3 (Amersham, Sigma, St. Louis, Mo, USA) being used for detection. Slides were scanned on an Illumina Beadstation and processed using BeadStudio (Illumina, Inc.)."

"The R software (http://cran.r-project.org/), a system for statistical computation and graphics, was used to analyze the data.(11) Data were normalized using Lumi,(12) a Bioconductor (Seattle, WA, USA) package designed to analyze Illumina microarray data that includes data input, quality control, variance stabilization, normalization, and gene annotation. The function ‘‘lumi- Expresso,’’ which uses a variance-stabilizing transformation (VST) algorithm, was used to take advantage of the technical replicates available on every Illumina microarray."

Normative gene expression in cartilage tissue for a set of BXD and BXH strains of mice generated using the Mouse WG-6 v2 Illumina Sentrix bead array. The data set includes 14 BXD strains (the Jackson Laboratory series generated by Dr. Ben Taylor), 10 of the BXH series, and the 3 parental strains, C57BL/6J (B), DBA/2J (D), and C3H/HeJ (H). Data were generated by JJ Suwanwela, Evan Williams, and Dr. Jake Lusis.

About the cases used to generate this set of data:

Based on the expression of Xist, probe ILM104280446, these samples are mixed sex pools. Expression of Xist varies from 7.2 to 9.0, consistent with mixed sex samples.

About the tissue used to generate this set of data: Please see publication and above text from the key paper.

Cartilage. JJ, please provide data on age and sex. Based on the expression of Xist, probe ILM104280446, these samples are mixed sex pools. Expression of Xist varies from 7.2 to 9.0, consistent with mixed sex samples.

Index TubeID Group Strain Age Sex Source 1 CASEIDHERE GDP STRAINHERE AGE SEX UCLA JL

About downloading this data set:

This is a confidential data set for both BXD and BXH strains of mice generated at UCLA by Jaijam Suwanwela, Evan Williams, and colleagues in the laboratory of Dr. Jake Lusis. Contact or Dr. Lusis for additional information.

About the array platfrom:

Illumina Mouse WG-6 v2

About data values and data processing:

Illumina rank invariant transform was further normalized by Jaijam Suwanwela using standard 2z + 8 method common to many data sets in GeneNetwork. The final values entered in GeneNetwork are a modified z score of rank invariant Log2 expression data, with a mean of 8 units and a SD of 2 units for each array. One unit of expression corresponds to approximately a 2-fold difference in expression. These values were entered by Evan G. Williams, Aug 2008, UCLA. QTL Reaper results were computed by EGW. All annotation files for this array in GeneNetwork were generated by Xusheng Wang and RW Williams.

Index TubeID Strain Original File ID QC1 QC2 QC3 QC4 QC5 QC6 QC7 Batch Id Used for batch control 1 R2595E.1 129S1/SvImJ R2595E.1.CEL 1.79 115 61.00% 37.50% 1.50% 1.46 0.77 1 Y

Data source acknowledgment:

Alfons J. Lusis and colleagues. Dissertation work of Jaijam Suwanwela

Information about this text file:

JJ needs to provide these data. Current skeleton text by RWW

GEO Series Data: This section to be used for GEO submission of the whole series of arrays

GSE Series: none

Status: unreviewed, unpublished

Title: Get from JJ

Organism(s): M. m. musculus, inbred strains, BXD and BXH type

Experiment type: Normative expression of genes in young adult mouse cartilage

Summary

Overall design

Contributor(s): Jaijam Suwanwela and Alfons J. Lusis, UCLA

Citation(s)

Submission date
Contact name: Jaijam Suwanwela and Alfons J. Lusis
E-mails: jaijam1220@gmail.com
Phone
FAX
URL
Organization name: UCLA
Department(s): Genetics
Laboratory(s): Lusis
Street address
City: Los Angeles
State/province: CA
ZIP/Postal code
Country: USA

Platforms: Illumina Mouse WG-6 v 2.0

Samples