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Series GSE30392 Query DataSets for GSE30392
Status Public on Nov 28, 2011
Title The NOD/SCID Xenograft Model Provides Clinically-Relevant Insights into Glucocorticoid-Induced Gene Expression in Childhood B-Cell Precursor Acute Lymphoblastic Leukemia
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Introduction. Glucocorticoids are critical drugs used to treat acute lymphoblastic leukemia, and response to glucocorticoids is highly predictive of outcome. Here we report a study evaluating the NOD/SCID xenograft mouse model to investigate glucocorticoid-induced gene expression. Methods. NOD/SCID mice were inoculated with ALL-3, a glucocorticoid-sensitive xenograft, and when highly engrafted were randomised to either dexamethasone 15mg/kg or vehicle control IP. Cells were harvested at 0, 8, 24 or 48 hours thereafter, RNA was extracted and hybridised onto Illumina WG-6_V3 chips. Results. The 8 hour dexamethasone-treated timepoint had the highest number of significantly differentially expressed genes with minimal changes seen across the time-matched controls. Replicate analysis revealed that using data from 3 replicates instead of 4 resulted in excellent recovery scores of >0.9 at timepoints with high signal. When assessed at the level of pathways, gene expression changes in the 8 hour xenograft samples were similar to patients treated with glucocorticoids. Conclusions. The NOD/SCID xenograft mouse model provides a reproducible experimental model system in which to investigate clinically-relevant mechanisms of in vivo glucocorticoid-induced gene regulation in ALL; the 8 hour timepoint provides the highest number of significantly differentially expressed genes; time-matched controls are redundant and excellent recovery scores can be obtained with 3 replicates.
 
Overall design At 0, 8, 24 or 48 hours, NOD/SCID xenograft mice were treated with vehicle control, or dexamethasone. We used 4 biological replicates per time point (3 at the 48hour time point), each of which went onto an Illumina HumanWG-6_V3_0_R1_11282955_A microarray. Samples from each of the 7 groups were divided across a total of 5 microarray slides
 
Contributor(s) Bhadri VA, Cowley MJ, Kaplan W, Trahir TN, Lock RB
Citation(s) 22093874
Submission date Jul 05, 2011
Last update date Feb 18, 2019
Contact name Vivek A Bhadri
E-mail(s) vbhadri@ccia.unsw.edu.au
Organization name Children's Cancer Institute Australia for Medical Research
Department Leukaemia Biology Program
Street address Lowy Cancer Research Centre
City Randwick
State/province NSW
ZIP/Postal code 2031
Country Australia
 
Platforms (1)
GPL6884 Illumina HumanWG-6 v3.0 expression beadchip
Samples (26)
GSM754214 xenograft_control_time0_rep1
GSM754215 xenograft_control_time0_rep2
GSM754216 xenograft_control_time0_rep3
Relations
BioProject PRJNA143443

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE30392_RAW.tar 6.3 Mb (http)(custom) TAR
GSE30392_non-normalized.txt.gz 5.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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