This folder contains supporting data for the manuscript:
Abruzzo LV, Herling CD, Calin GA, Oakes C, Barron LL, Banks HE, Katju V, Keating MJ, Coombes KR. Trisomy 12 CLL Expresses a Unique Set of Activated and Targetable Pathways. Submitted.
This manuscript describes features that make trisomy 12 cases of chronic lymphocytic leukemia (CLL) different from other cytogenetic subsets.
CLL cells were negatively selected from peripheral blood. Then total RNA was extracted, reverse-transcribed to cDNA, biotin-labeled, and hybridized to Illumina HumanHT-12 v4 microarrays. Data were exported using Illumina GenomeStudio software, preprocessed, and normalized using version 2.2.1 of the lumi
package in R version 2.12.0. Batch effects were removed by aligning the mean and standard deviation of each gene.
Here is a list of the files present in this folder. All data are stored as comma-separated-values files.
Although the full data set contains gene expression and clinical data on 114 patients with CLL, the analysis described in the manuscript only uses 97 of those cases. The subset consists of cases that have at most one of the common cytogenetic abnormalities (+12, del(13q), del(11q), del(17p), or none of the above). You can identify the subset using the Puritry
column of safeClinical.tsv
.