Overview

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.

Methods

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.

Files

Here is a list of the files present in this folder. All data are stored as comma-separated-values files.

  1. expressionData.csv contains the normalized and batch-corrected expression data, with 47,231 rows (for Illumina probes) and 114 columns (for different CLL patients).
  2. probeFeatures.csv contains annotations for the Illumina probes, which were updated in Summer 2017. This file contains 47,231 rows and 8 annotation columns.
  3. safeClinical.csv contains relevant clinical information about the samples. This file contains 114 rows, one for each CLL patient, and 26 columns of clinical data. All potentially identifying information has been removed from the clinical data set.

Subset

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.