The second analysis was performed with a total of 308 leukemia patient samples using Affymetrix expression chips that were divided into three groups.
We next investigated the consistency of gene expression measurements of leukemia samples when using different total RNA extraction methods by performing an unsupervised hierarchical clustering analysis.
For the research, Baylin and Zahnow's team worked with leukemia, breast and other cancer cell lines, and human tumor samples, using the lowest possible doses effective against the cancers.
We have previously shown that MerTK is ectopically expressed in pediatric T-ALL patient samples using a retrospective analysis of banked T-cell leukemia patient samples (21).
cDNA synthesis was performed in all samples, using oligo random hexanucleotides and M-MLV (Moloney Murine Leukemia Virus) reverse transcriptase (Promega Corp. Madison, USA), as previously described [ 30].
We tested our algorithm on VAFs obtained from deep read counts information for SNVs from an acute myeloid leukemia sample (AML1/UPN933124) using data from Ding et al. (2012).
Total RNA extracted from CLL-cell samples using an RNeasy mini kit (Qiagen, Crawley, UK) was reverse transcribed using Moloney murine leukemia virus reverse transcriptase (Promega, Southampton, UK) and an oligo dT 15 primer.
Patient leukemia samples were analyzed using 244 K microarrays (Agilent Technologies, Santa Clara, CA, USA).
In order to assess the frequencies of mature DCs in leukemia samples, we therefore used a second immunophenotypic panel.
cDNA was synthesized from 1 μg of mRNA from each sample using Moloney murine leukemia virus reverse transcriptase (M-MLV RT) and random hexamers (Promega, Madison, WI, USA).
