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, DNA-FISH on metaphase spreads
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, Lymphocyte development was analyzed in the thymus, bone marrow, lymph nodes and spleen of 4 to 8-week-old mice. All single-cell suspensions were treated with Fc-blocking antibody (CD16-32, 1:200 dilution) before cell surface staining, in phosphate-buffered saline (PBS) with 2% fetal bovine serum for 30 min at 4 C. T lineage cell populations from the thymus were identified based on the expression of the following markers: double-negative (DN) cells (CD4 -CD8 -), vol.1, p.2
, double-positive (DP) cells (CD4 + CD8 + ) and single-positive (SP) cells (CD4 + CD8 -and CD4 -CD8 + ). T cells from the spleen were identified based on the expression of CD3 + TCRb + . The following antibodies were used for cell surface staining: anti-CD4, anti-CD44 (IM7, 1:200 dilution), anti-CD25 (PC61, 1:200 dilution), anti-TCRb (H57-597,1:200 dilution) and anti-CD28 (E18, 1:200 dilution). Flow cytometry was performed on a FACS Canto II (BD Bioscience) and data were analyzed using FlowJo (TreeStar)
, DNA isolation and sequencing
, The resulting libraries were then sequenced on an Illumina HiSeq 2000 or HiSeq 2500 using a V3 or V4 flow cell generation generating two 100-or 125-bp paired-end reads. Basecalling was performed with Illumina RTA 1.18.64. Bcl conversions into Fastq were performed using bcl2fastq version 1.8.3. Tumors were sequenced with an average coverage of 36x (range = 18-52) and control samples were sequenced
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