The SuperSeries data of microarray (GSE122773), RNA-seq (GSE122774), ChIP-seq (GSE122775), and ATAC-seq (GSE122776) raw and processed data were deposited in Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo) as GSE122777. High-throughput sequencing was performed on the Illumina HiSeq 2500. We targeted 45 to 50 million reads per sample for RNA-seq and 25 to 30 million reads for ChIP-seq and ATAC-seq. Sequencing reads in FASTQ files were examined by FastQC (v0.11.5; www.bioinformatics.babraham.ac.uk/projects/fastqc).

For RNA-seq (n = 3 per genotype), total RNAs isolated from Nf1fl/fl;DhhCre and Runx1fl/fl;Runx3fl/fl;Nf1fl/fl;DhhCre mouse DRG/tumors were amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies). Paired-end reads were aligned to the mm10 reference genome using TopHat (v2.0.13). Aligned BAM files were converted into raw count files using feature counts (v1.4.6). The raw count tables were normalized using the Bioconductor’s edgeR-TMM normalization methods, and DEGs were detected using Bioconductor’s limma/voom package. The |fold change| > 2× and FDR P < 0.05 were used as cutoffs to detect DEGs. The abundance of each transcript variant was calculated using Kallisto (v0.43; https://pachterlab.github.io/kallisto).

For ChIP-seq (n = 1 per genotype), primary Nf1fl/fl;DhhCre mouse neurofibroma cells were used for the ChIP assay according to Magna ChIP instruction (Millipore, Billerica, MA) as described (40). Reads were trimmed using Trim Galore (v0.4.4; www.bioinformatics.babraham.ac.uk/projects/trim_galore) and aligned to the mouse reference genome (mm10) using Bowtie2 (v2.2.6; http://bowtie-bio.sourceforge.net/bowtie2). HOMER (v4.9; http://homer.ucsd.edu/homer) was used to predict and annotate differential peaks with the following parameters (-F 4 -L4 -c 2 -style factor -FDR 0.001). We considered differential peaks with FDR P < 0.001 as statistically significant.

ATAC-seq (n = 1 per genotype) was performed as described (41) using FACS-sorted EGFP+ Nf1fl/fl;DhhCre or Runx1fl/fl;Runx3fl/fl;Nf1fl/fl;DhhCre mouse DRG/tumor cells. Reads were trimmed using Trim Galore (v0.4.4) and aligned to the mm10 genome using Bowtie2 (v2.2.6). HOMER (v4.9) was used to predict and annotate differential peaks with the following parameters (−size 75 -mDist 50 -style factor -FDR 0.05). We considered differential peaks with FDR < 0.001 as statistically significant.

For microarray, tumor initiating–like cells were FACS-sorted from neurofibroma tumors, and total mRNA was extracted using the Qiagen Kit. Affymetrix Human Genome U133 Plus 2.0 array was used for transcriptome analysis. CEL files were preprocessed using Bioconductor’s affy package with Robust Multi-array Average normalization method. DEGs were predicted using Bioconductor’s limma package. The |fold change| > 2× and FDR P < 0.05 were used as cutoffs to detect DEGs.

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