Bulk RNA-seq
tumours, logMurine endometrial cancer
TUMOURS
Patient analysis: patient microbiopsy RNA was extracted with the RNA easy FFPE kit (Qiagen). The RNA-seq library was produced from 100 ng of RNA with the Illumina TruSeq Exome kit (RNA Library Prep for Enrichment & TruSeq RNA Enrichment) according to the manufacturer’s instructions and then sequenced with an Illumina NovaSeq 6000. FASTQ files were then processed with STAR (v.2.7.10a). Briefly, FASTQ files were mapped to the human reference genome (gencode.v.27) and aligned reads were converted for counting with STAR. The quality of FASTQ files was also checked, by FATSQC (v.0.11.9). RNA-seq analysis was performed with R (v.4.0.3) and the DESeq2 package (v.1.30.1). logMurine endometrial cancer model: tumours were collected, snap-frozen and cryoground. RNA was extracted with a standard kit (Macherey-Nagel). The RNA-seq library was produced from RNA with Illumina TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat, according to the manufacturer’s instructions, then sequenced with Illumina NOVASeq. FASTQ files were processed as described above, except for the reference genome which was Mus_musculus.GRCm38 (GENECODE release 25). Analysis was done with DESeq2 (v.1.30.1) and ggplot (v.3.1.3) packages in R (v.4.0.3). EMT scoring and heatmaps were done with log