GSM8773821: IMR90, SIN3A_11A_siFOXK1, Cut&Run, merge; Homo sapiens; OTHER
For ChIPseq, cells were fixed in 1% formaldehyde for 10 min at room temperature. Cells were quenched in ice cold PBS with 125 mM glycine. Chromatin was then sonicated using probe sonicator. Samples preparation for Cut&Run were done following manufacturer (Epycipher CUTANA™). For RNAseq, IMR90 cells were infected with retroviruses coding for empty vector, FOXK1 or FOXK2. 48h following the end of antibiotic selection, cells were harvested in TRIzol and RNA was extracted. For ATAC-seq, transposition was performed directly on nuclei following manufacturer recommendations (Tn5 Illumina). For ChIP-Seq samples, size distribution and molarity of immunoprecipitated and input samples were evaluated on a 2100 bioanalyzer (Agilent Technologies). ChIP-seq libraries and CUT&RUN librairies were prepared using the KAPA hyperprep library kit (Roche Diagnostics). The number of PCR cycles was calculated based on the quantification of the ligation products (Illumina adapters) by qPCR. Library size distribution was assessed on a 2100 bioanalyzer (Agilent Technologies) and libraries were quantified by qPCR. Equimolar libraries were sequenced in paired end reads (PE100), on a Novaseq 6000 system or HiSeq 4000 for K562 ChIP-Seq (Illumina), with a S4 flowcell and a coverage of 50M for ChIP-Seq and H2AUb Cut&Run library. 10M fragments were sequenced for BAP1 and H3K4me1 Cut&Run per library. For RNAseq, libraries were prepared using ribosomal RNA depletion (KAPA RNA HyperPrep kit) with a sequencing depth of a minimum of 50 million reads.