biostudies-arrayexpressChristophe RACHEZMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15196Chromatin association of several nuclear RNA exosome components and cofactors in BMEL cells is dependent on the presence of HP1 proteins. TKO2 cells invalidated for the expression of the three HP1 isoforms (Cbx1-/-; Cbx3-/-; Cbx5-/-) are compared to Het32 cells (Cbx1+/+; Cbx3+/+; Cbx5+/-) expressing HP1 as controls.biostudies-arrayexpressLibrary Construction - ChIP-seq libraries were prepared with DNA Library Prep Kit for Illumina by the Genom'IC core facility (Paris, France).Nucleic Acid Extraction - Samples were incubated overnight at 65°C to reverse crosslink, followed by proteinase K and RNase A treatment. DNA was isolated using a NucleoSpin PCR purification kit (Macherey Nagel).Sample Collection - BMEL cells were crosslinked by a double procedure of 2 mM Di-Succinimidyl-Glutarate (DSG, Merck) and 1% formaldehyde. Chromatin was sonicated for 15 cycles of 30 seconds on and 30 seconds off. Following extraction, chromatin immunoprecipitation (ChIP) was incubated overnight with 4 µg of antibody. followed by the addition of protein G beads (Dynabeads) incubated for an additional 1h. Beads were then washed 5 times for 5 min each on a rotating wheel.Sequencing - ChIP samples were processed for Illumina paired-end (PE40) sequencing performed at the Genom'IC core facility (Paris, France).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Bigwig files were generated from BAM files with bamCoverage (parameter: –normalizeUsing CPM) from Deeptools (v3.1.3). Peak calling was performed using MACS2 (v.2.1.1) (parameters: -p 0.05).Sequence Alignment - ChIP-seq reads were mapped to mm10 using bowtie2 (v2.3.4) (parameters: -N 0 -k 1 –very-sensitive-local). We then selected reads with a MAPQ equal or higher than 30 corresponding to uniquely mapped reads for further analysis.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500ChIP-seqMus musculusChristophe RACHEZfalseChIPseq of RNA Exosome components in BMEL cell lines invalidated or not for the expression of the three HP1 isoforms (CBX1, CBX3, CBX5)Chromatin association of several nuclear RNA exosome components and cofactors in BMEL cells is dependent on the presence of HP1 proteins. TKO2 cells invalidated for the expression of the three HP1 isoforms (Cbx1-/-; Cbx3-/-; Cbx5-/-) are compared to Het32 cells (Cbx1+/+; Cbx3+/+; Cbx5+/-) expressing HP1 as controls.2026-03-31T00:00:00Z2026-03-31T01:03:46.971Z2025-06-04T19:00:43.969ZE-MTAB-15196ERP173169E-MTAB-15194EFO_0002944EFO_0004170EFO_0002692EFO_0004917EFO_0005518EFO_0003816EFO_0004184