MassIVE MSV000098256

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RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions

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Description

We performed total proteome analysis in RB1 wild-type (RBWT) and RB1 knock-out (RBKO) hTERT1-RPE1 cells synchronized in the G1 phase via 6 days of contact inhibition. RBKO cells were generated with the CRISPR/Cas9 system, as previously described (PMID: 26314710). Four biological replicates were analyzed per genotype. Multiplexed mass spectrometry-based proteomics was performed using TMTpro barcoding reagents (PMID-33900084) and the SPS-MS3 method on an Orbitrap Fusion mass spectrometer. Prior to mass spectrometry analysis, the TMT set was fractionated offline by basic pH reversed-phase chromatography (bRPLC) into 24 fractions. Samples were labeled as follows TMT1 126 - RBKO G1_Replicate1 128n - RBWT G1_Replicate1 128c - RBWT G1_Replicate2 132c - RBKO G1_Replicate2 TMT2 129n - RBKO G1_Replicate3 131c - RBWT G1_Replicate3 132c - RBWT G1_Replicate4 133n - RBKO G1_Replicate4 [doi:10.25345/C5N01063X] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Retinoblastoma protein (RB), cohesin, CTCF, chromatin organization, loop formation, topologically associated domains (TADs), enhancer-promoter interactions, transcriptional regulation, TMTpro, Orbitrap Fusion, SPS-MS3 ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Ioannis Sanidas, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
Michael S. Lawrence, Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Broad Institute of MIT and Harvard, MA, United States
Wilhelm Haas, Massachusetts General Hospital and Harvard Medical School, United States
Submitting User: sambhavi
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