MassIVE MSV000098217

Partial Public PXD065063

In Depth Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2

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Description

A study to determine the molecular factors interacting with the active, upstream promoter of the transcription factor FOXP2 in HEK293 cells. Promoter-interacting proteins were tagged via proximity labeling with dCas9-APEX2 leveraging three gRNAs tiling the promoter and two negative controls: untargeted no gRNA with labeling (1) and with exclusion of biotin phenol to prevent labeling (2). Tagged proteins from three independent biological replicates were purified with streptavidin and peptides were prepared by on bead digestion with trypsin/LysC. Digested peptides were labeled with TMTpro 18-plex reagents according to the following scheme: g2 Rep1:126; g2 Rep2:127N; g1 Rep3:127C; g1 Rep1:128N; NoG+ Rep3:128C; NoG+ Rep1:129N; NoG- Rep1:129C; empty:130N; NoG+ Rep2:130C; NoG- Rep2:131N; g3 Rep3:131C; g3 Rep1:132N; g3 Rep2:132C; sample pool: 133N; g1 Rep2:133C; NoG- Rep3:134N; g2 Rep3:134C; empty:135N. Peptides were separated with online 2D-LC high pH/low pH twelve-step fractionation and directly injected to a Thermo Ascend tribrid mass spectrometer for data acquisition via RTS-SPS-MS3. [doi:10.25345/C59883086] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Transcription Factors ; Proximity Labeling ; Locus-Specific Chromatin Proteomics ; FOXP2 ; dCas9-APEX2 ; Tribrid Mass Spectrometer ; 2D-LC-TMT-RTS-SPS-MS3 ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Michael Snyder, Stanford University, United States
Tim MacKenzie, Stanford University, United States
Submitting User: tmackenz

Publications

Tim MG MacKenzie, Lucia Ramirez, Ruiqi Jian, Lihua Jiang, Michael P Snyder.
Comprehensive Characterization of the Promoter Proximal Proteome of Single Copy Locus FOXP2.
https://www.biorxiv.org/content/10.1101/2025.07.10.663086v1.

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