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Series GSE228463 Query DataSets for GSE228463
Status Public on Apr 12, 2023
Title Chromatin context-dependent regulation and modulation of prime editing [amplicon]
Organism Homo sapiens
Experiment type Other
Summary Prime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency of prime editing across target sites of interest has limited its adoption in the context of both basic research and clinical settings. Here, we set out to exhaustively characterize the impact of the cis-chromatin environment on prime editing efficiency. Utilizing a newly developed and highly sensitive method for mapping the genomic locations of a randomly integrated “sensor”, we identify specific epigenetic features that strongly correlate with the highly variable efficiency of prime editing across different genomic locations. Next, to assess the interaction of trans-acting factors with the cis-chromatin environment, we develop and apply a pooled genetic screening approach with which the impact of knocking down various DNA repair factors on prime editing efficiency can be stratified by cis-chromatin context. Finally, we demonstrate that we can dramatically modulate the efficiency of prime editing through epigenome editing, i.e. enhancing (or restricting) local chromatin accessibility in order to increase (or decrease) the efficiency of prime editing at a target site. Looking forward, we envision that the insights and tools described here will broaden the range of both basic research and therapeutic contexts in which prime editing is useful.
 
Overall design We randomly integrated a complex library of the synHEK3 reporters into a monoclonal K562 cell line constitutively expressing the PE2 prime editor. We further bottlenecked the pool to ~500 clones, each containing a unique combination of randomly inserted reporters, and performed T7-assisted reporter mapping on this population (T7-500-1). We further performed amplicon sequencing of synHEK3 reporters to measure the outcomes of prime editing (K562-HEK3-insCTT) as well as Cas9 editing (K562-HEK3-Cas9) in this pool of synHEK3 reporters. A few monoclonal lines were also derived from the 500-clone population. Files named "K562-SC1-5-OFF*" contain prime editing efficiencies measured in synHEK3 reporters in one of the monoclonal lines (Clone 5) in the settings of targeted gene silencing by CRISPRoffv2.1. "K562-HEK3-SC*" experiments measured the effects of various shRNAs on prime editing efficiencies in synHEK3 reporters in two monoclonal lines. Finally, the rest files are amplicon sequencing results of endogenous prime editing targets in the presense and absense of CRISPRa.
 
Contributor(s) Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid T, Kim H, Lalanne J, Nathans JF, Shendure J
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Submission date Mar 29, 2023
Last update date Jan 03, 2024
Contact name Xiaoyi Li
E-mail(s) xyli10@uw.edu
Organization name University of Washington
Department Department of Genome Sciences
Lab Jay Shendure
Street address 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platforms (3)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (145)
GSM7122326 T7-assisted reporter mapping library for synHEK3 reporters in a population derived from 500 clones [T7-500-1_S1]
GSM7122327 T7-assisted reporter mapping library for synHEK3 reporters in a population derived from 500 clones [T7-500-1_S1_2]
GSM7122328 Prime editing library of CTT insertions in synHEK3 reporters [K562-HEK3-insCTT]
This SubSeries is part of SuperSeries:
GSE228465 Chromatin context-dependent regulation and epigenetic modulation of prime editing
Relations
BioProject PRJNA949970

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE228463_CRISPRa_CXCR4_IL2RB_EGFR_CDKL5.csv.gz 598 b (ftp)(http) CSV
GSE228463_CRISPRa_K562_new.csv.gz 722 b (ftp)(http) CSV
GSE228463_CRISPRa_WTC11_new.csv.gz 346 b (ftp)(http) CSV
GSE228463_CRISPRoff_LRRC8C.csv.gz 4.0 Kb (ftp)(http) CSV
GSE228463_CRISPRoff_METTL2A.csv.gz 4.0 Kb (ftp)(http) CSV
GSE228463_CRISPRoff_USP7.csv.gz 4.0 Kb (ftp)(http) CSV
GSE228463_K562-HEK3-Cas9-Day1-XL281_S68_barcode_edit.txt.gz 2.2 Mb (ftp)(http) TXT
GSE228463_K562-HEK3-Cas9-Day2-XL281_S70_barcode_edit.txt.gz 1.8 Mb (ftp)(http) TXT
GSE228463_K562-HEK3-Cas9-Day4-XL281_S72_barcode_edit.txt.gz 1.6 Mb (ftp)(http) TXT
GSE228463_K562-HEK3-insCTT-DMSO_count.txt.gz 1.8 Mb (ftp)(http) TXT
GSE228463_PE2max_endogenous_121_K562.csv.gz 43.5 Kb (ftp)(http) CSV
GSE228463_PE_IL2RB_libraries.csv.gz 4.9 Kb (ftp)(http) CSV
GSE228463_T7-500-1_S1_ITR_corrected.txt.gz 121.2 Kb (ftp)(http) TXT
GSE228463_T7-500-1_processed.csv.gz 1.0 Mb (ftp)(http) CSV
GSE228463_T7-WT-Pool1.csv.gz 883.9 Kb (ftp)(http) CSV
GSE228463_T7-WT-Pool2.csv.gz 916.4 Kb (ftp)(http) CSV
GSE228463_sg1_top_alleles_count.txt.gz 123.0 Kb (ftp)(http) TXT
GSE228463_sg1_top_alleles_info.txt.gz 599 b (ftp)(http) TXT
GSE228463_shrna_freq_table.csv.gz 6.6 Kb (ftp)(http) CSV
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