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Items: 4

1.

Chromatin context-dependent regulation and epigenetic modulation of prime editing

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL30173 GPL15520 GPL18573
1324 Samples
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Series
Accession:
GSE228465
ID:
200228465
2.

Chromatin context-dependent regulation and modulation of prime editing [sci-RNA-seq3]

(Submitter supplied) 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.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL30173 GPL18573
1152 Samples
Download data: CSV
Series
Accession:
GSE228462
ID:
200228462
3.

Illumina NextSeq 500 (Homo sapiens)

Platform
Accession:
GPL18573
ID:
100018573
4.

DDR-focused pooled shRNA screen using a modified sci-RNA-seq3 [Batch1_Plate1300-2_enrich_P1-02E]

Organism:
Homo sapiens
Source name:
DDR-focused pooled shRNA screen using a modified sci-RNA-seq3
Platform:
GPL18573
Series:
GSE228462 GSE228465
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Sample
Accession:
GSM7121186
ID:
307121186
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