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Series GSE138860 Query DataSets for GSE138860
Status Public on Jun 01, 2020
Title CRISPR-mediated mutagenesis of RNA editing cis-regulatory elements
Organisms Homo sapiens; synthetic construct
Experiment type Other
Summary We used CRISPR KI technology to mutagenize the cis-regulatory elements including the editing stem and the editing complementary sequence of three RNA editing substrates-NEIL1, TTYH2, AJUBA. We designed single nucleotide variants, double-nucleotide variants and other mutant isoforms to interrogate the primary sequence and the secondary structures around the endogenous RNA editing sites. Gene specific primers were used to make the NGS library for each locus. The unique mutation of each tested isoform can be used as barcode and RNA editing level can be measured for each isoform from the pooled library. We found that RNA sequence and structure features synergistically determine the editing levels. Several features, such as mutation number, free energy, and probability of active conformation, play an important role in determining editing efficiency. This study systematically investigated the contribution of cis-regulatory elements to ADAR1 RNA editing by combining CRISPR-based saturation mutagenesis and deep sequencing technology.
 
Overall design Examination of the RNA editing level of three endogenous substrates whose cis-elements have been subject to saturation mutagenesis.
 
Contributor(s) Li JB, Sun T
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Submission date Oct 15, 2019
Last update date Jun 01, 2020
Contact name Jin Li
E-mail(s) jin.billy.li@stanford.edu
Organization name Stanford University
Department Genetics
Street address M341, 300 Pasteur Dr.
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (2)
GPL21697 NextSeq 550 (Homo sapiens)
GPL27609 NextSeq 550 (synthetic construct)
Samples (25)
GSM4120516 DNA of NEIL1 mutants from Watson strand donor knockin rep1
GSM4120517 DNA of NEIL1 mutants from Watson strand donor knockin rep2
GSM4120518 DNA of NEIL1 mutants from double strand donor knockin rep1
Relations
BioProject PRJNA577632
SRA SRP225697

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
GSE138860_173Neilwatson1g_counts.txt.gz 22.9 Kb (ftp)(http) TXT
GSE138860_174Neilwatson2g_counts.txt.gz 26.4 Kb (ftp)(http) TXT
GSE138860_175Neilds1g_counts.txt.gz 32.0 Kb (ftp)(http) TXT
GSE138860_176Neilds2g_counts.txt.gz 28.0 Kb (ftp)(http) TXT
GSE138860_177Neilcrick1g_counts.txt.gz 35.4 Kb (ftp)(http) TXT
GSE138860_178Neilcrick2g_counts.txt.gz 29.8 Kb (ftp)(http) TXT
GSE138860_AJUBA_editinglevel.txt.gz 4.5 Kb (ftp)(http) TXT
GSE138860_AJUBAdonorEDIT_counts.txt.gz 72.7 Kb (ftp)(http) TXT
GSE138860_NEIL1_deg_editinglevel.txt.gz 3.4 Kb (ftp)(http) TXT
GSE138860_NEIL1_editinglevel.txt.gz 7.5 Kb (ftp)(http) TXT
GSE138860_TTYH2_deg_editinglevel.txt.gz 1.6 Kb (ftp)(http) TXT
GSE138860_TTYH2_editinglevel.txt.gz 6.2 Kb (ftp)(http) TXT
GSE138860_TTYH2donorECS_counts.txt.gz 37.0 Kb (ftp)(http) TXT
GSE138860_TTYH2donorEDIT_counts.txt.gz 45.4 Kb (ftp)(http) TXT
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