A complementary genetic approach is an extension of the TRIBE technique called DART-seq Meyer 2019. Beyer applied DART-seq on HEK293 cells where the APOBEC domain was fused to the YTH domain from human YTHDF2 (WT and mutated). In essence, new C-to-U editing events that are significantly enriched in the YTHDF2-WT, but not in the binding domain mutant are bona fide candidates for m6A RNA modification
Usage
data(DARTseq)Format
a tibble with 18 elements:
id: Character string representing a unique identifier - created from contig, start, [end], and strand.
contig: Character string representing the contig of the variant
start: Numeric position of variant (>=0)
end: Numeric corresponds to "start + 1"
name: Character string. Name of used method call-2
score: Numeric value representing the test-statistc. Higher values indicate more divergent pileups
strand: Character representing strand information; "+", "-", or "."(no strand information available)
bases: Numeric tibble with representing counts for A, C, G, and T base calls.
cov: Numeric value indicating the read coverage for this site
backtrack1: Character - indicator if backtracking was used for condition 1.
backtrack2: Character - indicator if backtracking was used for condition 2.
backtrackP: Character - indicator if backtracking was used for condition pooled condition.
reset1: Character - indicator if default estimation was unstable with for condition 1.
reset2: Character - indicator if default estimation was unstable with for condition 2.
resetP: Character - indicator if default estimation was unstable with for pooled condition.
info: Character string separated with ";" provding additional data for this specific site. Empty field is equal to "*"
filter: ";"-separated character string showing feature filter information. Empty field is equal to "*"
ref: Character "A", "C", "G", "T", or "N" representing the reference base for this site - inverted when strand is "-".