The v1 guide RNA library was designed according to empirical data regarding effective guides for yeast CRISPRi using dCas9-Mxi.
library_v1/sequence-good-targets.txt file provides a table
of the 61,094 guides in the Ingolia lab v1 guide library, along with
information about target genes. In this table,
Guide gives a systematic name for each guide in the library, based
on the systematic name of the gene target and a unique number. See
below for more information about degenerate guides marked
TargetLoc gives the genomic location of the target sequence. This is listed in the format below, which is very similar to the information in BED-format annotations:
-, and a
+-strand target will end in …GG-3’ while a
--strand target will start with 5’-CC.
Yorf1 is the systematic name of the primary, most likely
target. This may be
NA when a guide has only dubious gene
targets, which are not candidates for Yorf1 (or Yorf2,
Offset1 is the distance in nucleotides from the center of the guide sequence to the beginning of the primary target.
StartType1 indicates whether the primary target location is
defined according to a transcription start site (
TSS) or just the
coding sequence (
Yorf2, Offset2, and StartType2 give the same information for a secondary, less likely target if one exists.
Yorf3, Offset3, and StartType3 give the same information for a tertiary, even less likely target if one exists (this is very rare).
Yorfs gives an ordered, comma-separated list of targets
PrimaryGuide gives the first choice for the guide systematic name, which generally matches Guide except in unusual circumstances involving dubious genes.
PrimaryGuideSource indicates which of the potential targets was used to define the primary guide identity.
Oligo gives the sequence of the guide oligo, with upstream and downstream constant sequence in lower-case and variable sequence in upper-case.
A small fraction of guides are degenerate, meaning that they target
non-unique sequences that occur in multiple places in the
genome. These degenerate guides have
DEGEN in their Guide
name. For these degenerate guides, the
table lists information about one genomic target location. The
library_v1/sequence-redundant-targets.txt table gives similar
information about other genomic targets. The redundant targets table
has the same information as the main table of good targets, and with
an additional column DegenGuide that gives the guide name in the