Guides v1

The v1 guide RNA library was designed according to empirical data regarding effective guides for yeast CRISPRi using dCas9-Mxi.

Guide-to-target assignments

The 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 DEGEN.

• 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:

  chromosome:start-end(strand)

  where:

  • chromosome is the reference sequence name
  • start is the starting position – the 5’-most nucleotide in the target in 0-based coordinates.
  • end is the ending position – the 5’-most nucleotide not in the target in 0-based coordinates.
  • strand is + or -, 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, Yorf3).

• 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 (CDS).

• 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.

Degenerate guides

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 sequence-good-targets.txt 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 main sequence-good-targets.txt table.