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. Author manuscript; available in PMC: 2022 Nov 14.
Published in final edited form as: Nat Protoc. 2022 Jan 12;17(2):476–512. doi: 10.1038/s41596-021-00653-8
pool name of the oligo pool
dialout dialout PCR primer set, corresponds to the primer sequences in the kosuri_dialout_primers.csv table and Supplementary Table 2. These primer sequences are derived from Kosuri, et al.62
design name of the subpool gene set, corresponds to the gene list text file name
group sgRNAs from subpools within the same group will be designed to have unique 5’ sgRNA sequence prefixes to enable the option of experimentally combining these subpools
prefix_length the desired minimum read length for 5’-to-3’ in situ sequencing to distinguish all library elements with a given minimum edit distance between prefixes. Usually a prefix length of 12 is long enough for large libraries up to ~80,000 sgRNAs. Smaller libraries can often use a much shorter prefix, reducing the number of necessary in situ sequencing cycles for demultiplexing the sgRNA identities.
edit_distance the minimum Levenshtein edit distance between all pairs of prefixes. A minimum Levenshtein distance of 2 is generally recommended to enable detection of single base insertion, deletion, or substitution errors.
num_genes total number of genes in the subpool, matching the number of gene IDs in the corresponding gene list
sgRNAs_per_gene number of desired targeting sgRNAs per gene
duplicate_oligos for oligo array synthesis it may be advantageous to synthesize multiple spots with the same oligo sequence to achieve a narrower distribution of oligo representation and/or to match the supplier’s synthesis scale