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 |