To get to this page below we selected in Step 1: Human(hg38), and for Step 2: input the HUGO gene symbol BAP1.
As you scroll from left to right, you will see titles for each column. Each of these columns have an up and down arrow where you can sort each coulmn. Below is a description for each category seen in the results table.
||Allows the user to select individual rows to export information using the Copy, CSV, View Data, and Design buttons at the top of the table.
||HUGO gene symbol of the gene being searched
||Guide RNA sequence
||Bacterial species and class of the CRISPR system
||The sgRNA target site genomic location (including the PAM sequence). This is a clickable genomic coordinate which will link to the UCSC Genome Browser
||Indicates whether or not the guide RNA targets a protein coding exon as indicated by True.
||Number of transcripts the guide RNA can target
||A clickable list of of Ensembl transcript IDs which link to the ENSEMBL database
||Predicted activity using the sgRNA Scorer 2.0 algorithm (-3 to 3). Higher the value, greater the predicted activity. 28146356
||Predicted activity using the Rule Set 2 algorithm (0 to 1). Higher the value, greater the predicted activity. 26780180
||Guidescan off-target score (0 to 1). Higher the value, higher the specificity. 28263296
||Favored Outcomes of Repair Events at Cas9 targets (FORECasT) score for predicting mutational outcomes (in frame indel %, lower values preferred for knockouts). 30480667
||Percentage of non-homologous end joining (NHEJ) mutation events observed from targeted sequencing. These events are filtered against SNPs/indels that are present in the control (untransfected) PCR amplicon.
||Percentage of out of frame (OOF) events of all NHEJ mutations observed from targeted sequencing.
||Number of publications that the selected guide RNA has been cited in.
||A list of Pubmed IDs (PMIDs) referencing the publication the guide RNA has been cited in.
||The number of pooled screen publications in which the selected guide RNA was over/under represented.
||A list of PMIDs referencing the pooled screen publication where the guide RNA has been cited in.
||The sources from which sgRNAs were compiled from. Please see Supplementary Table 1 of our publication with the full list of sources.
||If the guide has been used in a publication or has quantitative editing data, it has a status of validated, otherwise it is design. Simply typing in validated in the search box will filter only for guides that are validated.
If you are using a published guide RNA for your experiments: please cite BOTH the original source publication and our database.
If you are using a guide RNA that previousely published, but we had data for, please cite our database.
Gooden AA, Evans CN, Sheets TP, Clapp ME, Chari R (2020). dbGuide: A database of functionally validated guide RNAs for genome editing in human and mouse cells. bioRxiv
Updated: August 24th, 2020