same sgRNA for different genes in GeCKO lib

[Jack Ma]

Hi Neville or Ophir,

I just deep sequenced the GeKOv2 a and b library, and found different genes share same sgRNA. for example, the following genes have an sgRNA with identical sequence. What is your consideration to design the lib this way? and how to eliminate the bias introduced?

Best,

Jack

PCDHGB1_HGLibA_42838	ATGGGATTGAGCGCCCGCTA
PCDHGB5_HGLibA_42850	ATGGGATTGAGCGCCCGCTA
PCDHGA2_HGLibA_42817	ATGGGATTGAGCGCCCGCTA
PCDHGA12_HGLibA_42814	ATGGGATTGAGCGCCCGCTA
PCDHGC3_HGLibA_42860	ATGGGATTGAGCGCCCGCTA
PCDHGB7_HGLibA_42855	ATGGGATTGAGCGCCCGCTA
PCDHGB4_HGLibA_42846	ATGGGATTGAGCGCCCGCTA
PCDHGA3_HGLibA_42820	ATGGGATTGAGCGCCCGCTA
PCDHGA1_HGLibA_42804	ATGGGATTGAGCGCCCGCTA
PCDHGA10_HGLibA_42807	ATGGGATTGAGCGCCCGCTA
PCDHGA5_HGLibA_42823	ATGGGATTGAGCGCCCGCTA
PCDHGC5_HGLibA_42864	ATGGGATTGAGCGCCCGCTA
PCDHGA9_HGLibA_42834	ATGGGATTGAGCGCCCGCTA
PCDHGB6_HGLibA_42852	ATGGGATTGAGCGCCCGCTA
PCDHGB2_HGLibA_42841	ATGGGATTGAGCGCCCGCTA
PCDHGA8_HGLibA_42832	ATGGGATTGAGCGCCCGCTA
PCDHGA11_HGLibA_42810	ATGGGATTGAGCGCCCGCTA
PCDHGA7_HGLibA_42828	ATGGGATTGAGCGCCCGCTA
PCDHGC4_HGLibA_42861	ATGGGATTGAGCGCCCGCTA
PCDHGA6_HGLibA_42826	ATGGGATTGAGCGCCCGCTA
PCDHGB3_HGLibA_42844	ATGGGATTGAGCGCCCGCTA

[Ophir Shalem]

Hi Jack,

  When we designed the library we did our best to avoid off targets. In some cases, due to homology, our design algorithm could not find a unique sgRNA that does not have additional hits in other genes. We decided to leave these sgRNAs in the library, in cases that such sgRNAs come up in the screen you will need to do a more detailed follow up to figure which gene KO (or both) results in the observed phenotype.

  I've attached to this message the exon guides from GeCKOv2 library with off target scores and some additional information, sgRNAs with 0 score and those that have more than one hit.

  Hope this helps,

Ophir.

[d d]

Dear Ophir,
Can you provide the equivalent data files for the mouse Geckov2 community please? This woulld be very helpful.
Regards,
Donncha.