Guigo Lab BLaER1 pgRNA Library
(Pooled Library #183825)

• Purpose:

  The BLaER1 pgRNA CRISPR library is a CRISPR-Cas9 library to target lncRNAs and protein-coding genes with a potential role in B-cell to macrophage transdifferentiation. It can be a resource to perform knockout screens in other models, such as macrophage differentiation.

• Vector Backbone:

  pDECKO_mCherry - does not express Cas9

• Depositing Labs: Roderic Guigo
• Publication: Arnan and Ullrich et al. BMC Genomics . 2022. doi: 10.1186/s12864-022-08612-7.

Library Details

• Species: Human
• Genes targeted: 166 lncRNAs, 874 protein-coding genes (10 pgRNA per lncRNA or protein-coding gene)
• Controls: 4 positive controls plus pgRNAs against EGFP, mCherry and tdTomato (50 pgRNAs each); 100 negative controls (10 pgRNAs each)
• gRNAs: 11,750
• Lentiviral Generation: 3rd

Library Shipping

This library is delivered as suspended DNA in a microcentrifuge tube on blue ice. The tube's contents will not necessarily be frozen. For best results, minimize freeze-thaws.

• Volume: ∼25 µL
• Concentration: 40 ng/µL

Resource Information

• Protocols:
  • Library Amplification Protocol (10 KB)
  • PCR protocol for Illumina sequencing preparation (58 KB)
• Depositor Data:
  • List of targeted genes and gRNA sequences (1.6 MB)
  • Distribution of NGS Reads (848 KB)
• Terms and Licenses:
  • UBMTA

Depositor Comments

pgRNA Library schematic: (A) Workflow of the CRISPR screening experiment. The plasmid library is transfected into HeK293T cells to obtain a library of lentivirus. BLaER1-Cas9 cells are infected and selected with antibiotics, then induced for transdifferentiation into macrophages (3 or 6 days). Cells are labelled with antibodies against cell surface markers: CD19 (for B-lymphocytes) and Mac-1 (for macrophages). Transdifferentiation status is assessed and cell populations are isolated by Fluorescence-Activated Cell Sorting (FACS). (B) Scheme of pDECKO_mCherry plasmid and PCR amplification. H1 and U6 promoters drive the expression of the two gRNAs. In the first PCR step, staggered primers anneal to the U6 promoter and to the pDECKO backbone. In the second PCR step, primers containing the sample barcode and P5/P7 sequences for sequencing are added. (C) Position of pgRNAs targeting lncRNAs (targeting the promoter and the transcription start site) and pc-genes (targeting coding exons). (D) Library composition (number of targets of each biotype and pgRNA pairs designed per target).

Figure adapted from Arnan and Ullrich et al. 2022 BMC Genomics.

For more details on protocols and analysis, please see the publication (Arnan and Ullrich et al. 2022) or the preprint on bioRxiv .