Human Transcription Factor Knockout Library
(Pooled Library #162275, #162275-LV)

• Purpose:

  This lentiviral CRISPR knockout library targets 1,639 human transcription factors for comprehensive loss-of-function screens.

• Vector Backbone:

  lentiGuide-Puro (Plasmid #52963) - does not express Cas9

• Depositing Labs: Chunliang Li
• Publication: Zhang et al eLife. 2020 Oct 1;9. pii: 57858. doi: 10.7554/eLife.57858.

Library Details

• Species: Human
• Genes targeted: 1,639
• Total gRNAs: 11,364
• Controls: 100 non-targeting gRNAs
• 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: ∼20 µL
• Concentration: 50 ng/µL

Resource Information

• Protocols:
  • Library Amplification Protocol (DOCX, 15 KB)
  • Library Construction Protocol (XLSX, 8.6 KB)
  • Primers and PCR Protocol for Illumina Sequencing Preparation (XLSX, 9.4 KB)
• Depositor Data:
  • List of Targeted Genes and sgRNA Sequences (CSV, 394.8 KB)
  • Representative Illumina Sequencing Results (CSV, 437.4 KB)
• Scripts:
  • The depositing lab recommends using MAGeCK/MAGeCK-VISPR algorithms and DESeq2 for analysis.
• Articles Citing this Pooled Library:
  • Human TF KO Library (#162275)

Terms and Licenses

Academic/Nonprofit Terms:

• UBMTA

Industry Terms:

• Not Available to Industry

Trademarks:

• Zeocin® is an InvivoGen trademark.

Depositor Comments

Figure 1: Overview of the human transcription factor CRISPR knockout library.

Information for Lentiviral Prep (Catalog # 162275-LV)

Purpose

Ready-to-use lentiviral pooled library for CRISPR screening in human cells. Targets 1,639 transcription factors. Lentiviral particles carrying Human Transcription Factor Knockout Library in lentiGuide-Puro.

Delivery

• Volume: Varies depending on titer.
• Titer: ≥ 1 × 10⁷ TU/mL
• Storage: Store at -80 °C. Thaw just before use and keep on ice.
• Shipment: Viral particles are shipped frozen on dry ice. Pooled Library DNA (10 µL at 50 ng/µL) will also be included in the shipment.

Viral Production & Use

• Packaging Plasmids: psPAX2 (plasmid #12260)
• Envelope: pMD2.G (plasmid #12259)
• Buffer: OptiPRO SFM
• Selectable Marker: Puromycin

Biosafety

Requestor is responsible for compliance with their institution's biosafety regulations. Lentivirus is generally considered BSL-2. AAV is generally considered BSL-1, but may require BSL-2 handling depending on the insert. Biosafety Guide

Viral Quality Control

Pooled Library Representation:

• To confirm library representation and distribution, we perform next-generation sequencing on the purified plasmid DNA pool that was used to generate lentivirus.

Titering Method:

• ddPCR: 293T cells are transduced with serial dilutions of 162275-LV, harvested several days later, and genomic DNA is isolated. Copies of RRE are measured and normalized to RPP30.

PCR confirmation of insert:

• PCR was carried out with primers targeting U6 and EF1-alpha promoters. The PCR product was visualized on an agarose gel for size confirmation.
  • Forward primer: GAGGGCCTATTTCCCATGATT

  • Reverse Primer: CACGGCGACTACTGCACTTA

Visit our viral production page for more information.

Addgene Comments

Shipment specifications:

Pooled libraries containing at least 1.3 × 10⁸ infectious units are shipped on dry ice at a titer of ≥ 1 × 10⁷ TU/mL. The total volume is divided among several large aliquots and one 1.3 mL aliquot for testing. Each viral service request also includes virus associated DNA, which is a sample of the purified plasmid DNA pool that was used to generate lentivirus.

How to use this virus:

We recommend using the testing aliquot of virus to determine optimal infection conditions before performing screening-scale infections. Detailed methods for determining optimal infection conditions, screening, and validating hits are described in the original publication. Before using this virus, Addgene strongly recommends reading the original publication (Zhang et al., 2020 ).

How to use the virus associated DNA:

Distribution of this pooled lentiviral library includes virus associated DNA, which is a sample of the purified plasmid DNA pool that was used to generate lentivirus.

• This purified plasmid DNA pool can be sequenced and used as the starting plasmid DNA (pDNA) pool reference when performing screen analysis. As described in the original publication (Zhang et al., 2020 ), perform screen analysis by determining the log₂-fold-change of each single-guide RNA relative to the pDNA pool. The pDNA has been shown to serve as a good surrogate for an early time point and is more cost effective when performing many screens (Shalem et al., 2014 ).

• The purified plasmid DNA pool can be amplified to make more pooled plasmid library stock DNA. See our Library Amplification Protocol (DOCX, 15 KB) for more information.