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microTRE Screening Libraries
(Pooled Libraries #201012, #201013, #201014, #1000000220)

  • Purpose

    A massively parallel reporter assay (MPRA) library where barcode expression is dependent upon engagement of cellular transcription factors to a series of engineered, short, artificial transcriptional response elements (TREs) encoded alongside variable motifs and minimal promoters.

  • Vector Backbone


Item Catalog # Description Quantity Price (USD)
Pooled Library 201012 TRE-MPRA_minCMV library 1 $ 640 Add to Cart
Pooled Library 201013 TRE-MPRA_minPromega library 1 $ 640 Add to Cart
Pooled Library 201014 TRE-MPRA_minTK library 1 $ 640 Add to Cart
Pooled Library 1000000220 TRE-MPRA full library kit
  • #201012 (minCMV library)
  • #201013 (minPromega library)
  • #201014 (minTK library)
1 $ 1600 Add to Cart
Available to Academic and Nonprofits Only

Library Details

  • Species
    Synthetic, but based on human and mouse
  • Synthetic promoters
  • Unique barcodes
    Each of the three pooled libraries contains approximately 1.2 × 106 unique barcodes mapping to the TRE-barcode dictionary.
  • Insert size range
    59–148 bp

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

Depositor Comments

Panel A is a schematic diagram depicting HT-SELEX as the data source to generate 325 TFBMs. An additional 18 commercial TREs and 102 pseudo TREs make up the TRE-MPRA library, resulting in 6318 synthetic promoters. Panel B shows the schematic structure of a transcription unit. Four TFBMs are separated by two random spacer sets, followed by sequence to allow three helical rotations to comprise one TRE unit. Each TRE unit is combined with one of three minimal promoters to create a synthetic promoter. Luc2 and a 24 nucleotide barcode follows each synthetic promoter. Panel C depicts transfection of cells with the TRE-MPRA library followed by nucleic acid isolation and processing of sequencing data.
  • Figure 1. TRE-MPRA overview. A) Transcription factor binding motifs (TFBMs) included in the TRE-MPRA library were derived from the HT-SELEX dataset of Jolma et al., 2013. Candidate synthetic promoters were designed by combining homotypic TFBMs and one of three minimal promoters in multiple configurations. Commercially available TREs, as well as negative control promoters (‘pseudo’) were also included in the TRE-MPRA library. B) Four copies of a given TFBM were oriented on alternating sides of the DNA double helix using sets of random nucleotides and rotated along the helix relative to the minimal promoter (TRE unit). TRE units combined with minimal promoters (‘promoters’) regulate the expression of a Luc2 CDS containing 24 nucleotide barcodes in the 3’ UTR. Barcodes were mapped to associated TRE units using next-generation sequencing (NGS) during library preparation. C) Barcoded RNAs were extracted from transfected cells and sequenced via NGS alongside the input TRE-MPRA plasmid libraries. Resulting barcode counts were analyzed via MPRAnalyze (Ashuach et al., 2019) to produce estimates of promoter transcription rates and to compare activities between treatment with fetal bovine serum (FBS) or forskolin.

The Pooled NGS data provided by the depositor is from representative preps, and library composition changes very little between lots. NGS sequencing is required for the analysis pipeline, and datasets provided from the depositor can be used for comparative reference.

The necessary algorithms and barcode dictionary spreadsheet can be found on GitHub (Link opens in a new window).

Individual dual-luciferase plasmids, pGL4.R_TRE_minTK (211516), pGL4.R_TRE_minPro (211517), and pGL4.R_TRE_minCMV (211518), can be used to clone and validate individual TREs from the corresponding library.

How to cite this pooled library ( Back to top )

These pooled libraries were created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the plasmids were described, and include Addgene in the Materials and Methods of your future publications.

  • For your Materials & Methods section:

    microTRE Screening library was a gift from Justin English (Addgene #)
  • For your References section:

    Discovery and Validation of Context-Dependent Synthetic Mammalian Promoters. Zahm AM, Owens WS, Himes SR, Rondem KE, Fallon BS, Gormick AN, Bloom JS, Kosuri S, Chan H, English JG. bioRxiv. 2023 May 11:2023.05.11.539703. doi: 10.1101/2023.05.11.539703. Preprint. PubMed 37214829