Open Science

Recently Shared DNA Plasmids

Name & Description Get it at
pU6-(BbsI)_CBh-Cas9-T2A-EGFP
CRISPR/Cas9 expression vector with customizable gRNA. Co-expresses eGFP as a separate peptide to determine transfection efficiency.
DNASU
CMV-Gal4p65_MV1
Transcription activator with a Gal4 DNA binding domain, mCherry (RFP) tag, and p65 transcription activation domain.
DNASU

Deep Sequencing Data by Publication

Regulation of cancer epigenomes with a histone-binding synthetic transcription factor. Nyer DB, Daer R, Vargas D, Hom C, Haynes KA. (2017) Nature Genomic Medicine. doi:10.1038/s41525-016-0002-3
Gene Expression Omnibus (GEO): Accession Number GSE94120

Annotated Sequence Collections

Chromatin CRISPR Interference

Annotations of plasmids for transactivator and CRISPR complex expression, and a luciferase reporter gene integrated into the HEK293 genome.
Link: Benchling
Contributor(s): Rene Daer

  1. The impact of chromatin dynamics on Cas9-mediated genome editing in human cells. Daer RM, Cutts JP, Brafman DA, Haynes KA (2016) ACS Synthetic Biology. doi: 10.1021/acssynbio.5b00299

Gal4 DNA-binding Fusion Transcription Regulators

This set of mammalian optimized fusion transcription factors (gene activators) bind to the Gal4-UAS DNA sequence derived from yeast. Generally, the fusion ORF encodes (N to C) a Gal4 DNA binding domain (Gal4 DB), an mCherry fluorescent tag, and a regulator (transcription activation domain or epigenetic modifier).
Link(s): Benchling
Contributor(s): Cassandra Barret, Rene Daer

  1. The impact of chromatin dynamics on Cas9-mediated genome editing in human cells. Daer RM, Cutts JP, Brafman DA, Haynes KA (2016) ACS Synthetic Biology. doi: 10.1021/acssynbio.5b00299

Histone-binding Fusion Transcription Factors

This unique class of transcription factors (gene activators) are fusion proteins that bind to histone marks (H3K27me3) instead of DNA sequences. The first generation of these actuators, called Pc-TFs, was published by Haynes and Silver in 2011.
Link(s): Benchling
Contributor(s): Karmella Haynes

  1. Regulation of cancer epigenomes with a histone-binding synthetic transcription factor. Nyer DB, Daer R, Vargas D, Hom C, Haynes KA. (2017) Nature Genomic Medicine. doi:10.1038/s41525-016-0002-3
  2. Synthetic reversal of epigenetic silencing. Haynes KA & Silver PA. (2011) The Journal of biological chemistry, 286(31), 27176–27182. doi:10.1074/jbc.C111.229567

Quorum Sensing Collection

Sequences encoding quorum sensing homologues from various species. AHL synthases are cloned into a universal Sender vector that co-expresses RFP (mCherry). Regulators are expressed from a Receiver vector that also encodes a GFP regulated by the AHL-sensitive regulator’s target promoter.
Link(s)
: Benchling, iGEM Registry
Contributor(s): Brady Dennison, Ernesto Luna, Jiaqi Wu, Jimmy Xu