Dataset features

Specifications


Dataset type: Other
Number of samples: 22
Release date: Feb 1 2019
Last update date: Feb 1 2019
Access: Public
Dataset link Deep mutational scanning of Env from the HIV-1 strain DU422 for binding to CD4 and PG16

Experimental Protocol


The extracellular domains of Env (referred to here as gp140) from the clade C HIV-1 DU422 strain were encoded by a synthetic codon-optimized gene with a CD5 leader sequence, and fused at the C-terminus via a glycine/serine-rich linker to a hexahistidine tag and canonical transmembrane helix from class I MHC for surface display. The Env sequence was diversified by overlap-extension PCR to generate three single-site saturation mutagenesis libraries spanning the full length of gp140. The libraries were expressed in human Expi293F cells (a suspension derivative of HEK 293) and sorted by FACS for binding to soluble CD4 and bnAb PG16. Enrichment ratios were calculated for all single amino acid substitutions by comparing the frequencies of sequence variants in the sorted cell populations (from RNA transcripts) with the naive libraries (plasmid DNA). Experiments were independently duplicated.

Repositories


GEO

GSE117328

ENA

SRP154368

BioProject

PRJNA481765

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Contact


Erik Procko