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Table 1 shRNA target sites and the efficiency of CCR5 reduction in MAGI-CCR5 cells

From: Characterization of a potent non-cytotoxic shRNA directed to the HIV-1 co-receptor CCR5

Target region

Target sequence

Nucleotide position

CCR5 reduction on MAGI-CCR5

CCR5-1

aagtgtcaagtccaatctatgac

13

+++

CCR5-2

aagagcatgactgacatctacct

186

++

CCR5-3

ctgacaatcgataggtacctggc

366

-

CCR5-4

gtgacaagtgtgatcacttgggt

442

-

CCR5-5

ttgtcatggtcatctgctactgg

624

++

CCR5-6

cagtagctctaacaggttggaca

809

+

CCR5-7

aaggtcttcattacacctgcagc

517

+/-

CCR5-8

aagttcagaaactacctcttagt

909

+++

  1. Eight shRNAs against human CCR5 were selected by a published algorithm[7]. shRNA target sequences are shown in the second column. Corresponding nucleotide positions of the target sequence in CCR5 mRNA are shown in the 3rd column. MAGI-CCR5 cells were transduced with lentiviral vectors expressing shRNA under the U6 promoter. To determine the expression levels of CCR5 on cell surface, the cells were cultured for 4 days and stained with APC conjugated anti-human CCR5 monoclonal antibody. The reduction levels of in EGFP+ population was analyzed by flow cytometry and shown as following criteria (+++ more than 10 fold reduction, ++ 10 fold reduction, + 3–5 fold reduction, +/- 2 fold reduction, – no reduction).