ODN3, ox, r2
synthetic construct
Protocols: ODN 1: NNNNNNNNNNATCGAGAATCCCGGTGCCGATACCXACTCTTGYAGAANNNNNNNNNNCGTGTCAGATATATACATCCGAT (N: random ATGC, X and Y: 5hmU); The template ODN was purchased from ATDbio. The double stranded DNA was synthesized by single-extension PCR using 5'-ATCGGATGTATATATCTGACACG-as the primer. ODN 2: GCTCGCTTTGTTGGTTTCCTTGTTCTCTGTGCCCACTGCCTGACGGGCGGAAAGCAGCGCGAGCAAGCGAGACAGGACAC; The template ODN was purchased from Life Technologies. The double-stranded DNA was prepared by single-extension PCR using 5'-GTGTCCTGTCTCGCTTGCTCGCGCTGCTTT-3' as the primer where TTP (10 mM) was substituted by a mixture of TTP and 5hmdUTP (Trilink biotechnologies) in a ratio of 0:1, 1:1, 3:1, 7:1, 15:1, 1:0 to obtain fully, or partially 5hmU modified ODN pools. ODN 3: CTGTGGCTCTGCGTCCTTGTCCTNNNNNNACACAGCGCAN5NGAACGACGAGGCACAACAGAGAGCAACACCGCCGAGGA (N: random A or T or G or C, 5:5hmU); The template ODN was purchased from ATDbio. The double stranded DNA was synthesized by single-extension PCR using 5'-TCCTCGGCGGTGTTGCTCTCTGTTGTGCCT-3'as the primer. Purified by DNA Clean & Concentrator™-5 (Zymo Research). Detailed information is available in the liked publication. Briefly, the DNA was ligated with a custom adapter partially bearing Truseq LT adapter (Illumina) sequences, followed by KRuO4-mediated oxidation to oxidise 5hmU. Then single extension PCR was carried out to create libraries with and full length Truseq adapter sequence as well as information of 5hmU locations. The libraries were then amplified by PCR (6-8 cycles).
ENA first public
2018-06-08
ENA last update
2018-02-02
External Id
SAMEA104559082
INSDC center alias
Department of Chemistry University of Cambridge
INSDC center name
Department of Chemistry University of Cambridge
INSDC first public
2018-06-08T17:02:55Z
INSDC last update
2018-02-02T09:34:11Z
INSDC status
public
Mg2SO4 concentration
10
Submitter Id
E-MTAB-6456:ODN3, ox, r2
broker name
ArrayExpress
dATP dilution concentration
500
enzyme
Bst DNA Polymerase, Large Fragment
oligo
ODN3
oxidation treatment
ox
replicate
2
sample name
E-MTAB-6456:ODN3, ox, r2