Journal: Nucleic Acids Research

Article Title: Base-resolution detection of N 4 -methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing

doi: 10.1093/nar/gkv738

Figure Lengend Snippet: Comparison of MethylC-seq and 4mC-TAB-seq. ( A ) MethylC-seq converts C and a portion of 4mC to T. The remaining 4mC and almost all 5mC will be read as C. ( B ) 4mC-TAB-seq converts C, 5mC and a portion of 4mC to T, whereas about half of 4mC will be exclusively read as C. ( c ) Properties of 4mC and 5mC under different treatment conditions. Untreated or Tet-treated 4mC/5mC-containing model DNA is applied to either standard or optimized bisulfite treatment condition. Samples were PCR amplified, subcloned into TOPO vector and Sanger sequenced to quantify the number of 4mC or 5mC being read as C.

Article Snippet: C/5mC spike-in control (CpG methylated lambda DNA) was prepared by treating unmethylated lambda cl857 DNA (Promega) with M. SssI (NEB) according to the manufacturer's instructions.

Techniques: Amplification, Plasmid Preparation

Journal: Nucleic Acids Research

Article Title: Base-resolution detection of N 4 -methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing

doi: 10.1093/nar/gkv738

Figure Lengend Snippet: Data analysis of spike-in controls from MethylC-seq and 4mC-TAB-seq in the context of C. kristjanssonii genomic DNA. ( A ) Composition of pUC19 DNA, lambda DNA, and C. kristjanssonii genomic DNA. ( B ) The percentage of detected as cytosine reads on 4mC sites in untreated and Tet-treated samples. ( C ) The detected as cytosine reads percentage on unmodified cytosine sites (non-CpG context) and 5mC sites (CpG context) in untreated and Tet-treated samples. ( D ) Quantification of 4mC and 5mC in C. kristjanssonii genomic DNA, determined by LC-MS/MS and deep-sequencing respectively. Error bars indicate mean ± SD, n = 4.

Article Snippet: C/5mC spike-in control (CpG methylated lambda DNA) was prepared by treating unmethylated lambda cl857 DNA (Promega) with M. SssI (NEB) according to the manufacturer's instructions.

Techniques: Lambda DNA Preparation, Liquid Chromatography with Mass Spectroscopy, Sequencing

Journal: Nucleic Acids Research

Article Title: Base-resolution detection of N 4 -methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing

doi: 10.1093/nar/gkv738

Figure Lengend Snippet: 5mC-containing motif characterizations and distributions in C. kristjanssonii . ( A ) Motif sequence profile and sequence conservation analysis. Methylated cytosine is indicated with 5m. ( B ) Motif distributions in the reference genome, untreated- and Tet-treated samples. ( C ) Single cytosine methylation level distributions of each motif in the untreated sample.

Article Snippet: C/5mC spike-in control (CpG methylated lambda DNA) was prepared by treating unmethylated lambda cl857 DNA (Promega) with M. SssI (NEB) according to the manufacturer's instructions.

Techniques: Sequencing, Methylation

Journal: Reports of Biochemistry & Molecular Biology

Article Title: O6-Methylguanine-DNA Methyltransferase and ATP-Binding Cassette Membrane Transporter G2 Promotor Methylation: Can Predict the Response to Chemotherapy in Advanced Breast Cancer?

doi: 10.52547/rbmb.11.1.20

Figure Lengend Snippet: Shows amplified bisulfite converted DNA after MSP using methylated and unmethylated primers for ABCG2 on 2% agarose gel. Cases are run each methylated and unmethylated side by side. Lane 1: DNA ladder Lane 2: positive control, methylated converted DNA EpiTech control, showing target band at 235 bp. Lane 3: positive control, unmethylated converted DNA EpiTech control, showing target band at 135 bp. Lane 4: negative control for methylated primers, nuclease free water, showing no band. Lane 5: negative control for unmethylated primers, nuclease free water, showing no band. Lane 6: unmethylated band for case 1, Lane 7: no methylated band for case 1. Lane 12: unmethylated band at target location (at 135 bp) for case 4. Lane 13: methylated band at target location (at 235 bp) for case 4.

Article Snippet: Lane 1: positive control, methylated converted DNA EpiTech control, showing target band at 81bp.

Techniques: Amplification, Methylation, Agarose Gel Electrophoresis, Positive Control, Control, Negative Control

Journal: Reports of Biochemistry & Molecular Biology

Article Title: O6-Methylguanine-DNA Methyltransferase and ATP-Binding Cassette Membrane Transporter G2 Promotor Methylation: Can Predict the Response to Chemotherapy in Advanced Breast Cancer?

doi: 10.52547/rbmb.11.1.20

Figure Lengend Snippet: Shows amplified bisulfite converted DNA after MSP using methylated and unmethylated primers for MGMT on 2% agarose gel. Cases are run each methylated and unmethylated side by side. Lane 1: positive control, methylated converted DNA EpiTech control, showing target band at 81bp. Lane 2: positive control, unmetbylated converted DNA EpiTech control, showing target band at 93 bp. Lane 3: methylated band at target location (at 81 bp) for case 1. Lane 4: unmethylated band at target location (at 93 bp) for case 1. Lane 5: methylated band at target location (at 81 bp) for case 2. Lane 6: unmethylated band at target location (at 93 bp) for case 2. Lane 7: DNA ladder.

Article Snippet: Lane 1: positive control, methylated converted DNA EpiTech control, showing target band at 81bp.

Techniques: Amplification, Methylation, Agarose Gel Electrophoresis, Positive Control, Control