pcr-pyrosequencing on bisulfite-treated dna  (Pyrosequencing Inc)

Journal: Clinical and Translational Allergy

Article Title: DNA methylation biomarkers in asthma and rhinitis: Are we there yet?

doi: 10.1002/clt2.12131

Figure Lengend Snippet: DNA methylation studies in nasal epithelial cells

Article Snippet: 35 asthmatic children‐ non controls , Caucasian , 8.9 , 77% , Population , Physiciandiagnosis of asthma; reported wheezing symptoms in the previous 12 months; chesttightness and/or use of bronchodilators in the last 12 months , Nasal cell brushing‐Inferior turbinate , PCR‐pyrosequencing on bisulfite‐treated DNA , ↓ DNA methylation of the IL‐6 and iNOS promoters ‐ ↑ FENO , Baccarelli et al. (2012) .

Techniques: DNA Methylation Assay, Biomarker Discovery, Sampling, Methylation, Control, Virus, Infection, Microarray, Software, Genome Wide, Expressing, RNA Sequencing, Activation Assay

Journal: MethodsX

Article Title: Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter

doi: 10.1016/j.mex.2021.101445

Figure Lengend Snippet: Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter. a. Schematic representation of the targeted bisulfite massive parallel sequencing of 19 CpG sites in the LINE-1 promoter. The red frame indicates the analyzed CpG sites in this study, and the blue frame indicates the most frequently analyzed CpG sites as determined using the Qiagen pyrosequencing LINE-1 kit (explanations are in the text). The schematic profile of the plot was obtained from the LINE-1 methylation index across the 5’-UTR region in analyzed samples. b. Gel image of the results of the amplified LINE-1 sequences for five samples after the first PCR with attached adapters and the same samples with attached indices after the second PCR. M represents Sky-High DNA marker (Biolabmix, Russia) with size in bp indicated.

Article Snippet: Fig. 2 Relationship between the average LINE-1 methylation index (%) measured by the introduced method (NGS) and bisulfite DNA pyrosequencing.

Techniques: Sequencing, Methylation, Amplification, Marker

Journal: MethodsX

Article Title: Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter

doi: 10.1016/j.mex.2021.101445

Figure Lengend Snippet: Relationship between the average LINE-1 methylation index (%) measured by the introduced method (NGS) and bisulfite DNA pyrosequencing.

Article Snippet: Fig. 2 Relationship between the average LINE-1 methylation index (%) measured by the introduced method (NGS) and bisulfite DNA pyrosequencing.

Techniques: Methylation

Journal: MethodsX

Article Title: Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter

doi: 10.1016/j.mex.2021.101445

Figure Lengend Snippet: Relationship between methylation indices of individual CpG sites as measured by the introduced method and average LINE-1 methylation index (%) as assessed by bisulfite DNA pyrosequencing (at positions 318, 321, and 328) trophoblast and ACTA2+ cells.

Article Snippet: Fig. 2 Relationship between the average LINE-1 methylation index (%) measured by the introduced method (NGS) and bisulfite DNA pyrosequencing.

Techniques: Methylation

Journal: MethodsX

Article Title: Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter

doi: 10.1016/j.mex.2021.101445

Figure Lengend Snippet: Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter. a. Schematic representation of the targeted bisulfite massive parallel sequencing of 19 CpG sites in the LINE-1 promoter. The red frame indicates the analyzed CpG sites in this study, and the blue frame indicates the most frequently analyzed CpG sites as determined using the Qiagen pyrosequencing LINE-1 kit (explanations are in the text). The schematic profile of the plot was obtained from the LINE-1 methylation index across the 5’-UTR region in analyzed samples. b. Gel image of the results of the amplified LINE-1 sequences for five samples after the first PCR with attached adapters and the same samples with attached indices after the second PCR. M represents Sky-High DNA marker (Biolabmix, Russia) with size in bp indicated.

Article Snippet: Fig 2 Fig. 3 Relationship between methylation indices of individual CpG sites as measured by the introduced method and average LINE-1 methylation index (%) as assessed by bisulfite DNA pyrosequencing (at positions 318, 321, and 328) trophoblast and ACTA2+ cells.

Techniques: Sequencing, Methylation, Amplification, Marker

Journal: MethodsX

Article Title: Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter

doi: 10.1016/j.mex.2021.101445

Figure Lengend Snippet: Relationship between the average LINE-1 methylation index (%) measured by the introduced method (NGS) and bisulfite DNA pyrosequencing.

Article Snippet: Fig 2 Fig. 3 Relationship between methylation indices of individual CpG sites as measured by the introduced method and average LINE-1 methylation index (%) as assessed by bisulfite DNA pyrosequencing (at positions 318, 321, and 328) trophoblast and ACTA2+ cells.

Techniques: Methylation

Journal: MethodsX

Article Title: Method of targeted bisulfite massive parallel sequencing of the human LINE-1 retrotransposon promoter

doi: 10.1016/j.mex.2021.101445

Figure Lengend Snippet: Relationship between methylation indices of individual CpG sites as measured by the introduced method and average LINE-1 methylation index (%) as assessed by bisulfite DNA pyrosequencing (at positions 318, 321, and 328) trophoblast and ACTA2+ cells.

Article Snippet: Fig 2 Fig. 3 Relationship between methylation indices of individual CpG sites as measured by the introduced method and average LINE-1 methylation index (%) as assessed by bisulfite DNA pyrosequencing (at positions 318, 321, and 328) trophoblast and ACTA2+ cells.

Techniques: Methylation

Journal: Genes & Diseases

Article Title: Recent advances in elucidating the genetics of common variable immunodeficiency

doi: 10.1016/j.gendis.2019.10.002

Figure Lengend Snippet: Genetic alterations identified through different next generation platforms in CVID samples. A Disintegrin and Metalloproteinase (ADAM); Activation induced cytidine deaminase (AICDA); Adenosine deaminase 2 (ADA2); AKT serine/threonine kinase 1 (AKT1); ATM Serine/Threonine kinase (ATM); B-cell lymphoma 2 like 1 (BCL2L1); B-cell lymphoma 6 (BCL6); C–C chemokine receptor type 7 (CCR7); CD40 ligand (CD40LG); CD 81 molecule (CD81); Cat eye syndrome chromosome region, candidate 1 (CECR1); Complement factor H related 5 (CFHR5); Chromodomain helicase DNA binding protein 7 (CHD7); Cytotoxic T-lymphocyte associated protein 4 (CTLA4); DNA methyltransferase 3 beta (DNMT3B); Dedicator of cytokinesis 8 (DOCK8); Desmoglein 1 (DSG1); Ectopic P-granules autophagy protein 5 (EPG5); Forkhead Box O(FOXO); Intercellular adhesion molecule 1 (ICAM1); Interferon (IFN); DNA Ligase 1 (LIG1); Fatty acid synthase (FASN); Fibrillin-1 (FBN1); Inhibitor of nuclear factor kappa B kinase regulatory subunit gamma (IKBKG); IKAROS family zinc finger 1 (IKZF1); Interleukin 1 alpha (IL1A); Interferon regulatory factor 2 binding protein 2 (IRF2BP2); Lymphocyte transmembrane adaptor 1 (LAX1); Lipopolysaccharide-responsive beige-like anchor protein (LRBA); Leucine rich repeat containing 8 VRAC subunit A (LRRC8A); Mitogen-activated protein kinase 8 (MAPK8); Mannan binding lectin serine peptidase 2 (MASP2); Mediterranean fever (MEFV); MX domain like GTPase 1 (MX1); NBPF member 15 (NBPF15); Neutrophil cytosolic factor 2 (NCF2); Nuclear factor kappa B subunit 1 (NFKB1); Nuclear factor kappa B subunit 2 (NFKB2); NLR family pyrin domain containing 3 (NLRP3); NLR family pyrin domain containing 12 (NLRP12); Paired Box 5 (PAX5); Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta (PIK3CD); Phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1); Phospholipase C, gamma (PLCG); Protein kinase C delta (PRKCD); Protein tyrosine phosphatase receptor type C (PTPRC); Recombination activating 1 (RAG1); Recombination activating 2 (RAG2); Retinoblastoma associated (RBA); Potassium calcium-activated channel subfamily N member 4 (KCNN4); Ribosomal protein S6 kinase beta-2 (RPS6KB2); Splicing factor 3b subunit 1 (SF3B1); Signal transducer and activator of transcription 1 (STAT1); Signal transducer and activator of transcription 3 (STAT3); Syntaxin binding protein 2 (STXBP2); Transcription factor 3 (TCF3); Toll like receptor 1 (TLR1); TNF receptor superfamily member 13B (TNFRSF13B); TRAF3 interacting protein 2 (TRAF3IP2); Tubulin beta 1 class VI (TUBB1); Tyrosine kinase 2 (TYK2); Unc-13 homolog D (UNC13D); Zinc finger and BTB domain containing 24 (ZBTB24).

Article Snippet: High-Throughput DNA methylation and Bisulfite-modified DNA pyrosequencing , 23 CVID patients , Impaired demethylation in AICDA, BCL6, STAT3, FOXO, AKT1 and NFKB2 , 2019 , .

Techniques: Activation Assay, Binding Assay, Next-Generation Sequencing, Genome Wide, Sequencing, DNA Sequencing, Mutagenesis, Variant Assay, Expressing, RNA Sequencing, Cell Differentiation, DNA Methylation Assay, Methylation Sequencing

Journal: Genes & Diseases

Article Title: Recent advances in elucidating the genetics of common variable immunodeficiency

doi: 10.1016/j.gendis.2019.10.002

Figure Lengend Snippet: Advantages and limitations of different genomic, transcriptomic and proteomics based platforms in Common variable immunodeficiency disease. ELISA, Enzyme-linked immunosorbent assay; SNP, Single nucleotide polymorphism.

Article Snippet: High-Throughput DNA methylation and Bisulfite-modified DNA pyrosequencing , 23 CVID patients , Impaired demethylation in AICDA, BCL6, STAT3, FOXO, AKT1 and NFKB2 , 2019 , .

Techniques: Enzyme-linked Immunosorbent Assay, Genome Wide, Biomarker Discovery, Sequencing, Electrophoresis, Next-Generation Sequencing, Amplification, High Throughput Screening Assay, Gene Expression, Generated, Microarray, Hybridization, Sample Prep, Transcriptome Wide Gene Expression, DNA Methylation Assay, Methylation, Quantitative Proteomics, Fourier Transform Infrared Spectroscopy, Spectroscopy