Journal: BMC Cancer

Article Title: The autophagy GABARAPL1 gene is epigenetically regulated in breast cancer models

doi: 10.1186/s12885-015-1761-4

Figure Lengend Snippet: Epigenetic modifications in GABARAP family gene promoters. a Quantification of GABARAP , GABARAPL1 , GABARAPL2 expression using qRT-PCR in BC MCF-7 and MDA-MB-453 cancer cells and MCF-10A immortalized cells. b and c GABARAP family gene methylation using methylCollector kit in MCF-7, MDA-MB-453 and MCF-10A cells. (I: input; M: methylated fraction). d Visualization of H3 deacetylation using ChIP experiment and anti-H3 acetylated (H3-ac) antibody in the GABARAP family gene in MCF-7 and MDA-MB-453 cells (I: input; IgG: negative control of IP). e Detection of DNMT1 and HDAC1 recruitment on GABARAPL1 promoter using ChIP experiment and anti-DNMT1 or anti-HDAC1 antibody (I: input; IgG : negative control)

Article Snippet: Histone 3 acetylation was quantified using the EpiQuik Tissue Acetyl-Histone H3 ChIP Kit (P-2012, Epigentek).

Techniques: Expressing, Quantitative RT-PCR, Methylation, Negative Control

Journal: Genetics

Article Title: Development of a Multiparent Population for Genetic Mapping and Allele Discovery in Six-Row Barley

doi: 10.1534/genetics.119.302046

Figure Lengend Snippet: Genetic diversity in the BRIDG6 parents and six-row spring barley in the National Small Grains Collection Core. (A) The proportion of variants differing between Rasmusson (the common parent) and each BRIDG6 donor parent. Donor parents are sorted from the greatest (top) to least (bottom) genetic distance from Rasmusson. Analysis was conducted using 588,482 GBS SNPs prior to filtering steps required for subsequent analyses. (B) Principal component analysis (PCA) of the BRIDG6 parents and 1172 six-row National Small Grains Collection Core accessions, which are plotted as small gray open circles. Rasmusson, is plotted as a large black open circle, and BRIDG6 parents are open circles colored by subpopulation assignments in orange (Admixed), purple (Asian), green (Central European), blue (Coastal Mediterranean), red (East African), and dark gray (Unassigned). Analysis was conducted using 6648 iSelect 9K SNPs. (C) PCA of the BRIDG6 donor parents and 6059 recombinant inbred lines. BRIDG6 parents and the population are colored as described in (B), except large points represent parents and small points represent the population. Analysis was conducted using 5332 GBS SNPs with maximum 10% missing data.

Article Snippet: The BRIDG6 parents and six-row barley accessions in The Core were genotyped using the barley Infinium 9K iSelect SNP chip ( Comadran et al. 2012 ).

Techniques: Recombinant

Journal: The BMJ

Article Title: Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation

doi: 10.1136/bmj.n214

Figure Lengend Snippet: Explanation of genotyping using SNP chip technology. Example cluster plots for common variant (top) and rare variant (bottom). Each circle represents one person’s DNA assayed at specific position on SNP chip when known variant (G to C) exists. Automated clustering across multiple individuals is used to determine which DNA base is present in each person at that position. Pink circles in main cluster represent most common reference base (G), orange circles represent heterozygous variant (C), and pale purple circles represent uncertain or missing results due to experimental noise

Article Snippet: We subsequently downloaded SNP chip data (provided by 23andMe from 2012 to 2019 using Illumina arrays) and genome sequencing data (provided by Veritas Genetics) for 21 people.

Techniques: Variant Assay

Journal: The BMJ

Article Title: Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation

doi: 10.1136/bmj.n214

Figure Lengend Snippet: Current medical context of SNP chip screening

Article Snippet: We subsequently downloaded SNP chip data (provided by 23andMe from 2012 to 2019 using Illumina arrays) and genome sequencing data (provided by Veritas Genetics) for 21 people.

Techniques:

Journal: The BMJ

Article Title: Use of SNP chips to detect rare pathogenic variants: retrospective, population based diagnostic evaluation

doi: 10.1136/bmj.n214

Figure Lengend Snippet: Positive predictive value (PPV) of UK Biobank Axiom SNP chip for detecting variants at different population frequencies. Similar trend was seen with UK Biobank BiLEVE chip (supplementary figure A) and Personal Genome Project consumer data (supplementary figure B)

Article Snippet: We subsequently downloaded SNP chip data (provided by 23andMe from 2012 to 2019 using Illumina arrays) and genome sequencing data (provided by Veritas Genetics) for 21 people.

Techniques: