Journal: Molecular Cell

Article Title: Human NLRP1 is a sensor of pathogenic coronavirus 3CL proteases in lung epithelial cells

doi: 10.1016/j.molcel.2022.04.033

Figure Lengend Snippet:

Article Snippet: A549 ACE2 & TMPRSS2 Cells , a549-hace2tpsa , Invivogen.

Techniques: Virus, Variant Assay, Clinical Proteomics, Recombinant, Microscopy, Plasmid Preparation, Mutagenesis, Construct, Software

Journal: The Journal of molecular diagnostics : JMD

Article Title: Validation of a Next-Generation Sequencing Pipeline for the Molecular Diagnosis of Multiple Inherited Cancer Predisposing Syndromes.

doi: 10.1016/j.jmoldx.2017.05.001

Figure Lengend Snippet: Figure 4 Pipeline analysis for targeted NGS of multiple inherited cancer syndromes using the TruSight Cancer panel. In our analysis pipeline, .fastq files are used for alignment and variant calling in Isaac Enrichment, Burrows-Wheeler Aligner (BWA) Enrichment, and NextGENe software, and .vcf files are then imported to GeneticistAssistant for variant filtering. Supervised analysis of filtered variants will allow the identification of disease-associated variants and/or of pathogenic variants associated with cancer predisposing syndromes outside the clinical context (incidental finding), with both being supported (if needed) by visual inspection of .bam files in Golden Helix GenomeBrowse (GB). Variants called because of sequencing errors are discarded on visual inspection of .bam files in Golden Helix GB. 1000G, 1000 Genomes Project; ACMG, American College of Med- ical Genetics and Genomics; Alt.var.freq., percentage of reads with alter- native allele; CDS, coding sequence; EVS, Exome Variant Server; ExAC, Exome Aggregation Consortium; In-house freq., variant frequency among all of the samples in our in-house database; MAF, minor allele frequency.

Article Snippet: Library Preparation and Sequencing For library preparation, we followed the manufacturer’s instructions (TruSight Rapid Capture Kit; Illumina Inc., San Diego, CA).

Techniques: Variant Assay, Software, Sequencing

Journal: Epigenetics

Article Title: Battle of epigenetic proportions: comparing Illumina's EPIC methylation microarrays and TruSeq targeted bisulfite sequencing.

doi: 10.1080/15592294.2019.1656159

Figure Lengend Snippet: Figure 1. Coverage of epigenetic and genetic elements for EPIC (black) and TruSeq (red).

Article Snippet: To fill this gap, we conducted a comparison study in which we processed cord blood samples from four newborns in duplicates using both the Illumina HumanMethylationEPIC BeadChip and the Illumina TruSeq Methyl Capture EPIC Kit, and evaluated both platforms in regard to coverage, reproducibility, and identification of differential methylation.

Techniques:

Journal: Epigenetics

Article Title: Battle of epigenetic proportions: comparing Illumina's EPIC methylation microarrays and TruSeq targeted bisulfite sequencing.

doi: 10.1080/15592294.2019.1656159

Figure Lengend Snippet: Figure 2. Concordance of methylation level estimates between EPIC and TruSeq samples stratified by read depth.

Article Snippet: To fill this gap, we conducted a comparison study in which we processed cord blood samples from four newborns in duplicates using both the Illumina HumanMethylationEPIC BeadChip and the Illumina TruSeq Methyl Capture EPIC Kit, and evaluated both platforms in regard to coverage, reproducibility, and identification of differential methylation.

Techniques: Methylation