One powerful method, Precision nuclear Run-On sequencing (PRO-seq), maps the locations of RNA polymerase active sites genome-wide at high resolution. PRO-seq provides a snapshot of strand-specific transcriptional activity and does not rely on immunoprecipitation of the polymerase of interest. ...
We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) (PRO-cap) genome-wide at high resolution. The density of RNA polymerases at a particular genomic...
can focus on the coding regions of all of the base pairs of the genome (whole exome sequencing (WES)), or can involve the analysis of the entire tumor genome, including the intronic regions (whole genome sequencing (WGS)). The choice between these approaches depends on several factors, inc...
and the annotation of our biomarkers for drug modulatory effects. Third, we now have a longer duration follow-up on subjects, and also used longitudinal, not just cross-sectional, calculations for predictions. Fourth, we used newer methodologies, such as RNA sequencing, as well as machine...
SP, signal peptide; PD, prodomain; TM, transmembrane domain. 4.3. Precision medicine: present and future Genomics is without a doubt the current key technology in personalized medicine (Fig. 1B). The newest generation Illumina sequencer [71] allows for complete genome sequencing in less than a...
Single-cell RNA-sequencing (scRNA-seq) data were preprocessed by undergoing quality control, denoising, clustering, cell typing and differentially expressed gene (DEG) calculation. DEGs for each cell type were calculated between healthy and sick samples. Using DEGs alongside information on drugs, sc...
Dr. Ottaviani went on to show how MED1 and ER are depleted from the chromatin upon siCDK12, indicating CDK12 knockdown disrupts MED1 and ER recruitment to the chromatin. Following CDK12 knockdown, apoptosis was significantly increased as evidenced by both RNA sequencing and PARP cleavage western...
Precision ID; HID Ion AmpliSeq; short tandem repeats; GlobalFiler; single-nucleotide polymorphisms; ancestry SNPs; identity SNPs; next-generation sequencing; massively parallel sequencing; forensic genetics1. Introduction Since the discovery of DNA fingerprinting in the 1980s, the field of forensic ...
Next-generation sequencing Clinical NGS (specifically, DNA-seq) analysis was performed using the Tempus xT 648-gene panel1,3,21 (Tempus Labs, Inc., Chicago, IL, USA) using the same FFPE tissue specimen as was used for the LMD-RPPA analysis. The sample for DNA-seq was prepared from tissu...
We used RNA-Seq (Illumina HiSeq 2000 RNA Sequencing Version 2) Level 3 data from TCGA (http://cancergenome.nih.gov/) project, normalized with RSEM46. The 40 genes studied were selected from the autophagy pathway (hsa04140) curated by KEGG (http://www.genome.jp/). We considered tissue...