Search Results for: Quantitative PCR

The Division of Veterinary Resources’ (DVR) mission is to contribute to the advancement of NIH biomedical research programs by providing excellence in animal care, customer service, and specialized research services to support intramural research efforts. Read More...

The Biomedical Engineering and Physical Science (BEPS) shared resource supports NIH’s intramural basic and clinical scientists on applications of engineering, physics, imaging, measurement, and analysis. BEPS is centrally located on the main NIH campus Read More...

The Division of Veterinary Resources Animal Surgery has supported large animal research and clinical care for more than 40 years. DVR surgeons provide outstanding and highly specialized large animal (rabbits, ungulates, etc.) research support in a Read More...

The Center for Advanced Tissue Imaging (CAT-I) is an NIAID and NCI supported effort involving collaborative studies between experts in the Laboratory of Immune System Biology, DIR, NIAID and investigators in the DIR, NIAID and Read More...

The Spatial Imaging Technology Resource (formerly the Nanoscale Protein Analysis Section of the Collaborative Protein Technology Resource or CPTR) provides expertise and service in state-of-the-art protein analysis technologies to advance CCR research in basic discovery Read More...

CREx News & Updates November 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More Site Spotlight FACILITY HIGLIGHTS Learn more about services from the NINDS Quantitative Magnetic Resonance Imaging Core. NINDS Read More...

Protein and Metabolite Characterization Core (PMCC), formerly known as the Protein Characterization Lab (PCL),  offers various technologies to CCR investigators to characterize proteins and metabolites. The core develops and applies state-of-the-art analytical technologies, primarily mass Read More...

Proteomic Data Common (PDC) represents the NCI’s largest public repository of proteogenomic comprehensive tumor datasets, essentially a Proteogenomic Cancer Atlas. It was developed to advance our understanding of how proteins help shape the risk, Read More...

The Mass Spectrometry Unit of the Collaborative Protein Technology Resource uses mass spectrometry for the study of proteins. We perform collaborative experiments with CCR researchers in areas such as: interactomes, quantitative global proteome analyses, and Read More...

The PPS encompasses all scientific analyses related to pharmacology, once the specimen has been collected and stored. There is a multi-step process to evaluate how the drug is being handled by the body after administration. Read More...

The CCR Building 41 Flow Cytometry Core is a full-service facility within the Center for Cancer Research that supports over 150 users representing 26 laboratories. The Core Facility provides instrument and software training, technical expertise, assay development, and Read More...

The core provides access to several different state-of-the-art 3D microscopes as well as computers to visualize and process image data. The facility houses equipment for 2D or 3D imaging of fixed and living specimens. High Read More...

The Optical Microscopy Analysis Core (OMAC), formerly known as the Optical Microscopy Analysis Lab (OMAL),  focuses its research and development activities to quantitatively understand the molecular basis of three-dimensional (3D) cell organization, motility, invasion, and Read More...

The function of the SAIP is to collaborate with NCI investigators in the development of mouse models, new molecular imaging probes for early detection and therapy, monitor tumors in vivo, and perform drug efficacy studies Read More...

Back Services: Biophysics Facility offers fluorometers as open-access instruments.  First-time users must complete a short training session before gaining access to the instrument reservation calendar. Location: Building 50, room 3226 Description: Some substances reemit light after Read More...

The NIH Metabolomics Consortium (NIH-MC) is a shared research resource that performs metabolomics analysis (and related small molecule research) for investigators at all Institutes and Centers across the NIH Intramural Research Program. The NIH-MC is Read More...

Back Services: Biophysics Facility offers Octet as an open-access instrument.  First-time users must complete a short training session before gaining access to the instrument reservation calendar.  Training includes a full analysis of a Read More...

The OSTR offers cutting-edge technology platforms to the CCR scientific community through centralized facilities. The videos accessed through this page are designed to introduce the various scientific methodologies OSTR makes available through the cores on Read More...

Home About the Biophysics Core Biophysics Core Services [tabby title="Instrumentation"] NHLBI Biophysics Core The Biophysics Core Facility: Overview Core Facilities provide scientific resources, cutting-edge technologies and novel approaches to support DIR scientists. Availability of Read More...

03/11/2021 - Abstract: Targeted quantitative proteomics using multiple/parallel reaction monitoring (MRM, PRM) is already being applied by many researchers in biology, biochemistry, and clinical research laboratories. These methods allow rapid and precise quantitation of proteins Read More...

07/15/2021 - Register Now Faculty: Michael Angelo, MD, PhD – Stanford University, Moonshot Cancer Atlas Moderator: Carsten Krieg, PhD – Medical University of South Carolina Target Audience This series will serve as an excellent resource for all stakeholders Read More...

03/09/2022 - Please join us on March 9 when Johns Hopkins University’s Elana J. Fertig, Ph.D., will demonstrate how CoGAPS, an established method for identifying transcriptional signatures related to cell type and state, can be Read More...

03/31/2021 - Link to recording: https://web.microsoftstream.com/video/78e8e458-f5c7-4aa4-b5ea-9cd94b20452a Helen Shearman, PhD, Senior Field Application Scientist, will be presenting a one-hour overview demonstration on Read More...

05/20/2024 - Hybrid (in-person location in Rockville, MD) Virtual attending via  WebEx Meeting, link will be available two weeks prior to the meeting date . Attend the  2024 Co-Clinical Imaging Research Resource Program (CIRP) Read More...

06/06/2024 - This webinar introduces SimBiology as a modeling environment for mechanistic pharmacokinetic (PK), pharmacodynamic (PD), and quantitative systems pharmacology (QSP) modeling and simulation. Participants will learn how to use the SimBiology Model Builder app to Read More...

02/29/2024 - This class provides an overview of the methods used to visualize the association among two or more quantitative variables. This class will focus on scatterplots, scatterplot matrix, and visualizing paired data. Upon completion of Read More...

Bray-Curtis dissimilarity quantitative Takes into consideration abundance and presence absence Jaccard - qualitative - presence / absence - percentage of taxa not found in both samples Weighted UniFrac quantitative similar to Bray-Curtis but takes into consideration Read More...

12/05/2023 - This class provides an overview of the methods used to visualize the association among two or more quantitative variables. This class will focus on scatterplots, scatterplot matrix, and visualizing paired data. Upon completion of Read More...

Differential expression involves the comparison of normalized expression counts of different samples and the application of statistical measures to identify quantitative changes in gene expression between the different samples.

Reads not perfect Duplicate molecules (PCR artifacts skew quantitation) Multimapped reads - Some regions of the genome are thus classified as unmappable Aligners try very hard to align all reads, therefore fewest artifacts occur when Read More...

Picard is a set of command line tools for manipulating high- throughput sequencing (HTS) data and formats such as SAM/ BAM/CRAM and VCF. (mark pcr duplicates) Samtools provide various utilities for manipulating alignments in Read More...

07/11/2023 - This class provides a basic overview of the methods used to visualize the association among two or more quantitative variables. This class will focus on scatterplots, scatterplot matrix, and visualizing paired data. Read More...

04/04/2023 - This class provides a basic overview of the methods used to visualize the association among two or more quantitative variables. This class will focus on scatterplots, scatterplot matrix, and visualizing paired data. Read More...

02/21/2023 - Please plan to attend the Earl Stadtman Investigator Program search seminar by: Stephanie Harmon, Ph.D. Molecular Imaging Branch (MIB), CCR hosted by the MIB  Dr. Harmon is a Staff Scientist in the MIB Read More...

01/05/2023 - This class provides a basic overview of the methods used to visualize the association among two or more quantitative variables. This class will focus on scatterplots, scatterplot matrix, and visualizing paired data. Participants are Read More...

The plot below shows the sequence duplication levels. High levels of duplication may indicate an enrichment bias such as over-amplification in the PCR step. However, in RNA sequencing, duplicate sequences could be biologically meaningful as Read More...

The Lasergene Molecular Biology package includes the following applications: SeqBuilder Pro, SeqMan Ultra, MegAlign Pro, GeneQuest, GenVision, SeqNinja, and DNASTAR Navigator. These applications provide tools to perform in silico gel electrophoresis and cloning, plasmid vector Read More...

Geneious Prime is a graphical user interface (GUI) based bioinformatics package that contains a suite of tools for molecular biology and Next Generation Sequencing analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{Esum}} Classic Computational Molecular Read More...

04/10/2025 - This one hour online training introduces participants to the tools and techniques for analyzing and quantifying microscopy images using MATLAB’s low-code algorithms. Participants will learn how to preprocess images, segment regions Read More...

03/12/2025 - Clustering is one of the fundamental unsupervised machine learning algorithms. It is often used to group quantitative proteomic or RNAseq expression data to suggest sub-types of a particular cancer. This presentation covers building a Read More...

10/08/2024 - Mass spectrometry is a powerful tool for analyzing protein regulation and function. This workshop, divided into two parts, will explain the fundamentals of mass spectrometry experiments and how proteins are identified. We will further Read More...

09/13/2023 - FORGEdb is a web-based tool that can rapidly integrate data for individual genetic variants, providing information on associated regulatory elements, transcription factor (TF) binding sites and target genes for over 37 million variants.   Read More...

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq Read More...

Normalization - the process of scaling data to account for uncontrolled factors affecting variation. Effect size - "the quantitative measure of the magnitude of a phenomenon" (Biostar Handbook). P-value - "the probability Read More...

Alignment RNASeq Mapping Challenges The majority of mRNA derived from eukaryotes is the result of splicing together discontinuous exons, and this creates specific challenges for the alignment of RNASEQ data. Mapping Challenges Reads not perfect Read More...

Before diving into the construction of bar plot, box & whisker plot, and histogram, we should do a quick review of the types of variables that we commonly work with in data analysis. Categorical variables Read More...

10/04/2022 - Speaker: Steven D Cappell NIH Stadtman Investigator Center for Cancer Research – National Cancer Institute – Bethesda MD My laboratory is integrating quantitative image analysis with genetic, biochemical, and systems biology approaches to understand how cells Read More...

10/03/2022 - Join Drs. Andrey Fedorov and Hugo Aerts for the upcoming October NCI Imaging and Informatics Community Webinar. Their presentation includes updates to the  Imaging Data Commons  (IDC)—a repository of the  NCI Cancer Research Read More...

04/07/2022 - Join Dr. Maryellen L. Giger at the April NCI Imaging and Informatics Community Webinar for a discussion on the development, validation,  database  needs, and ultimate future implementation of artificial intelligence (AI) in the clinical Read More...

10/27/2021 - Wrapping up its final webinar of 2021, the NCI Cancer Research Data Commons (CRDC) Cancer Genomics Cloud (CGC) welcomes Cold Spring Harbor Laboratory fellow Dr. Pascal Belleau. He will share his findings from recent work Read More...

04/02/2013 -   Geneious is an integrated and extensible software platform for the organization, visualization and analysis of DNA and protein sequence information. Researchers can analyze any NGS data alongside traditional Sanger data and combine technologies in Read More...

03/06/2013 -   Geneious is an integrated and extensible software platform for the organization, visualization and analysis of DNA and protein sequence information. Researchers can analyze any NGS data alongside traditional Sanger data and combine technologies in Read More...

In this session of the BTEP Coding Club, Brian Luke, PhD, Senior Principal Computational Scientist with the Advanced Biomedical Computational Science (ABCS) group, showed us the basic techniques involved in clustering using R and RStudio Read More...

CLC Genomics Workbench (Qiagen) is a graphical user interface (GUI) based bioinformatics software. It houses tools for molecular biology and Next Generation Sequencing (NGS) analysis (see Listing of Analysis Functions below). {{Sdet}}{{Ssum}}Listing of Read More...

SnapGene is a point and click proprietary software program used for designing and documenting molecular biology experiments. SnapGene is a multipurpose software program used for, but not limited to, the following: DNA sequence alignment, annotation, Read More...

SnapGene is a point and click proprietary software program used for designing and documenting molecular biology experiments. SnapGene is a multipurpose software program. SnapGene is a point and click proprietary software program used for designing Read More...

02/12/2026 - The NLM Division of Intramural Research (DIR) is pleased to welcome Tiarnán Keenan, MD, PhD, Stadtman Tenure-Track Investigator and Director of the Medical Retina Fellowship Program at the National Eye Institute Read More...

01/15/2026 - Gil Kanfer, PhD, of the NCI CCR High-Throughput Imaging Facility (HiTIF), in the Laboratory of Receptor Biology and Gene Expression (LRBGE) , will present the spatial biology analysis stack HiTIF is building to support Center Read More...

01/21/2025 - About the Speaker: Hari completed his PhD in Cell Biology at the University of Toronto, where he used single-molecule imaging techniques to reveal how multimolecular interactions govern early signaling events in individual immune cells. Read More...

11/13/2024 - The National Library of Medicine (NLM) Division of Intramural Research (DIR) is pleased to welcome Manisha Desai, PhD, Section Chief of Biostatistics and Director of the Quantitative Sciences Unit at Stanford University School of Read More...

There are several metrics that can be used to assess overall quality. The base workflow from Seurat suggests the following: nCount_RNA - the absolute number of RNA molecules (UMIs) per cell (i.e., count Read More...

03/22/2024 - This 3-hour seminar is tailored for biologists, data analysts, and researchers who are eager to dive into the essentials of computational flow cytometry analysis using R. Flow cytometry is a crucial technique in cell Read More...

03/01/2024 - Jens Rittscher is Professor of Engineering Science at the University of Oxford with his appointment held jointly between the Institute of Biomedical Engineering and the Nuffield Department of Medicine. He is a group leader Read More...

Lesson 6 . Learning Objectives Introduce several beta diversity metrics Discover different ordination methods Learn about statistical methods that are applicable Beta diversity Beta diversity is between sample diversity. This is useful for answering the question, how Read More...

Differential Expression Differential expression involves the comparison of normalized expression counts of different samples and the application of statistical measures to identify quantitative changes in gene expression between the different samples. Normalization and Statistical Significance Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn * What are sequence adapters? * Do we need to trim them before alignment? * How can I trim with a new adapter sequence? Be Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn * What are sequence adapters? * Do we need to trim them before alignment? * How can I trim with a new adapter sequence? Be Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: FASTQC for assaying quality of sequence reads MultiQC for combining multiple FASTQC reports into one report Trimmomatic for removing sequence data based Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: FASTQC for assaying quality of sequence reads MultiQC for combining multiple FASTQC reports into one report Trimmomatic for removing sequence data based Read More...

Unix, what is it, and why should biologists take the time to learn it? The Unix operating system forms the basis of many bioinformatics analyses resources, such as the NIH High Performance Cluster (HPC) Biowulf/ Read More...

09/22/2022 - The avalanche of easy-to-create genomics data has impacted almost all areas of medicine and science, from cancer patients and microbial diagnostics to molecular monitoring for astronauts in space. In this lecture, new discoveries from Read More...

06/29/2022 - The CCR Genomics, Sequencing and Single Cell Analysis Core Facilities are pleased to host a virtual technology seminar with Illumina. Presentation overview : For decades cancer methylation studies have provided insights into tumorigenic pathways and Read More...

01/19/2022 - For our next CDSL Webinar we will have a guest lecture by  Dr. Russell Rockne from Beckman Research Institute, City of Hope National Medical Center. Abstract: Temporal dynamics of gene expression inform cellular and Read More...

12/01/2021 - Speaker: James Lacey, Ph.D., M.P.H. Dr. James Lacey is a City of Hope professor and director of the Division of Health Analytics within the Department of Computational and Quantitative Medicine. His Read More...

06/10/2021 - Meeting Link:  https://cbiit.webex.com/cbiit/j.php?MTID=mc11b56eb7f7e732aa44c78427402dd2e Abstract: Long read, single molecule sequencing from Pacific Biosciences (PacBio) and Oxford Nanopore are revolutionizing Read More...

05/03/2021 - Abstract: We will discuss technical advantages of a personalized and tumor-informed multiplex PCR next generation sequencing assay, called Signatera™, that enables a sensitive, specific, and dynamic detection of molecular disease burden in cell-free DNA ( Read More...

04/20/2021 - Abstract: Single-cell genome-wide profiling offers an approach to map transitional cell states during cell differentiation, disease onset, and drug response. Lineage-tracing, in which cells are labeled with hereditary markers, offers an approach to establishing Read More...

03/08/2021 - Zoom Registration Description NHGRI will host a new seminar series this year on the “Bold Predictions for Human Genomics by 2030” that are described in NHGRI’s “ Strategic Vision for Improving Human Health at the Read More...

06/28/2020 - The overarching goal of our work is to implement data analysis and informatics tools for integration of biological mass spectrometry data (proteomics and metabolomics) with genomic / transcriptomic information to advance cancer research. We are Read More...

{{Sdet}}{{Ssum}}Sequence comparison{{Esum}} CLC Genomics Workbench What file types can I start my analysis with? FASTA Genbank Geneious Prime What file types can I start my analysis with? FASTA Genbank Lasergene What file Read More...

There are a number of core facilities available to NCI researchers. See more information from the Office of Science and Technology Resources. We most commonly see data from the following cores: CCR Sequencing Facility (CCR-SF) Read More...

Learning Objectives This tutorial was designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples. Throughout this tutorial we Read More...

Lesson 1: Introduction to Unix and the Shell Lesson Objectives Course overview. Introduce Unix and describe how it differs from other operating systems. Introduce and get set up on DNAnexus and the GOLD system. Discuss ways Read More...

In lesson 9, we learned that reference genomes came in the form of FASTA files, which essentially store nucleotide sequences. In this lesson, we will learn about the FASTQ file, which is the file format that Read More...

Lesson 10: Introducing the FASTQ file and assessing sequencing data quality Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 9 Review In the previous lesson, we explored the reference genomes and Read More...

/* Whole document: */ body{ font-family: Times; font-size: 16pt; } Stat Transformations: Bar plots, box plots, and histograms Objectives Review the grammar of graphics template Learn about the statistical transformations inherent to geoms Review data types Create bar Read More...

03/08/2016 - BTEP Workshop on Exome-Seq Data Analysis and Variant Annotation (2-day) This workshop will cover the basics and best practices of exome-seq analysis including downstream interpretation of variants using a variety of in-house, open-source and Read More...