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Search Results for: Gene expression

Total Results Found: 169

Total Results Found: 169

Past Seminars

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2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( Read More...

Visium Spatial Gene Expression Technology

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What is Visium FFPE v2 with CytAssist? Visium FFPE v2 is sequencing-based spatial profiling technology developed by 10x Genomics. This assay can take mouse or human tissue sections on normal glass slides as input and Read More...

Using NCBI GEO Datasets to Analyze Gene Expression

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Bioinformatics

06/20/2014 - NCI CCR  http://bioinformatics.nci.nih.gov/training/  and the NIH Library Bioinformatics Support Program http://nihlibrary.nih.gov/Bioinformatics  are partnering to sponsor training on the use of NCBI GEO Datasets to analyze Read More...

BTEP Coding Club: Gene Expression Example.

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Bioinformatics

We want to add the columns gene_symbol and Description from one data table to another data table containing our differential expression results. First, let's load our data. gene_info_fp<-file. Read More...

Introduction to Gene Expression Microarray Data Analysis

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Bioinformatics

10/02/2012 - Microarray Technology and Preprocessing Quality Control Normalization Using MAS5 and RMA Filtering Batch Effect Correction Basic Statistical Tests for Differentially Expressed Genes T-test ANOVA SAM Calculating False Discovery Rate Principal Components Analysis and Clustering Read More...

Differential Expression Analysis with Seurat

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Bioinformatics

05/22/2024 - This seminar provides an overview of differential expression testing with Seurat. Topics to be covered include preparing data for differential gene expression, d ifferential gene analysis between specific groups, d ifferential gene analysis for Read More...

Protein Expression Laboratory

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Protein Expression Laboratory The Protein Expression Laboratory develops, improves, and delivers protein-centric services. Our goal is to help client investigators achieve their research goals with the lowest possible cost in the shortest time. All PEL Read More...

CCR Protein Expression Laboratory (PEL)
Frederick, Maryland

Core Facility

The Protein Expression Laboratory produces proteins to help CCR investigators achieve their research goals with the lowest possible cost in the shortest time. PEL is operated by Leidos Biomedical Research Inc. on behalf of NCI Read More...

Publications

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Confocal

2025 Sebastian R, Sun EG, Fedkenheuer M, Fu H, Jung S, Thakur BL, Redon CE, Pegoraro G, Tran AD, Gross JM, Mosavarpour S, Kusi NA, Ray A, Dhall A, Pongor LS, Casellas R, Aladjem MI. Mechanism Read More...

Spatial Biology

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Employing spatial biology techniques enables acquisition of transcript and protein data from intact tissue sections, and in turn, spatial distribution information and cellular interaction patterns are revealed.

Data Wrangling with R: Data Challenges

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Bioinformatics

There are some immediate problems with the data. The column names begin with numbers, which are not syntactic with R. The gene names are hybrids of Ensembl ID and gene symbols and will match neither Read More...

Research

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Confocal

Research Mission The goal of OMAL’s research is to understand molecular mechanisms driving carcinogenesis and the reversal of this process through treatment, by utilization and advancement of optical microscopy techniques. These techniques include multiplex Read More...

GEO Analysis Tools: New and Improved

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Bioinformatics

10/30/2024 - In this session of the BTEP Coding Club, Emily Clough, PhD, GEO Curator, will explore updates to analysis tools available within the Gene Expression Omnibus (GEO), a public repository for gene expression and epigenomics Read More...

Pathway Analysis

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Bioinformatics

09/10/2024 - The training will overview the current status of pathway tools, with focus on software available to NIH community.  It will discuss the biological interoperation of mutation and expression data in the context Read More...

CCR Genomics Technology Laboratory (GTL)
Frederick, MD

Core Facility

The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated Read More...

Genomics Technology Laboratory

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The Genomics Laboratory (formerly Laboratory of Molecular Technology) is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, together with associated laboratory automation systems, data analysis, and information management Read More...

Xenium Spatial Profiling Technology

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What is Xenium? Xenium is a high-resolution, imaging-based in situ spatial profiling technology from 10x Genomics that allows for simultaneous expression analysis of RNA targets (currently in range of 100’s) within the same tissue section. Read More...

Spatial Biology

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Employing spatial biology techniques enables acquisition of transcript and protein data from intact tissue sections, and in turn, spatial distribution information and cellular interaction patterns are revealed.

CCR Radiation Oncology Branch Bioinformatics Core
Bethesda, Maryland

Collaborative

Radiation Oncology Branch is part of CCR. Bioinformatics core is a collaborative resource to support ROB branch and provide service to ROB investigators from NCI and other Institutes access to new technologies, bioinformatics, statistical analysis Read More...

Software & Techniques

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Confocal

Techniques The Laboratory of Cancer Biology and Genetics Microscopy Core houses multiple systems that can be used to analyze cell structure, protein expression, and cell dynamics using immunofluorescence. These include inverted epifluorescence microscopes, a confocal Read More...

Contact Us

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Our Team Tatiana S. Karpova Ph.D.Core Headkarpovat@nih.govBuilding 41, Room C615240-760-6637 David A. Ball Ph.D.Core Biologistballa@nih.govBuilding 41, Room B114D240-760-6577 Mohamadreza Fazel, Ph.D.Core Biologistmohamadreza. Read More...

Publications

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Confocal

2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...

RNA-Seq Analysis Using Galaxy

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Bioinformatics

06/03/2025 - Class Description Introduction to RNA-Seq data analysis Step-by-step live demonstration of RNA-Seq analysis using the Galaxy platform   What You’ll Learn: How to independently carry out the basic gene expression Read More...

Pathway Analysis with Reactome

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Bioinformatics

04/08/2025 - Reactome is a free, open-source, curated and peer-reviewed pathway database that includes bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge. This lesson will showcase the capabilities of Reactome in garnering biological Read More...

Introduction to RNA Sequencing

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Bioinformatics

02/18/2025 - This class will introduce basic experimental and analytical considerations for bulk RNA sequencing, a technique that is used to profile gene expression at the tissue level. Information taught serves as the foundation for participants Read More...

BTEP course: Learning Objectives

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Bioinformatics

After this class, participants will Become familiar analyzing single cell RNA sequencing data using Partek Flow including Importing of data into a Partek Flow project QA/QC, filtering, and normalizing of single cell RNA data Read More...

Data Wrangling with R: Our challenge

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Bioinformatics

First, we will want to fix the three immediate problems discussed above. Once those have been fixed, we are going to create a bar plot, using ggplot2 to plot the total gene counts per sample. Read More...

Data Wrangling with R: Unite and separate

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Bioinformatics

There are two additional functions from Tidyr that are very useful for organizing data: unite() and separate() . These are used to split or combine columns. For example, you may have noticed that our feature column Read More...

CCR Genomics Core
Bethesda, MD

Core Facility

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...

Bloomington Drosophila Stock Center
Bloomington, IN

Repositories

Trans NIH Facility

The Bloomington Drosophila Stock Center (BDSC) collects, maintains, and distributes genetically defined strains of Drosophila melanogaster for research and education. The BDSC supports a large, worldwide community of scientists using Drosophila as a model organism Read More...

NCI Genomics and Pharmacology Facility
Bethesda, MD

Core Facility

The Genomics and Pharmacology Facility is part of the NCI's Center for Cancer Research (CCR), within the Developmental Therapeutics Branch. Its mission is to manage and assess molecular interaction data obtained through multiple platforms, increase Read More...

CLIA Molecular Diagnostics Laboratory
Frederick, Maryland

Core Facility

CLIA-Certified Technologies Offered: Fragment Analysis for Micro-satellite Instability Detection, Pharmacoscan Array for Pharmacogenomics, Mutation Detection for PCR and Sanger Sequencing, DNA extraction from whole blood, saliva, FFPE tissues, buccal swabs, nails, hair, PBMCs, buffy coats, Read More...

CLIA Molecular Diagnostics Laboratory (CMDL)

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The CLIA Molecular Diagnostics Laboratory (CMDL) provides an array of services for groups at the NIH Clinical Center, Fort Detrick, and Hood College, among others. They support cancer- and disease-related research by making Read More...

July 2021

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CREx News & Updates July 2021   Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGHLIGHTS Learn more about services from the NHLBI Read More...

10X Genomics

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[embed]https://youtu.be/yTl1Q0D7aZ0[/embed] 10x Genomics' supports multiple cancer research areas from single nucleotide and structural variant detection to single cell whole transcriptome gene expression analysis of thousands of individual Read More...

NHLBI Transgenic Core
Bethesda, MD

Core Facility

Trans NIH Facility

The NHLBI Transgenic Core’s main mission is to keep up with the latest advancements in genome engineering technologies and to provide state-of-the-art services to assist NIH scientists in generating genetically engineered animal models. In Read More...

December 2024 Newsletter

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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Advance your research with the NIH Mouse Imaging Facility (MIF) The NIH Mouse Imaging Read More...

Mass Spectrometry for Proteins

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Mass Spectrometry Section of the Collaborative Protein Technology Resource (Bldg. 37) Core Capabilities: Identification of proteins in complexes, organelles, subcellular fractions, or fluids. Global relative protein quantitation. Quantitation by isotopic labeling of cells in culture (SILAC) Read More...

August 2024 Newsletter

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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. If you haven’t Read More...

Molecular Targets Database and Tools
Rockville, MD

Repositories

Trans NIH Facility

Thousands of molecular targets have been measured in the NCI panel of 60 human tumor cell lines. Measurements include protein levels, RNA measurements, mutation status, and enzyme activity levels. You can choose to search for a Read More...

Laboratory of Genome Integrity (LGI): Flow Cytometry Core
Bethesda, MD

Core Facility

The Flow Cytometry Core (LGI) offers established technologies to support studies using flow cytometry and cell sorting. Established Technologies Applications that run on FACS Caliburs include: Immunophenotyping (up to 4-color), Intracellular markers, including cytokines and Read More...

July 2024 Newsletter

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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. We would greatly appreciate Read More...

October 2021

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CREx News & Updates October 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGLIGHTS Learn more about services from the CPTR Read More...

November 2024 Newsletter

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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Derive Greater Insights and Accelerate your Research Using Bioinformatic Tools! CREx is an NIH Read More...

NCI Patient-Derived Models Repository (PDMR)
Bethesda, MD

Collaborative

Repositories

The National Cancer Institute (NCI) is developing a national repository of Patient-Derived Models (PDMs) comprised of patient-derived xenografts (PDXs), patient-derived organoids (PDOrg), and in vitro patient-derived tumor cell cultures (PDCs) and cancer-associated fibroblasts (CAFs). These Read More...

March 2023 Newsletter

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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New Resources on CREx NCI CLIA Molecular Diagnostics Laboratory (CMDL) The NCI CMDL is available to assist all Read More...

Image Analysis

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HALO HALO is a powerful 2D image analysis tool with AI capabilities to perform annotations and analysis on bright-field and immunofluorescent images for digital pathology and numerous other applications.  It offers a set of algorithms Read More...

Policies

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General Usage Policies Principal investigators should read this document and sign it. PI’s/postdocs should attach a short-written summary of the project to the signed doc. If the project changes, Read More...

Publications

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Confocal

2016-2024 Publications using images obtained in OMC

Class Documents

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Bioinformatics

Most BTEP courses include detailed course materials including lesson content, additional resources, and lesson associated data. These course materials are listed here so that learners can easily return to and review concepts taught in class Read More...

Resources

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Bioinformatics

BTEP strives to maintain links to resources that should be of interest to CCR Bioinformatics Community.  Some of the resources to will be accessible through more than one of these lists, but since the lists Read More...

Introducing Bioinformatics for Beginners

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Bioinformatics

What is bioinformatics? Bioinformatics integrates biology, statistics, and computer science to develop and apply theory, methods, and tools for the collection, storage, and analysis of biological and related data. Bioinformatics plays a critical role in Read More...

Bulk RNA Sequencing Analysis using Partek Flow

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Bioinformatics

11/19/2024 - Partek Flow enables scientists to construct analysis workflows for multi-omics sequencing data including DNA, bulk and single cell RNA, spatial transcriptomics, ATAC and ChIP. It is a point-and-click software hosted on Biowulf, the NIH Read More...

Generative AI for Modeling Single-Cell State and Response

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Bioinformatics

10/16/2024 - Dear Colleagues,   Thanks to advances in single-cell genomics, researchers can construct large-scale organ atlases, giving you more accurate ways to study genetic mutations and alterations related to drug responses and disease. These Read More...

BTEP course: Course overview

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Bioinformatics

Course Overview Partek Flow is a start-to-finish solution for analyzing high dimensional multi-omics sequencing data. It is a point-and-click software and is suitable for those who wish to avoid the steep learning curve associated with Read More...

Data Wrangling with R: Help Session Lesson 6

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Bioinformatics

Let's grab some data. library ( tidyverse ) acount_smeta % dplyr :: rename ( "Feature" = "...1" ) acount #differential expression results dexp % filter ( ! Feature %in% dexp $ feature ) ## # A tibble: 48,176 × 9 ## Feature SRR1039508 SRR1039509 SRR1039512 SRR1039513 SRR1039516 SRR1039517 ## ## 1 Read More...

Data Wrangling with R: Lesson 6: Continuing with Dplyr

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Bioinformatics

Help Session Lesson 6 Let's grab some data. library ( tidyverse ) acount_smeta % dplyr :: rename ( "Feature" = "...1" ) acount #differential expression results dexp % filter ( ! Feature %in% dexp $ feature ) ## # A tibble: 48,176 × 9 ## Feature SRR1039508 SRR1039509 SRR1039512 Read More...

FAQ

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CRTP

No summary available.

NIH Intramural Sequencing Center (NISC)
Rockville, MD

Trans NIH Facility

NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to Read More...

NIH Biowulf Computational Cluster
Bethesda, MD

Trans NIH Facility

The NIH Biowulf Cluster provides researchers with a world-class system to assist in solving complex biomedical problems as diverse as gene variation in worldwide human populations, deep learning to model protein structures, and PET brain Read More...

NIH Clinical Center, Center for Cellular Engineering
Bethesda, MD

Core Facility

Trans NIH Facility

The Center of Cellular Engineering (CCE) is a comprehensive facility that develops and manufactures a wide range of cell and gene therapies for early phase clinical trials. The CCE is currently manufacturing chimeric antigen receptor ( Read More...

CCR Sequencing Facility
Frederick, MD

Core Facility

The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at Read More...

February 2023 Newsletter

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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More. New Resources on CREx NIMH Human Brain Collection Core (HBCC) The HBCC obtains human brain tissue, hair, and blood Read More...

NCATS Functional Genomics Laboratory
Rockville, MD

Core Facility

Trans NIH Facility

The Functional Genomics Laboratory (formerly, the RNAi Screening Facility) of the National Center for Advancing Translational Sciences (NCATS) assist investigators with all stages of project planning and execution, beginning with assay development through genome-wide siRNA Read More...

June 2024 Newsletter

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CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx Program Manager The CREx Team is happy to announce Deepika Velampati as the new CREx Program Read More...

BD Genomics Rhapsody System

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Total end-to-end system for single-cell research [embed]https://youtu.be/vMzhSzg1rUw[/embed] The BD Rhapsody Single-Cell Analysis system empowers and streamlines your research with a complete system of tools, including reagents and analysis software, Read More...

NCI LASP Genome Modification Core (GMC)
Frederick, MD

Core Facility

NCI LASP Genome Modification Core (GMC) is a CCR-dedicated facility that provides advice, training, and reagents to NCI scientists seeking to utilize CRISPR and other nucleases to generate genome modifications in primary cells, cell lines, Read More...

Biopharmaceutical Development Program (BDP)
Frederick, MD

Collaborative

The Biopharmaceutical Development Program (BDP) provides resources for the development of investigational biological agents. The BDP supports feasibility through development and Phase I/II cGMP manufacturing plus regulatory documentation.The BDP was established in 1993. We Read More...

NCI Center for Structural Biology: Protein Technology Core
Frederick, MD

Collaborative

The primary objective of the Protein Technology Core (PTC) is to establish an experimental screening pipeline for single-domain antibodies termed nanobodies. Nanobodies are antibody fragments consisting of a single monomeric variable antibody domain. The PTC, Read More...

STARS Request

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Supplemental Technology Award Review System (STARS) Overview STARS Request Form STARS System The Supplemental Technology Award Review System (STARS) is a web-based interface for submission and review of S&S supplement requests by CCR Read More...

CCR Spatial Imaging Technology Resource (SpITR)
Bethesda, MD

Collaborative

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...

CCR Protein Characterization Laboratory (PCL)
Frederick, MD

Core Facility

Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...

NCI Genomic Data Commons (GDC)
Bethesda, MD

Repositories

Trans NIH Facility

The NCI Genomic Data Commons (GDC) was established by the NCI Center for Cancer Genomics (CCG) to support the receipt, harmonization, distribution, and analysis of genomic and clinical data from cancer research programs. The GDC Read More...

NCI LASP Mouse Modeling & Cryopreservation (MMC)
Frederick, MD

Core Facility

Repositories

The Mouse Modeling Core assists NIH investigators by generating and preserving genetically-engineered mouse strains. Services include scientific consultation, gene-targeting in mouse embryonic stem cells, micro-injection of nucleic acids, proteins, or ES cells into mouse embryos, Read More...

Technology Video Library

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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...

Multi-Angle Light Scattering (MALS)

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Back Services: We offer a limited sample processing service using standard SEC-MALS and FFF protocols.  This service is intended for the occasional users of this system.  Researchers who expect to use this instrument Read More...

Publications

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Confocal

2024 L. Balagopalan, T. Moreno, H. Qin, B. C. Angeles, T. Kondo, J. Yi, K. M. McIntire, N. Alvinez, S. Pallikkuth, M. E. Lee, H. Yamane, A. D. Tran, P. Youkharibache, R. E. Cachau, N. Taylor, Read More...

Personnel

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Stephen Lockett, Ph.D. Director, OMAL locketts@nih.gov 301-846-5515 Valentin Magidson, Ph.D. Scientist magidsonv@mail.nih.gov 301-846-6092 Will Heinz, Ph.D. Scientist heinzwf@nih.gov 301-846-1239 David Read More...

Resources

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Confocal

General Microscopy Resources Confocal Listserv Email discussion list focused on confocal microscopy, but also including topics on fluorescence microscopy and digital imaging. MicroscopyU Online learning platform by Nikon.  An online source for Microscopy education. Leica Read More...

BTEP Video Archive of Past Classes

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Bioinformatics

Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...

The Advanced Biomedical Computational Science (ABCS) Group

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Bioinformatics

The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: • Subject matter expertise in genomics, proteomics, and imaging. • Machine learning/ Read More...

Data Wrangling with R: Accessors

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Bioinformatics

As you can see from the image, there are several accessor functions to access the data from the object: assays() - access matrix-like experimental data (e.g., count data). Rows are genomic features (e.g., Read More...