Search Results for: mRNA quantification

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...

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...

10/26/2021 - Meeting Link: https://cbiit.webex.com/cbiit/j.php?MTID=m14c6833bc06f89408464fac5bb2e8ce9 Human cells generate remarkable regulatory and functional complexity from a finite set of genes. Production of Read More...

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...

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...

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...

09/08/2023 - Hybrid Seminar Friday, September 8, 2023 • 9:00-10:00 a.m. Building 549 Auditorium (In-person attendance encouraged)   Speaker: Brian Kelsall, M.D. Senior Investigator, Mucosal Immunobiology Section Laboratory of Molecular Immunology National Institutes of Allergy Read More...

By using the metacharacter asterisk "*" we can run feature counts on all the HBR and UHR samples in one command line. featureCounts -a refs/ERCC92.gtf -g gene_name -o counts.txt bam/ Read More...

By using the metacharacter asterisk "*" we can run feature counts on all the HBR and UHR samples in one command line. featureCounts -a refs/ERCC92.gtf -g gene_name -o counts.txt bam/ Read More...

By using the metacharacter asterisk "*" we can run feature counts on all the HBR and UHR samples in one command line. featureCounts -a refs/ERCC92.gtf -g gene_name -o counts.txt bam/ Read More...

12/13/2017 - PLEASE NOTE:  This workshop is a  BYOC  ( Bring Your Own LapTop Computer ) class, and  requires installation of Partek Genomics Suite on your laptop ahead of the workshop. Government issued or personal computers are permitted. Read More...

RNA-Seq (RNA sequencing), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. (Wikipedia) Strictly speaking this could be any type of RNA (mRNA, rRNA, Read More...

RNASEQ looks at steady state mRNA levels which is the sum of transcription and degradation Protein levels are assumed to be driven by mRNA levels RNASEQ can measure relative abundance not absolute abundance RNASEQ is Read More...

The total number of detected transcripts expressed in a cell is dependent on the amount of mRNA in a cell. Cells naturally vary in the total amount of mRNA expressed. However, the chemistry of the Read More...

Mostly Computational intensive task requiring signigicant computer hardware. Quality Control Sample quality and consistency Is Trimming appropriate - quality/adaptors Alignment/Mapping Reference Target (Sequence and annotation) Alignment Program Alignment Parameters Mark Duplicates Post-Alignment Quality Read More...

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.

06/13/2024 - The schedule for this week consists of one presentation: Lorenz Adlung, UMC Hamburg-Eppendorf, will discuss: scMod: Marrying machine learning and deterministic modelling of longitudinal single-cell data Single-cell-based methods such as flow cytometry or single-cell Read More...

To add to the mRNA mapping problem is the existance of alternate splicing events. Attempting to identify alternate splicing in RNASEQ data is not something for the novice to attempt! .... get professional help

Remember ~90% of RNA is ribosomal RNA. Therefore enrich your total RNA sample by: polyA selection (oligodT affinity) of mRNA (eukaryote), or rRNA depletion - RiboZero is typically used (costs extra)

Getting the data Unpacking the data QA/QC with FASTQC and MULTIQC Adapter trimming Alignment Getting a Reference Genome Genome Indexing Spliced reads Non-spliced reads No Reference Genome? Working with a Transcriptome (non-model organisms) Pseudo-alignment ( Read More...

We will analyze these data by doing: 1. Alignment (hisat2) 2. Quantification (featureCounts) 3. Differential expression (DESeq) Use of a spike-in control Using a spike-in allows us to determine how well we can measure and reproduce data with Read More...

We will analyze these data by doing: 1. Alignment (hisat2) 2. Quantification (featureCounts) 3. Differential expression (DESeq) Use of a spike-in control Using a spike-in allows us to determine how well we can measure and reproduce data with Read More...

We will analyze these data by doing: 1. Alignment (hisat2) 2. Quantification (featureCounts) 3. Differential expression (DESeq) Use of a spike-in control Using a spike-in allows us to determine how well we can measure and reproduce data with Read More...

03/23/2023 - Learn how scientists are using ddPCR technology for absolute quantification of copy number variation, pathogen detection, detection of rare mutations, genome editing, and NGS data validation. We will go over ddPCR basics, and workflow Read More...

05/04/2022 - Presenter: Thomas Gonatopoulos-Pournatzis, Ph.D. Stadtman Investigator NIH Distinguished Scholar Head Functional Transcriptomics Section RNA Biology Laboratory NCI-Frederick Dr. Gonatopoulos-Pournatzis studies the regulatory pathways and functional roles of alternative splicing and other pre-mRNA processing Read More...

06/24/2020 - Join us for a webinar:  How to Analyze Single Cell RNA-Seq Data: Point, Click, Done Register:  https://www.partek.com/webinar/how-to-analyze-single-cell-rna-seq-data-point-click-done/ Single cell mRNA sequencing allows for the identification of different cell subtypes Read More...

06/02/2015 - This workshop will cover some basic concepts involved in the integration of different types of NGS data in order to obtain a better overall picture of the underlying biology. Specifically, the course will examine Read More...

04/01/2025 - Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which Read More...

06/06/2024 - The Brooks Lab developed a computational tool called FLAIR (Full-Length Alternative Isoform Analysis of RNA) to produce confident transcript isoforms from long-read RNA-seq data with the aim of alternative isoform detection and quantification. With 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...

The QIIME2 platform can be used for different types of -omics data. For this course, we will be focusing on targeted amplicon sequencing of the 16S rRNA gene. The 16S rRNA gene (~1500 bp) codes for Read More...

11/16/2023 - This class will provide a demonstration of how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Read More...

Factor in at least 3 replicates (absolute minimum), but 4 if possible (optimum minimum). Biological replicates are recommended rather than technical replicates. Always process your RNA extractions at the same time. Extractions done at different times lead Read More...

RNA-SEQ Overview What is RNASEQ ? RNA-Seq (RNA sequencing), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. (Wikipedia) Strictly speaking this could be any Read More...

Data Analysis Overview RNASEQ - Data Analysis WorkFlow Mostly Computational intensive task requiring signigicant computer hardware. Quality Control Sample quality and consistency Is Trimming appropriate - quality/adaptors Alignment/Mapping Reference Target (Sequence and annotation) Read More...

There are a number of specific solutions that have been devised to address the issues created by attempting to map mRNA to DNA genomes. Each of these has its advantages and disadvantages. Align against the Read More...

Course setup Intro to DNAnexus and the GOLD learning system Learning Objectives Unix Bootcamp Brief Review of R (for R scripts in later analyses) Introduction to RNA Sequencing Central Dogma of Molecular Biology What is Read More...

03/30/2023 - Partek Flow provides a singular web based point and click environment for analyzing and visualizing high dimensional multi-omics sequencing data, making bioinformatics easily accessible to all researchers. Partek Flow software is available to NCI Read More...

06/16/2022 - For the Advanced Training, topics covered depend upon survey results: find key hubs using over-connectivity analysis; using Microarray repository for gene comparisons against public data; building networks with MetaCore; constructing your own pathway maps; Read More...

05/11/2022 - Many new studies include RNA sequencing data. In this webinar we will go through the process of downloading and importing SRA data using the SRA toolkit, how to use an aligner to convert fastq 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...

10/19/2021 - For the Advanced Training, topics covered depend upon survey results: find key hubs using over-connectivity analysis; using Microarray repository for gene comparisons against public data; building networks with MetaCore; constructing your own pathway maps; Read More...

10/12/2021 - Speaker :  Tali Mazor, Ph.D., Scientist, Knowledge Systems Group, Dana-Farber Cancer Institute Tali Mazor, Ph.D., of the Dana-Farber Cancer Institute will discuss the functions and features of the cBioPortal for Cancer Genomics. This Read More...

04/28/2021 - Register/Join This month’s Cancer Genomics Cloud (CGC) webinar welcomes two bioinformaticians, Dr. Vesna Pajic and Nevena Vukojicic, to show attendees how CGC features can be used to perform multi-omics analysis. Dr. Pajic Read More...

11/10/2020 - This two-part lecture will provide an overview of RNA-Seq technology, its various application and shortcomings, as well as detailing the steps involved in analyzing the resulting data. Part II This second part of the Read More...

09/24/2020 - For the Advanced Training, topics covered depend upon survey results: find key hubs using over-connectivity analysis; using Microarray repository for gene comparisons against public data; building networks with MetaCore; constructing your own pathway maps; Read More...

07/27/2020 - The GDC RNA-Seq Analysis pipeline quantifies protein-coding gene expression. RNA-Seq data is aligned to the reference genome to detect splice junctions and then re-aligned to increase quality. Gene expression quantification and fusion detection are Read More...

03/29/2017 - The CCR Bioinformatics Training and Education Program (BTEP) is pleased to organize a workshop on Partek Flow for scientists at NCI-Frederick . Partek Flow software is designed specifically for the analysis needs of next generation Read More...

02/20/2013 - Ingenuity Pathways Analysis (IPA)  is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research. This training session will cover Advanced uses of Read More...

02/05/2013 - This training session will focus on Gene Expression analysis and the rich set of results possible from RNA-Seq based studies. In addition to differential gene expression, researchers also have the opportunity to discover SNPs, Read More...

10/30/2012 - Due to the weather related shutdown of the FEDERAL GOVERNMENT (NIH) this seminar has been POSTPONED ... we will attempt to reschedule at a later date. (10-30-2012)   Topics to be covered   I. Genomic and Read More...

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Long read sequencing was recently named 2022’s method of the year by Nature Methods . Long read sequencing technologies, those that generate sequence reads with lengths of 10s of kilobases or longer have several advantages over Read More...

12/03/2024 - This one and a half hour online training  will provide a demonstration of how to build a Bulk RNA-Seq data analysis pipeline using a fastq file. Partek  Flow   Read More...

10/24/2024 - Recent advances in artificial intelligence (AI) have revolutionized the use of hematoxylin and eosin (H&E)-stained tumor slides for precision oncology, enabling data-driven approaches to predict molecular characteristics and therapeutic outcomes. In Read More...

Now that we have loaded the package, we can import our data. Generally, in R programming, functions that involve data import begin with "read / Read". Seurat includes a number of read functions for Read More...

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...

03/05/2024 - This in-person workshop will show participants how to identify cell types based on statistics, visualization, and canonical markers. One Peripheral blood mononuclear cells (PBMCs) sample will be used to illustrate a basic Single Cell Read More...

10/11/2023 - Partek Flow is your 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 analyzing 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...

STAR 2-pass mode --sjdbGTFfile is the path to the file with annotated transcripts in standard GTF format, STAR extracts splice junctions from this file, improves accuracy of mapping. Using annotations is highly recommended whenever they Read More...

The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . The UHR is total RNA isolated from a diverse set of 10 cancer cell lines. The HBR Read More...

The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . The UHR is total RNA isolated from a diverse set of 10 cancer cell lines. The HBR Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . The UHR is total RNA isolated from a diverse set of 10 cancer cell lines. The HBR Read More...

This page contains content taken directly from the Biostar Handbook by Istvan Albert. Always remember to start the bioinformatics environment. conda activate bioinfo We will be analyzing differential expression of genes on Chr22 from the Read More...

This page contains content taken directly from the Biostar Handbook by Istvan Albert. Always remember to start the bioinformatics environment. conda activate bioinfo We will be analyzing differential expression of genes on Chr22 from the Read More...

High resolution single cell profiling assays have provided an unprecedented view of many biological systems and processes, but the spatial context in which this biology is occurring is often crucial. Spatial profiling, including spatial transcriptomic Read More...

02/20/2020 - Learn how to easily analyze your gene expression data yourself - using Qlucore Omics Explorer NCI/CCR:To get access to Qlucore, put a request into NCI at Your Service under Get Help https:// Read More...

09/26/2019 - Qlucore Omics Explorer is an interactive analysis and visualization tool that helps the user to find groups, structures, variable networks and discriminating variables. You can use your own data and analyze public data. Omics Read More...

09/19/2018 - TOPIC: Single Cell RNA-Seq Data Analysis in Partek Flow Partek (partek.com) Flow software provides a point-and-click interface for analysis of next -gen sequencing data. Users can customize analysis pathways for sequence alignment, differential Read More...

03/20/2017 - BTEP Workshop on RNA-Seq Data Analysis (2-day) This 2-day workshop, which includes both lecture and hands-on components, will cover the fundamentals of and best practices for RNA-Seq Data Analysis. Learn everything from experimental design Read More...

12/07/2015 - This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of RNA-Seq Data Analysis. Learn everything from experimental design to statistical analysis. This workshop will include Read More...

12/01/2015 - REGISTRATION FULL - Please signup for Session 2 December 7/8 This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of RNA-Seq Data Analysis. Learn everything from experimental Read More...

02/19/2015 - This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of RNA-Seq Data Analysis. Learn everything from experimental design to statistical analysis. This workshop will include Read More...

02/18/2014 - This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of RNA-Seq Data Analysis. Learn everything from experimental design to statistical analysis. This workshop will include Read More...

09/17/2013 - Ingenuity Pathways Analysis (IPA)  is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research.   Agenda for Day 1 (Tuesday September 17th) Large Scale ( Read More...

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...

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...

This lesson provides an introduction to R in the context of single cell RNA-Seq analysis with Seurat. Learning Objectives Learn about options for analyzing your scRNA-Seq data. Learn about resources for learning R programming. Learn Read More...

Lesson 2: Getting Started with QIIME2 Lesson Objectives Obtain sequence data and sample metadata Import data and metadata Discuss other useful QIIME2 features including view QIIME2, provenance tracking, and the QIIME2 forum. DNAnexus DNAnexus provides a Read More...

Retrieve R "helper" scripts developed for Biostars environment. curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r curl -O http://data.biostarhandbook. Read More...

Now that we have downloaded the HBR and UHR dataset and know where analysis tools are, let's start learning about RNA sequencing, by first learning about our reference genome and annotation files. Let's Read More...

Now that we have downloaded the HBR and UHR dataset and know where analysis tools are, let's start learning about RNA sequencing, by first learning about our reference genome and annotation files. Let's Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinfo environment. conda activate bioinfo Then create a new directory for files we will be working with today in Read More...

We will build a database out of all features of the 2014 Ebola genome under accession number KM233118. This data will go into a new directory named "db_2014". mkdir -p db_2014 # Get the 2014 Ebola Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

How to download data from the Sequence Read Archive (NCBI/SRA) to your account on NIH HPC Biowulf You will need: active, unlocked Biowulf account (hpc.nih.gov) active Globus account for transferring files OR Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment and create a directory for today's work. conda activate bioinfo mkdir blast cd blast What is Read More...

Whether you are measuring mRNA expression, protein expression, DNA methylation, expressed miRNAs, protein binding to DNA or RNA, etc., you will likely end up with a list of genes or gene products from which you Read More...

06/19/2017 - Harvesting the Wealth of TCGA Data The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA Read More...

02/21/2017 - This BTEP Workshop will cover the fundamentals and best practices of Exome-Seq analysis, including downstream interpretation of variants using a variety of in-house and NCI-licensed software solutions. There will be hands-on training on CCBR Read More...

09/01/2016 - This 2-day workshop, including a BYOD (Bring Your Own Data) exercise, will provide an introduction and hands-on training for Cytoscape, which is an open source software platform for visualizing  networks and integrating these networks Read More...

04/04/2016 - This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of RNA-Seq Data Analysis. Learn everything from experimental design to statistical analysis. This workshop will include Read More...

01/07/2016 - REGISTRATION IS FULL FOR THIS WORKSHOP (25 ATTENDEES; 6 WAITLIST) The Cancer Genome Atlas (TCGA) is a large-scale study that has cataloged genomic data accumulated for many different types of cancers, and includes mutations, copy number Read More...

03/18/2014 - The Cancer Genome Atlas (TCGA) is a large-scale study that has catalogued genomic data accumulated from more than 20 different types of cancer including mutations, copy number variation, mRNA and miRNA gene expression, and DNA Read More...