Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Extraction: Advanced Methods

Extraction: Advanced Methods

Metal ions can be separated from one another by complexation with organic ligands–the chelating agent– to form uncharged chelates. Here, the chelating agent must contain hydrophobic groups and behave as a weak acid, losing a proton to bind with the metal. Since most organic ligands used in this process are insoluble or undergo oxidation in the aqueous phase, the chelating agent is initially added to the organic phase and extracted into the aqueous phase. The metal-ligand complex is formed in...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

ZW4864-mediated inhibition of the β-catenin/BCL9/BCL9L complex reveals therapeutic potential in bladder cancer.

Molecular oncology·2026

Same author

Spatial and Functional Immune Profiling Identifies Impaired Vascular Repair in Human Myocardial Infarction.

Biomedicines·2026

Same author

Intertwining of the IGF system and animal welfare.

Scientific reports·2026

Same author

Exploring the Therapeutic Potential of <i>Moringa oleifera</i> Against Lung Cancer Through Network Modeling and Molecular Docking Analysis.

International journal of molecular sciences·2025

Same author

Phase-specific kidney graft failure prediction with machine learning model.

Frontiers in artificial intelligence·2025

Same author

Exploring the Prognostic Significance of IL10 Variants and Their Mechanistic Regulation in Diabetic Nephropathy.

Journal of cellular and molecular medicine·2025

Same journal

Potential role of the <i>Trpv4 c.1491+1G>A</i> mutation in pulmonary fibrosis in a gene-edited mouse model.

Frontiers in genetics·2026

Same journal

Utilization of whole exome sequencing to identify hereditary mutations in Palestinian families with hereditary cancers.

Frontiers in genetics·2026

Same journal

Research of N-acetyl-L-cysteine on CD40-CD40L pathway in pulmonary fibrosis induced by silicon dioxide.

Frontiers in genetics·2026

Same journal

Novel variants in LSS related hypotrichosis simplex 14.

Frontiers in genetics·2026

Same journal

Network-based analysis identifies shared mechanisms between ischemic stroke and myocardial infarction and therapeutic ingredients of Buyang Huanwu Decoction.

Frontiers in genetics·2026

Same journal

GWAS analysis of a depression cohort defined by an EHR-phenotyping algorithm reveals the role of immune regulations in depression risk.

Frontiers in genetics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 11, 2026

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

TCGADownloadHelper: simplifying TCGA data extraction and preprocessing.

Alexandra Anke Baumann^1,2, Olaf Wolkenhauer^1,3,4, Markus Wolfien^2,5

¹Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany.

Frontiers in Genetics

|May 19, 2025

Summary

This summary is machine-generated.

This study introduces a simplified pipeline for downloading and preprocessing The Cancer Genome Atlas (TCGA) data. The new method uses the Genomic Data Commons portal and custom scripts to make complex genomic data more accessible for cancer research.

Keywords:

Jupyter Notebook genomic data commons (GDC) portal lung cancer sample preprocessing the cancer genome atlas (TCGA)

More Related Videos

Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies

Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies

Published on: September 15, 2023

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Related Experiment Videos

Last Updated: May 11, 2026

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project

Published on: April 8, 2017

Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies

Author Spotlight: Unveiling Transmembrane Protein Family-Related Markers in Gastric Cancer and Implications for Targeted Therapies

Published on: September 15, 2023

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Area of Science:

Genomics
Bioinformatics
Cancer Research

Background:

The Cancer Genome Atlas (TCGA) offers extensive genomic data for various cancer types.
Navigating TCGA data presents challenges due to complex file naming and data type linkage.
Existing tools for TCGA data handling lack a comprehensive, integrated approach.

Purpose of the Study:

To develop a streamlined pipeline for efficient TCGA data download and preprocessing.
To simplify the process of linking disparate data types to individual case IDs.
To enhance the usability of TCGA genomic data for researchers, especially those new to the field.

Main Methods:

Utilized the Genomic Data Commons (GDC) portal's cart system for file selection and the GDC Data Transfer Tool for downloads.
Developed a pipeline integrating Python scripts in a Jupyter Notebook and a Snakemake pipeline for ID mapping and automated preprocessing.
Modified manifest files to focus on specific data subsets and replaced opaque file IDs with human-readable case IDs using the GDC Sample Sheet.

Main Results:

Successfully created a pipeline that simplifies TCGA data extraction and preprocessing.
Reduced the complexity of handling multimodal datasets for individual patients.
Significantly decreased the effort required for data preprocessing, minimizing errors.

Conclusions:

The developed pipeline enhances the efficiency and usability of TCGA data for cancer research.
Provides a clear, step-by-step methodology beneficial for researchers new to genomic data analysis.
Facilitates broader utilization of TCGA data by overcoming common data handling hurdles.