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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genomic Imprinting and Inheritance02:30

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Parallel Resonance01:23

Parallel Resonance

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The parallel RLC circuit is an arrangement where the resistor (R), inductor (L), and capacitor (C) are all connected to the same nodes and, as a result, share the same voltage across them. The parallel RLC circuit is analyzed in terms of admittance (Y), which reflects the ease with which current can flow. The admittance is given by:
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Parallel Processing01:20

Parallel Processing

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The brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
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Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing
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BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell

Fatma Uzbas1, Florian Opperer1, Can Sönmezer1,2

  • 1Institute of Stem Cell Research, Helmholtz Center Munich, 85764, Neuherberg, Germany.

Genome Biology
|August 8, 2019
PubMed
Summary
This summary is machine-generated.

We developed Barcode Assembly foR Targeted Sequencing (BART-Seq), a cost-effective method for parallel targeted sequencing. BART-Seq precisely identifies stem cell differentiation mechanisms and BRCA mutations in breast cancer patients.

Keywords:
BarcodingHigh-throughput screeningHuman pluripotent stem cellsMultiplex PCRSingle-cell RNA sequencingTargeted transcriptomics

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Transcriptome Analysis of Single Cells
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Area of Science:

  • Molecular Biology
  • Genomics
  • Stem Cell Biology

Background:

  • High-throughput sequencing is crucial for understanding complex biological systems.
  • Current targeted sequencing methods can be expensive and lack scalability for large sample numbers.
  • Analyzing single-cell transcriptomes and genomic regions requires sensitive and quantitative techniques.

Purpose of the Study:

  • To introduce a novel, inexpensive, and highly sensitive technique for parallel targeted sequencing.
  • To demonstrate the utility of this technique in analyzing stem cell differentiation and genetic screening.
  • To provide a scalable solution for analyzing thousands of bulk or single-cell samples.

Main Methods:

  • Development of a multiplexing strategy using DNA barcodes and invariant primer sets.
  • Implementation of a novel workflow named Barcode Assembly foR Targeted Sequencing (BART-Seq).
  • In silico optimization of primer sets and barcode matrices for extensive multiplexing.

Main Results:

  • BART-Seq successfully analyzed developmental states of thousands of single human pluripotent stem cells.
  • The technique identified mechanisms of differentiation induction upon Wnt/β-catenin pathway activation.
  • BART-Seq precisely identified BRCA mutations in genetic screening of breast cancer patients.
  • The method demonstrated superior dynamic range and scalability compared to global transcriptomics.

Conclusions:

  • BART-Seq is a versatile and powerful tool for targeted sequencing across diverse research applications.
  • This technique enables high-precision genetic screening and detailed analysis of cellular states.
  • BART-Seq offers a cost-effective and scalable solution for large-scale biological studies.