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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

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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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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Genomic DNA in Prokaryotes00:46

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
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Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Competitive Genomic Screens of Barcoded Yeast Libraries
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Competitive Genomic Screens of Barcoded Yeast Libraries

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Barcode identification for single cell genomics.

Akshay Tambe1, Lior Pachter2

  • 1Division of Biology and Biological Engineering, California Institute of Technology, 116 Kerckhoff Laboratory, Pasadena, CA, 91125, USA.

BMC Bioinformatics
|January 19, 2019
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to correct errors in DNA barcodes used in single-cell sequencing. The approach enhances the accuracy of single-cell RNA sequencing data, especially with high error rates.

Keywords:
Barcode identificationBarcodesCircularizationK-mer countingSingle-cellde Bruijn graph

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Single-cell sequencing relies on DNA barcode tags to identify cellular origin.
  • Grouping reads by barcode is essential but challenging due to sequencing errors.
  • High rates of mismatch and deletion errors in barcodes impede accurate data analysis.

Purpose of the Study:

  • To develop a robust method for identifying and correcting errors in DNA barcodes.
  • To improve the accuracy of read assignment in single-cell sequencing experiments.
  • To enhance the recovery of single-cell transcriptome data.

Main Methods:

  • Utilizes de Bruijn graphs of circularized barcode k-mers for error identification.
  • Employs circularization to generate error-free k-mers, even with short barcodes.
  • Assigns reads to consensus fingerprints derived from k-mers.

Main Results:

  • Demonstrates improved recovery of accurate single-cell transcriptome estimates.
  • Shows enhanced performance with high per-read error rates.
  • Confirms robustness across various error types (mismatch, insertion, deletion) and cell abundances.

Conclusions:

  • The circularization approach significantly improves single-cell RNA-Seq data accuracy.
  • The method is effective even with substantial barcode errors.
  • A software package, Sircel, implementing this approach is publicly available.