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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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Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
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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 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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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.
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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
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Cost-effective high-throughput single-haplotype iterative mapping and sequencing for complex genomic structures.

Daniel W Bellott1, Ting-Jan Cho1, Jennifer F Hughes1

  • 1Whitehead Institute, Cambridge, Massachusetts, USA.

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|March 23, 2018
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Summary
This summary is machine-generated.

A new protocol, single-haplotype iterative mapping and sequencing (SHIMS) 2.0, enables small labs to generate high-quality reference sequences from complex genomic regions efficiently. This cost-effective method significantly reduces time and expense compared to previous approaches.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Accurate reference sequences for complex genomic regions are crucial for genetic studies.
  • Previous clone-based methods like SHIMS 1.0 were accurate but resource-intensive, limiting accessibility.

Purpose of the Study:

  • To introduce SHIMS 2.0, a streamlined and cost-effective protocol for sequencing complex genomic regions.
  • To enable smaller laboratories to generate high-quality reference sequences.

Main Methods:

  • Developed a parallelized library preparation protocol compatible with short-read sequencing.
  • Implemented a barcoding strategy allowing multiplexing and separate assembly of individual clones.
  • Utilized bacterial artificial chromosome (BAC) or fosmid clones.

Main Results:

  • SHIMS 2.0 allows sequencing and assembly of 192 BACs/fosmids within a week.
  • The protocol significantly reduces cost and time (by two orders of magnitude) compared to SHIMS 1.0.
  • High sequencing accuracy is maintained.

Conclusions:

  • SHIMS 2.0 democratizes access to high-quality genomic reference sequences for complex regions.
  • This improved protocol empowers smaller labs with advanced sequencing capabilities.
  • Facilitates advancements in genomics research across various species.