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Single-cell RNA sequencing typos (#277)
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* Fix data analysis/analysts typo.

* Add missing word in prokaryote to eukaryote comparison.

* Fix capitalization.

* Added a missing word.
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toniecrumley committed May 22, 2024
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# Single-cell RNA sequencing

This chapter provides a short introduction to the most widely used single-cell ribonucleic acid ({term}`RNA`) sequencing assays and associated basic molecular biology concepts. Multimodal or spatial assays are not covered here, but are introduced in the respective advanced chapters. All sequencing assays have individual strengths and limitations which must be known by data analysis to be aware of possible biases in the data.
This chapter provides a short introduction to the most widely used single-cell ribonucleic acid ({term}`RNA`) sequencing assays and associated basic molecular biology concepts. Multimodal or spatial assays are not covered here, but are introduced in the respective advanced chapters. All sequencing assays have individual strengths and limitations which must be known by data analysts to be aware of possible biases in the data.

## The building block of life

Expand All @@ -20,11 +20,11 @@ Since the early definition of cell theory, researchers discovered that there exi
Eukaryotic cells contain a nucleus, where the nuclear membrane encapsulates the chromosomes; while prokaryotic cells only have a nucleoid region, but no nucleus.
The nucleus hosts the cells' genomic deoxyribonucleic acid {term}`DNA` and is the reason for the eukaryotes' name: _Nucleus_ is Latin for kernel or seed. Eukaryotes are organisms composed of a single cell (unicellular) or multiple cells (multicellular), whereas prokaryotes are single-celled organisms. Eukaryotic cells are further distinguished from prokaryotic cells by their high degree of compartmentalization, i.e. membrane-bound organelles are carrying out highly specialized functions and providing crucial support for cells.

Compared to prokaryotic cells, eukaryotic cells have on average about 10,000 the volume with a rich mix of organelles and a cytoskeleton constituted of microtubules, microfilaments, and intermediate filaments.
Compared to prokaryotic cells, eukaryotic cells have on average about 10,000 times the volume with a rich mix of organelles and a cytoskeleton constituted of microtubules, microfilaments, and intermediate filaments.
The DNA replication machinery reads the hereditary information that is stored in the DNA in the nucleus to replicate themselves and keep the life cycle going. The eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by the microtubular spindle during nuclear division.
Understanding the hereditary information hidden in DNA is key to understanding many evolutionary and disease-related processes.
_sequencing_ is the process of deciphering the order of DNA nucleotides and is primarily used to unveil the genetic information that is carried by a specific DNA segment, a complete genome, or even a complex microbiome.
DNA _sequencing_ allows researchers to identify the location and function of genes and regulatory elements in the DNA molecule and the genome, and uncovers genetic features such as open reading frames (ORFs) or CpG islands, which indicate promotor regions. Another very common application area is evolutionary analysis, where homologous DNA sequences from different organisms are compared. DNA sequencing can additionally be applied for the associations between mutations and diseases or sometimes even disease resistance, deeming one of the most useful applications.
_Sequencing_ is the process of deciphering the order of DNA nucleotides and is primarily used to unveil the genetic information that is carried by a specific DNA segment, a complete genome, or even a complex microbiome.
DNA _sequencing_ allows researchers to identify the location and function of genes and regulatory elements in the DNA molecule and the genome, and uncovers genetic features such as open reading frames (ORFs) or CpG islands, which indicate promotor regions. Another very common application area is evolutionary analysis, where homologous DNA sequences from different organisms are compared. DNA sequencing can additionally be applied for the associations between mutations and diseases or sometimes even disease resistance, deeming it one of the most useful applications.

A very popular example is sickle cell disease, a group of blood disorders, which results from an abnormality in the oxygen-carrying protein hemoglobin in red blood cells.
This leads to serious health issues including pain, anemia, swelling in the hands and feet, bacterial infections and strokes. The cause of sickle cell disease is the inheritance of two abnormal copies of the β-globin gene (HBB) that makes hemoglobin, one from each parent.
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