Wednesday 31 October 2018
Tuesday 30 October 2018
Monday 29 October 2018
Thursday 25 October 2018
Wednesday 24 October 2018
PRC1 and PRC2
Cited from the paper "A distal intergenic region controls pancreatic endocrine differentiation by acting as a transcriptional enhancer and as a polycomb response element"
PcG-dependent repression is mediated by two major complexes known as PRC1 and PRC2 that act in an interdependent manner. PRC2 contains Ezh2 and Ezh1 in its non-canonical form, both of which catalyzes the trimethylation of Lysine 27 on histone 3 (H3K27me3). This histone mark contributes to the recruitment of the PRC1 complex, which promotes H2A ubiquitylation, interference with transcriptional machinery, and chromatin compaction [4–8].
PcG-dependent repression is mediated by two major complexes known as PRC1 and PRC2 that act in an interdependent manner. PRC2 contains Ezh2 and Ezh1 in its non-canonical form, both of which catalyzes the trimethylation of Lysine 27 on histone 3 (H3K27me3). This histone mark contributes to the recruitment of the PRC1 complex, which promotes H2A ubiquitylation, interference with transcriptional machinery, and chromatin compaction [4–8].
Index Sorting
Cited from How to Use FlowJo’s Script Editor with Index Sorted Data
Index sorting is a method that deposits individual cells from a heterogenous mixture into wells of a plate (96, 384, and so on). Sorted cells are usually selected by some criteria (such as GFP+ and CD11b+, but CD3-) and then channeled into an empty well. Cells that do not meet the specified criteria are shunted to a waste tube.
The cytometer that sorts the cells will export a file that specifies the locations of sorted cells into their respective wells by using some sort of keyword (such as Index_Sort_Positions, Tray_X, Tray_Y, and so on).
Index sorting is a method that deposits individual cells from a heterogenous mixture into wells of a plate (96, 384, and so on). Sorted cells are usually selected by some criteria (such as GFP+ and CD11b+, but CD3-) and then channeled into an empty well. Cells that do not meet the specified criteria are shunted to a waste tube.
The cytometer that sorts the cells will export a file that specifies the locations of sorted cells into their respective wells by using some sort of keyword (such as Index_Sort_Positions, Tray_X, Tray_Y, and so on).
Tuesday 23 October 2018
Fluorescence-activated Nuclear Sorting (FANS)
Cited from Cell Type-Specific Gene Expression Profiling Using Fluorescence-Activated Nuclear Sorting
Fluorescence-activated cell sorting (FACS) is a powerful method for the analysis of cell type-specific transcriptome profiles, DNA or histone modifications, and chemical compounds.
However, many tissues are recalcitrant to cell separation and are therefore not readily accessible for FACS analysis. Here, we lay out a detailed protocol for the generation of transcriptional profiles from fluorescently labeled nuclei.
Here, the nuclei of cells of interest are labeled by transgenic expression of nuclear-localized fluorescent protein constructs and are separated from surrounding unlabeled nuclei from a crude extract by a cell sorter.
Most techniques of nuclear sorting use some kind of tissue fixation. The isolated polyadenylated RNA therefore most likely is composed of newly transcribed mRNA about to be exported from the nucleus as well as cytoplasmic RNA that was cross-linked to the nuclear envelope.
Fluorescence-activated cell sorting (FACS) is a powerful method for the analysis of cell type-specific transcriptome profiles, DNA or histone modifications, and chemical compounds.
However, many tissues are recalcitrant to cell separation and are therefore not readily accessible for FACS analysis. Here, we lay out a detailed protocol for the generation of transcriptional profiles from fluorescently labeled nuclei.
Here, the nuclei of cells of interest are labeled by transgenic expression of nuclear-localized fluorescent protein constructs and are separated from surrounding unlabeled nuclei from a crude extract by a cell sorter.
Most techniques of nuclear sorting use some kind of tissue fixation. The isolated polyadenylated RNA therefore most likely is composed of newly transcribed mRNA about to be exported from the nucleus as well as cytoplasmic RNA that was cross-linked to the nuclear envelope.
Gene and Protein Names in Humans and Mice
Cited from Guidelines for Formatting Gene and Protein Names
In general, symbols for genes are italicized (e.g., IGF1), whereas symbols for proteins are not italicized (e.g., IGF1).
Although the general rule that gene symbols are italicized and protein symbols are not italicized holds true regardless of the type of organism, there are several variations among organisms in the composition and capitalization of alphanumeric characters within the gene and protein symbols.
Humans, non-human primates, chickens, and domestic species: Gene symbols contain three to six italicized characters that are all in upper-case (e.g., AFP). Gene symbols may be a combination of letters and Arabic numerals (e.g., 1, 2, 3), but should always begin with a letter; they generally do not contain Roman numerals (e.g., I, II, III), Greek letters (e.g., α, β, γ), or punctuation. Protein symbols are identical to their corresponding gene symbols except that they are not italicized (e.g., AFP).
Mice and rats: Gene symbols are italicized, with only the first letter in upper-case (e.g., Gfap). Protein symbols are not italicized, and all letters are in upper-case (e.g., GFAP).
Fish: In contrast to the general rule, full gene names are italicized (e.g., brass). Gene symbols are also italicized, with all letters in lower-case (e.g., brs). Protein symbols are not italicized, and the first letter is upper-case (e.g., Brs).
Flies: Gene names and symbols begin with an upper-case letter if: (1) the gene is named for a protein or (2) the gene was first named for a mutant phenotype that is dominant to the wild-type phenotype (e.g., Rpp30). Gene names and symbols begin with a lower-case letter if the gene was first named for a mutant phenotype that is recessive to the wild-type phenotype (e.g., kis). Gene symbols are italicized. Symbols for proteins that were named for genes begin with an upper-case letter, but there are no accepted formatting guidelines for proteins that were not named for genes. Protein symbols are not italicized.
Worms: Gene symbols are italicized and generally composed of three to four letters, a hyphen, and an Arabic number (e.g., abu-1). Protein symbols are not italicized, and all letters are in upper-case (e.g., ABU-1).
Bacteria: Gene symbols are typically composed of three lower-case, italicized letters that serve as an abbreviation of the process or pathway in which the gene product is involved (e.g., rpo genes encode RNA polymerase). To distinguish among different alleles, the abbreviation is followed by an upper-case letter (e.g., the rpoB gene encodes the β subunit of RNA polymerase). Protein symbols are not italicized, and the first letter is upper-case (e.g., RpoB).
In general, symbols for genes are italicized (e.g., IGF1), whereas symbols for proteins are not italicized (e.g., IGF1).
Although the general rule that gene symbols are italicized and protein symbols are not italicized holds true regardless of the type of organism, there are several variations among organisms in the composition and capitalization of alphanumeric characters within the gene and protein symbols.
Humans, non-human primates, chickens, and domestic species: Gene symbols contain three to six italicized characters that are all in upper-case (e.g., AFP). Gene symbols may be a combination of letters and Arabic numerals (e.g., 1, 2, 3), but should always begin with a letter; they generally do not contain Roman numerals (e.g., I, II, III), Greek letters (e.g., α, β, γ), or punctuation. Protein symbols are identical to their corresponding gene symbols except that they are not italicized (e.g., AFP).
Mice and rats: Gene symbols are italicized, with only the first letter in upper-case (e.g., Gfap). Protein symbols are not italicized, and all letters are in upper-case (e.g., GFAP).
Fish: In contrast to the general rule, full gene names are italicized (e.g., brass). Gene symbols are also italicized, with all letters in lower-case (e.g., brs). Protein symbols are not italicized, and the first letter is upper-case (e.g., Brs).
Flies: Gene names and symbols begin with an upper-case letter if: (1) the gene is named for a protein or (2) the gene was first named for a mutant phenotype that is dominant to the wild-type phenotype (e.g., Rpp30). Gene names and symbols begin with a lower-case letter if the gene was first named for a mutant phenotype that is recessive to the wild-type phenotype (e.g., kis). Gene symbols are italicized. Symbols for proteins that were named for genes begin with an upper-case letter, but there are no accepted formatting guidelines for proteins that were not named for genes. Protein symbols are not italicized.
Worms: Gene symbols are italicized and generally composed of three to four letters, a hyphen, and an Arabic number (e.g., abu-1). Protein symbols are not italicized, and all letters are in upper-case (e.g., ABU-1).
Bacteria: Gene symbols are typically composed of three lower-case, italicized letters that serve as an abbreviation of the process or pathway in which the gene product is involved (e.g., rpo genes encode RNA polymerase). To distinguish among different alleles, the abbreviation is followed by an upper-case letter (e.g., the rpoB gene encodes the β subunit of RNA polymerase). Protein symbols are not italicized, and the first letter is upper-case (e.g., RpoB).
Friday 12 October 2018
Pre or Pro Protein/Domain
Cited from Re: What is the function of a protein's prodomain? Why are they called that?
"pre-" was adopted as the prefix that means "before N-terminal cleavage during a secretion event".
Many proteins require additional proteolytic processing to become fully functional. This also involves cleavage of a peptide from the N-terminus, but is not part of the secretory process. So the prefix "pro-" was adopted to describe the protein prior to this processing event.
"preproprotein" (the N-terminal is cleaved during secretion, then cleaved again to make the protein active).
Caspase is a good example. It is synthesised as an inactive proprotein. In this case the term "prodomain" is used, because the N-terminal region is folded into a discrete structural unit with a specific function (the definition of a domain). Usually the prodomain mediates interaction with other proteins in a complex. Proteolytic cleavage then removes the prodomain, activates the caspase and triggers a cascade in which caspases activate other caspases, leading eventually to the cleavage of key target proteins (caspase substrates) and cell death. Other proteins besides caspases also contain prodomains that mediate a particular process for the protein.
"pre-" was adopted as the prefix that means "before N-terminal cleavage during a secretion event".
Many proteins require additional proteolytic processing to become fully functional. This also involves cleavage of a peptide from the N-terminus, but is not part of the secretory process. So the prefix "pro-" was adopted to describe the protein prior to this processing event.
"preproprotein" (the N-terminal is cleaved during secretion, then cleaved again to make the protein active).
Caspase is a good example. It is synthesised as an inactive proprotein. In this case the term "prodomain" is used, because the N-terminal region is folded into a discrete structural unit with a specific function (the definition of a domain). Usually the prodomain mediates interaction with other proteins in a complex. Proteolytic cleavage then removes the prodomain, activates the caspase and triggers a cascade in which caspases activate other caspases, leading eventually to the cleavage of key target proteins (caspase substrates) and cell death. Other proteins besides caspases also contain prodomains that mediate a particular process for the protein.
Tuesday 2 October 2018
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