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- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/00%3A_Front_Matter
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/00%3A_Front_Matter/02%3A_InfoPageThe LibreTexts libraries are Powered by NICE CXOne and are supported by the Department of Education Open Textbook Pilot Project, the UC Davis Office of the Provost, the UC Davis Library, the Californi...The LibreTexts libraries are Powered by NICE CXOne and are supported by the Department of Education Open Textbook Pilot Project, the UC Davis Office of the Provost, the UC Davis Library, the California State University Affordable Learning Solutions Program, and Merlot.
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/04%3A_Cell_migration_assayThen, a pipette tip or another object is used to create a scratch through the monolayer, leaving an area of a consistent width open and free of cells. Relevant section of caption for published figure ...Then, a pipette tip or another object is used to create a scratch through the monolayer, leaving an area of a consistent width open and free of cells. Relevant section of caption for published figure reads: “(a) Representative bright-field images of HaCaT keratinocyte migration subjected to nontarget (siNT) or Dsg3 siRNA (siDSG3) and treated with solvent or with the p38MAPK inhibitor SB202190 (SB20).
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/09%3A_DNA_MicroarrayThe two samples are then applied at the same time to the microarray, which is a solid surface that contains many thousands of “spots” of DNA, each of a specific sequence. The five early-stage samples ...The two samples are then applied at the same time to the microarray, which is a solid surface that contains many thousands of “spots” of DNA, each of a specific sequence. The five early-stage samples on the left are in one cluster, and the other five, the late-stage samples, are in a second cluster. The early-stage cluster shows overexpressed genes in red at the top of the figure and green downregulated genes at the bottom of the figure.
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/07%3A_Cox_proportional_hazards_analysisGenerally speaking, a survival analysis is a mathematical method that models a) the length of time until an event occurs and b) whether that event occurs at all as a function of a number of variables ...Generally speaking, a survival analysis is a mathematical method that models a) the length of time until an event occurs and b) whether that event occurs at all as a function of a number of variables of interest.
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/14%3A_ImmunohistochemistryWhen a researcher is ready to perform IHC, the wax is removed from the sample and antigen retrieval is performed, often by heating. Several different methods can be used at this point, but all result ...When a researcher is ready to perform IHC, the wax is removed from the sample and antigen retrieval is performed, often by heating. Several different methods can be used at this point, but all result in a colored substance being deposited on the sample only at the locations were the protein of interest is located. A positive control that contains the protein of interest tells the researcher if the antibody works well in IHC and/or if the conditions used for staining are optimal.
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/22%3A_QIBCTotal nuclear intensity for DAPI, mean nuclear intensities for RPA1 (chromatin-bound fraction [CB]), and γ-H2AX were determined for each of >5,000 individual cells and were plotted in a scatter diagra...Total nuclear intensity for DAPI, mean nuclear intensities for RPA1 (chromatin-bound fraction [CB]), and γ-H2AX were determined for each of >5,000 individual cells and were plotted in a scatter diagram. However, simultaneous treatment with HU and an ATR inhibitor leads to more cells with very high amounts of γH2AX, a hallmark of ATM activation.
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/05%3A_CoimmunoprecipitationThe lysate is incubated with the anti-A beads as well as control beads that have been attached to an antibody that does not bind protein A. Then the beads are washed to remove any proteins that are bi...The lysate is incubated with the anti-A beads as well as control beads that have been attached to an antibody that does not bind protein A. Then the beads are washed to remove any proteins that are binding non-specifically, and finally the proteins still bound to the beads are eluted. This leaves the researcher with a solution of protein A and any other proteins that are bound to protein A.
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/08%3A_CRISPRHowever, if the researcher provides a DNA sequence containing homology arms flanking the sequence of interest, the cell can use HDR to repair the break, resulting in a change to or insertion into the ...However, if the researcher provides a DNA sequence containing homology arms flanking the sequence of interest, the cell can use HDR to repair the break, resulting in a change to or insertion into the genome. The diagram shows that the LHA corresponds to the sequence upstream of exon 1 in the TRAC locus, and the RNA begins toward the 3’ end of exon 1.
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/10%3A_Flow_CytometryThe authors want to know how the level of CAIX expression in the tumor affects the presence in the mouse lungs of a certain subset of cells that highly express the proteins CD11b and Gr1 on their surf...The authors want to know how the level of CAIX expression in the tumor affects the presence in the mouse lungs of a certain subset of cells that highly express the proteins CD11b and Gr1 on their surface. Panel B is a dot plot that quantifies the results from Panel A by showing the overall % of the CD45 + cells in each sample that are CD11b + Gr1 + . Based on this data, the authors conclude that when the primary tumor does not express CAIX, fewer CD11b + Gr1 + cells are found in the lung.
- https://bio.libretexts.org/Bookshelves/Biotechnology/Encyclopedia_of_Biological_Methods_(Mattaini)/32%3A_Western_blotthe thickness of the band, semi-quantitatively measures the amount of the protein of interest present in the sample. The labels on the top show which sample was run in each lane, whereas the samples o...the thickness of the band, semi-quantitatively measures the amount of the protein of interest present in the sample. The labels on the top show which sample was run in each lane, whereas the samples on the side show which antibody was used in that piece of the blot.
