Journal: Genome Biology

Article Title: Quartet DNA reference materials and datasets for comprehensively evaluating germline variant calling performance

doi: 10.1186/s13059-023-03109-2

Figure Lengend Snippet: Coverage of quartet benchmark regions on coding region and clinically related genes

Article Snippet: The pbsv discover stage was run with –tandem-repeats parameter using tandem repeat annotation file human_GRCh38_no_alt_analysis_set.trf.bed ( https://github.com/PacificBiosciences/pbsv/tree/master/annotations ).

Techniques: Variant Assay

Journal:

Article Title: An Optimized Set of Human Telomere Clones for Studying Telomere Integrity and Architecture

doi:

Figure Lengend Snippet: Diagram showing the derivation of fiberFISH distances. The fiberFISH distance in kb (D) between the test clone signal and the telomere (TTAGGGital)n signal is given by D=Z(X/Y), where Z is the known size of the test clone in kb, Y is the length of the test-clone signal in mm and X is the distance between the test-clone signal and the telomere signal in mm.

Article Snippet: Proc Natl Acad Sci USA 86:6240–6244 [ PMC free article ] [ PubMed ] Rosenberg M, Hui L, Ma JL, Nusbaum HC, Clark K, Robinson L, Dziadzio L, et al (1997) Characterization of short tandem repeats from thirty-one human telomeres.

Techniques:

Journal:

Article Title: An Optimized Set of Human Telomere Clones for Studying Telomere Integrity and Architecture

doi:

Figure Lengend Snippet: Comparison of FISH results obtained with a cosmid clone compared to a BAC clone for the 19p and 10q telomeres. All probes are labeled with digoxigenin and detected with antidigoxigenin rhodamine (red). A, Hybridization of cosmid clone, cF20643 (left), and BAC clone, RG129F16 (right), corresponding to the 19p telomere. B, Hybridization of cosmid clone, c2136c3 (left), and BAC clone, GS261B16 (right), corresponding to the 10q telomere. In both A and B, notice the difference in signal intensity between the two telomere clones; the BAC clone shows a larger signal compared to that of the cosmid clone.

Article Snippet: Proc Natl Acad Sci USA 86:6240–6244 [ PMC free article ] [ PubMed ] Rosenberg M, Hui L, Ma JL, Nusbaum HC, Clark K, Robinson L, Dziadzio L, et al (1997) Characterization of short tandem repeats from thirty-one human telomeres.

Techniques: Comparison, Labeling, Hybridization, Clone Assay

Journal:

Article Title: An Optimized Set of Human Telomere Clones for Studying Telomere Integrity and Architecture

doi:

Figure Lengend Snippet: Three-color interphase FISH ordering at the human 1p telomere. Interphase cells from a chromosome 1 monochromosomal hybrid cell line were hybridized with three probes from the telomeric region of chromosome 1p. GS-232-B23 is labeled with biotin and detected with avidin-Cy5 (purple), PAC GS-63-M14 is labeled with Spectrum Orange (red) and BAC GS-145-I23 is labeled with digoxigenin and detected with anti-digoxigenin FITC (green). The order of these clones was determined to be tel-GS145I23-GS63M14-GS232B23-cen.

Article Snippet: Proc Natl Acad Sci USA 86:6240–6244 [ PMC free article ] [ PubMed ] Rosenberg M, Hui L, Ma JL, Nusbaum HC, Clark K, Robinson L, Dziadzio L, et al (1997) Characterization of short tandem repeats from thirty-one human telomeres.

Techniques: Labeling, Avidin-Biotin Assay, Clone Assay

Journal:

Article Title: An Optimized Set of Human Telomere Clones for Studying Telomere Integrity and Architecture

doi:

Figure Lengend Snippet: FiberFISH results showing telomere-specific probe signals in green and (TTAGGG)n probe signals in red. A, Control hybridization showing 4p cosmid (B31: ∼33 kb insert) ∼80 kb from the (TTAGGG)n repeat sequence. B, control hybridization showing 16p cosmid (cGG4: ∼36 kb insert) ∼100 kb from the (TTAGGG)n repeat. C, test hybridization showing 7p PAC (164-D18) ∼130 kb from the (TTAGGG)n repeat.

Article Snippet: Proc Natl Acad Sci USA 86:6240–6244 [ PMC free article ] [ PubMed ] Rosenberg M, Hui L, Ma JL, Nusbaum HC, Clark K, Robinson L, Dziadzio L, et al (1997) Characterization of short tandem repeats from thirty-one human telomeres.

Techniques: Control, Hybridization, Sequencing