bac dna miniprep kit  (Zymo Research)


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    Name:
    ZR BAC DNA Miniprep Kit
    Description:
    The ZR BAC DNA Miniprep Kit efficiently isolates BAC plasmid DNA or other large plasmids e g PAC from E Coli using a procedure that is simple rapid user friendly and reliable It features a modified alkaline lysis protocol with color coded reagents that allow easy visualization of complete bacterial cell lysis and neutralization The innovative Zymo Spin IC XL columns are optimized for high yield endotoxin free plasmid DNA recovery BAC DNA purified using the ZR BAC DNA Miniprep Kit is ideal for sequencing PCR endonuclease digestion etc
    Catalog Number:
    d4048
    Price:
    None
    Applications:
    DNA Purification
    Size:
    25 units
    Category:
    Life Science Reagents and Media
    Buy from Supplier


    Structured Review

    Zymo Research bac dna miniprep kit
    ZR BAC DNA Miniprep Kit
    The ZR BAC DNA Miniprep Kit efficiently isolates BAC plasmid DNA or other large plasmids e g PAC from E Coli using a procedure that is simple rapid user friendly and reliable It features a modified alkaline lysis protocol with color coded reagents that allow easy visualization of complete bacterial cell lysis and neutralization The innovative Zymo Spin IC XL columns are optimized for high yield endotoxin free plasmid DNA recovery BAC DNA purified using the ZR BAC DNA Miniprep Kit is ideal for sequencing PCR endonuclease digestion etc
    https://www.bioz.com/result/bac dna miniprep kit/product/Zymo Research
    Average 97 stars, based on 18 article reviews
    Price from $9.99 to $1999.99
    bac dna miniprep kit - by Bioz Stars, 2020-10
    97/100 stars

    Images

    1) Product Images from "Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues"

    Article Title: Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues

    Journal: Current Genomics

    doi: 10.2174/138920212802510510

    Screen dump of the UCSC Genome Browser (GoldenPath) display showing the BAC ends mapped to the targeted region of chromosome 2: 92,269,115 bp to 92,335,426 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-100H17 (arrow) in a region comprised entirely of satellite DNA, while BAC RP11-469P16 (arrowhead) is predicted to contain a cluster of long interspersed repeated DNA sequences (LINEs)(circled).
    Figure Legend Snippet: Screen dump of the UCSC Genome Browser (GoldenPath) display showing the BAC ends mapped to the targeted region of chromosome 2: 92,269,115 bp to 92,335,426 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-100H17 (arrow) in a region comprised entirely of satellite DNA, while BAC RP11-469P16 (arrowhead) is predicted to contain a cluster of long interspersed repeated DNA sequences (LINEs)(circled).

    Techniques Used: BAC Assay, Sequencing

    Screen dump of the UCSC Genome Browser display showing the BAC ends mapped to the region chromosome 4: 49,093,534 bp to 49,183,369 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-360M1 (high-lighted) in a region comprised almost entirely of satellite DNA and completely free of interspersed repeated DNA sequences such as short interspersed repeats (SINEs) or LINEs.
    Figure Legend Snippet: Screen dump of the UCSC Genome Browser display showing the BAC ends mapped to the region chromosome 4: 49,093,534 bp to 49,183,369 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-360M1 (high-lighted) in a region comprised almost entirely of satellite DNA and completely free of interspersed repeated DNA sequences such as short interspersed repeats (SINEs) or LINEs.

    Techniques Used: BAC Assay, Sequencing

    In situ hybridization analysis of DNA probes prepared from BAC clones. The BAC clones RP11-294C12 and RP11-242E13 hybridized to metaphase spreads prepared from short term cultures of human lymphocytes showed specific hybridization to the target regions on the X (arrowhead) and Y (arrow) chromosome, respectively. A) Schematic representation of the FISH target regions on the X and Y chromosome. B) Hybridization of both probes to metaphase chromosomes. C) Hybridization signals in diploid interphase cell nuclei. (Bars = 10 µm).
    Figure Legend Snippet: In situ hybridization analysis of DNA probes prepared from BAC clones. The BAC clones RP11-294C12 and RP11-242E13 hybridized to metaphase spreads prepared from short term cultures of human lymphocytes showed specific hybridization to the target regions on the X (arrowhead) and Y (arrow) chromosome, respectively. A) Schematic representation of the FISH target regions on the X and Y chromosome. B) Hybridization of both probes to metaphase chromosomes. C) Hybridization signals in diploid interphase cell nuclei. (Bars = 10 µm).

    Techniques Used: In Situ Hybridization, BAC Assay, Clone Assay, Hybridization, Fluorescence In Situ Hybridization

    FISH performance of BAC-derived DNA probes targeting the centromeric heterochromatin of chromosome 2. A-B) A DNA probe prepared from BAC clone RP11-469P16 shows multiple signals in normal interphase cell nuclei ( A ) or on metaphase spreads ( B ). Arrows in B ) point at the target region on chromosome 2. C ) A DNA probe prepared from BAC clone RP11-100H17 binds exclusively to the chromosome 2-specific target region (arrows). (Bars = 10 µm).
    Figure Legend Snippet: FISH performance of BAC-derived DNA probes targeting the centromeric heterochromatin of chromosome 2. A-B) A DNA probe prepared from BAC clone RP11-469P16 shows multiple signals in normal interphase cell nuclei ( A ) or on metaphase spreads ( B ). Arrows in B ) point at the target region on chromosome 2. C ) A DNA probe prepared from BAC clone RP11-100H17 binds exclusively to the chromosome 2-specific target region (arrows). (Bars = 10 µm).

    Techniques Used: Fluorescence In Situ Hybridization, BAC Assay, Derivative Assay

    2) Product Images from "Bioinformatics Tools Allow Targeted Selection of Chromosome Enumeration Probes and Aneuploidy Detection"

    Article Title: Bioinformatics Tools Allow Targeted Selection of Chromosome Enumeration Probes and Aneuploidy Detection

    Journal: Journal of Histochemistry and Cytochemistry

    doi: 10.1369/0022155412470955

    Culture genotype of chromosome 10 in a PTC cell line. Chromosome numbers and signal counts of the chromosome 10-specific DNA probe prepared from BAC RP11-168p20 hybridized to cell line S48TK18A6 (scored by three independent scorers).
    Figure Legend Snippet: Culture genotype of chromosome 10 in a PTC cell line. Chromosome numbers and signal counts of the chromosome 10-specific DNA probe prepared from BAC RP11-168p20 hybridized to cell line S48TK18A6 (scored by three independent scorers).

    Techniques Used: BAC Assay

    In situ hybridization results for selected DNA probes. Red shaded areas on the idiograms in (A–B) and (F–G) indicate the hybridization target sites. (A) In situ hybridization using fluorescent probes for the highly repeated satellite III DNA segment (flanked by the PCR primers WYR2 and WYR4) shows bright signals on the long arm of the Y chromosome. (B) Combining biotinylated in situ hybridization probes for the Y chromosome-specific DNA segment (large signal) with probes for X chromosome-specific DNA flanked by the PCR primers WXR1 and WXR2 (small signal) allows chromosome identification based on the size of the signal. (C) A digoxigenin-labeled DNA probe prepared from BAC RP11-348g24 resulted in specific signals on the X chromosome in the presence of a significant amount of cross-hybridization to other chromosomes in metaphase spreads. High level of cross-hybridization was also evident in interphase nuclei. (D) In contrast to the result shown in (C), a probe prepared from BAC RP11-294c12 bound almost exclusively to the centromeric heterochromatin of the human X chromosome. (E) Combining differentially labeled DNA probes in a single hybridization experiment, the Y chromosomal target appears in green, whereas the X chromosomal centromeric repeat DNA is shown in red. (F) In situ hybridization of an autosome-targeting DNA probe prepared from BAC clone RP11-96f8 showed multiple signals and a high level of cross-hybridization in the interphase cell nuclei. (G) The biotinylated probe prepared from BAC RP11-168p20 exhibited strong signals on both homologues of chromosome 10. (H) A combination of three differently labeled probes was hybridized simultaneously. Chromosome 10 signals are shown in red; X chromosomal and Y chromosomal signals are shown in green and blue, respectively. (I–K) The same probe as in (G) (BAC RP11-168p20) was hybridized to the cell line S48TK18A6. Multiple signals indicate chromosomal abnormalities. (I) shows DAPI picture, (J) shows green avidin-FITC signal, and (K) shows the superposition of both. (L–N) A chromosome X probe (BAC clone RP11-294c12) labeled with biotin/avidin-FITC, a Cy-5 labeled chromosome Y probe (RP11-242e13), and a chromosome 10-specific probe prepared from BAC RP11-168p20 (labeled with Spectral Orange-dUTP) were hybridized onto a deparaffinized 12-week placenta tissue section. (L) The chromosome 10 probe (red signals) and bound chromosome X probe (green signals) in this female placental tissue section. (M–N) In our triple probe FISH experiment, the chromosome 10 probe is represented by orange signals, the chromosome X probe by green signals, and the chromosome Y probe by red signals in the male cell nuclei. (Size marker bars indicate 10 µm.)
    Figure Legend Snippet: In situ hybridization results for selected DNA probes. Red shaded areas on the idiograms in (A–B) and (F–G) indicate the hybridization target sites. (A) In situ hybridization using fluorescent probes for the highly repeated satellite III DNA segment (flanked by the PCR primers WYR2 and WYR4) shows bright signals on the long arm of the Y chromosome. (B) Combining biotinylated in situ hybridization probes for the Y chromosome-specific DNA segment (large signal) with probes for X chromosome-specific DNA flanked by the PCR primers WXR1 and WXR2 (small signal) allows chromosome identification based on the size of the signal. (C) A digoxigenin-labeled DNA probe prepared from BAC RP11-348g24 resulted in specific signals on the X chromosome in the presence of a significant amount of cross-hybridization to other chromosomes in metaphase spreads. High level of cross-hybridization was also evident in interphase nuclei. (D) In contrast to the result shown in (C), a probe prepared from BAC RP11-294c12 bound almost exclusively to the centromeric heterochromatin of the human X chromosome. (E) Combining differentially labeled DNA probes in a single hybridization experiment, the Y chromosomal target appears in green, whereas the X chromosomal centromeric repeat DNA is shown in red. (F) In situ hybridization of an autosome-targeting DNA probe prepared from BAC clone RP11-96f8 showed multiple signals and a high level of cross-hybridization in the interphase cell nuclei. (G) The biotinylated probe prepared from BAC RP11-168p20 exhibited strong signals on both homologues of chromosome 10. (H) A combination of three differently labeled probes was hybridized simultaneously. Chromosome 10 signals are shown in red; X chromosomal and Y chromosomal signals are shown in green and blue, respectively. (I–K) The same probe as in (G) (BAC RP11-168p20) was hybridized to the cell line S48TK18A6. Multiple signals indicate chromosomal abnormalities. (I) shows DAPI picture, (J) shows green avidin-FITC signal, and (K) shows the superposition of both. (L–N) A chromosome X probe (BAC clone RP11-294c12) labeled with biotin/avidin-FITC, a Cy-5 labeled chromosome Y probe (RP11-242e13), and a chromosome 10-specific probe prepared from BAC RP11-168p20 (labeled with Spectral Orange-dUTP) were hybridized onto a deparaffinized 12-week placenta tissue section. (L) The chromosome 10 probe (red signals) and bound chromosome X probe (green signals) in this female placental tissue section. (M–N) In our triple probe FISH experiment, the chromosome 10 probe is represented by orange signals, the chromosome X probe by green signals, and the chromosome Y probe by red signals in the male cell nuclei. (Size marker bars indicate 10 µm.)

    Techniques Used: In Situ Hybridization, Hybridization, Polymerase Chain Reaction, Labeling, BAC Assay, Avidin-Biotin Assay, Fluorescence In Situ Hybridization, Marker

    Related Articles

    Amplification:

    Article Title: Production of gellan gum, an exopolysaccharide, from biodiesel-derived waste glycerol by Sphingomonas spp.
    Article Snippet: .. From the promising glycerol degrading bacterial isolates, genomic DNA was extracted and purified using ZR Bacterial DNA MiniPrep Kit (Zymo Research, USA).The extracted DNA was amplified using the 16S rRNA gene based primers (27F-5ʹ-AGAGTTTGATCCTGGCTCAG-3ʹ and 1492R-5ʹ-ACGGCTACCTTGTTACGACTT-3ʹ) in a thermocycler (Bio-Rad, USA). .. Partial sequencing of the amplicons was performed at Inqaba Biotec, South Africa, followed by BLAST analysis.

    BAC Assay:

    Article Title: Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues
    Article Snippet: .. In typical experiments, the BAC DNAs are extracted from overnight cultures following an alkaline lysis protocol [ ] or using a BAC DNA miniprep kit (Zymo Research; Irvine, CA). .. The DNAs are confirmed on a 1% agarose gel and quantitated spectrophotometrically.

    Article Title: Molecular and Biochemical Characterization of Salt-Tolerant Trehalose-6-Phosphate Hydrolases Identified by Screening and Sequencing Salt-Tolerant Clones From the Metagenomic Library of the Gastrointestinal Tract
    Article Snippet: .. ZR BAC DNA Miniprep Kit (Zymo Research) was used to extract fosmid based on the manufacturer’s directions. .. High-Throughput Sequencing and Bioinformatics Analysis The fosmid DNA of salt-tolerant clones was sequenced with the Illumina Solexa Genome Analyzer platform.

    Article Title: The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II
    Article Snippet: .. To obtain bacmids for insect cell expression, plasmids were transformed into chemically competent DH10Bac cells and purified using ZR BAC DNA miniprep kit (Zymo Research). .. Baculoviruses encoding CSB variants, CSA/DDB1, or CUL4A/RBX1 were amplified in three stages (P1, P2, and P3) in Sf9 cells (Expression Systems).

    Article Title: Circadian timing-dependent myoblast differentiation and muscle regeneration
    Article Snippet: .. To make a BAC control library, a mouse 110 kb BAC clone encoding Nctc1 and Igf2 were purchased from Thermo Fisher Scientific (RPCI23.C) and the DNA was prepared with a ZR BAC DNA Miniprep kit (Zymo Research (D4048) as control. .. Ten micrograms of DNA was digested with BamHI for 16 hr, followed by phenol-chloroform extraction and ethanol precipitation twice.

    Article Title: Bioinformatics Tools Allow Targeted Selection of Chromosome Enumeration Probes and Aneuploidy Detection
    Article Snippet: .. DNA Probe Preparation The BAC DNAs were extracted from overnight cultures following an alkaline lysis protocol ( ) or using a ZR BAC DNA Miniprep Kit (Zymo Research; Irvine, CA). .. The isolation of high molecular weight BAC DNAs was confirmed on 1% agarose gels and quantitated by Hoechst fluorometry using a Hoefer TK 100 instrument (Hoefer; South San Francisco, CA).

    Purification:

    Article Title: Production of gellan gum, an exopolysaccharide, from biodiesel-derived waste glycerol by Sphingomonas spp.
    Article Snippet: .. From the promising glycerol degrading bacterial isolates, genomic DNA was extracted and purified using ZR Bacterial DNA MiniPrep Kit (Zymo Research, USA).The extracted DNA was amplified using the 16S rRNA gene based primers (27F-5ʹ-AGAGTTTGATCCTGGCTCAG-3ʹ and 1492R-5ʹ-ACGGCTACCTTGTTACGACTT-3ʹ) in a thermocycler (Bio-Rad, USA). .. Partial sequencing of the amplicons was performed at Inqaba Biotec, South Africa, followed by BLAST analysis.

    Article Title: The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II
    Article Snippet: .. To obtain bacmids for insect cell expression, plasmids were transformed into chemically competent DH10Bac cells and purified using ZR BAC DNA miniprep kit (Zymo Research). .. Baculoviruses encoding CSB variants, CSA/DDB1, or CUL4A/RBX1 were amplified in three stages (P1, P2, and P3) in Sf9 cells (Expression Systems).

    Incubation:

    Article Title: Comparative Genome Analysis of Bacillus sporothermodurans with Its Closest Phylogenetic Neighbor, Bacillus oleronius, and Bacillus cereus and Bacillus subtilis Groups
    Article Snippet: .. Growth of B. sporothermodurans isolates was performed on brain heart infusion agar (Hampshire, Oxoid, UK) and incubated at 37 °C for 48 h. Bacillus oleronius was grown on nutrient agar (Oxoid, UK) at 37 °C for 24 h. Genomic DNA was extracted using the ZR Bacterial DNA Miniprep kit (Zymo Research, Irvine, CA, USA). .. The DNA was quantified using the Qubit instrument and the dsDNA BR Assay kit (Life Technologies, Grand Island, NY, USA).

    Alkaline Lysis:

    Article Title: Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues
    Article Snippet: .. In typical experiments, the BAC DNAs are extracted from overnight cultures following an alkaline lysis protocol [ ] or using a BAC DNA miniprep kit (Zymo Research; Irvine, CA). .. The DNAs are confirmed on a 1% agarose gel and quantitated spectrophotometrically.

    Article Title: Bioinformatics Tools Allow Targeted Selection of Chromosome Enumeration Probes and Aneuploidy Detection
    Article Snippet: .. DNA Probe Preparation The BAC DNAs were extracted from overnight cultures following an alkaline lysis protocol ( ) or using a ZR BAC DNA Miniprep Kit (Zymo Research; Irvine, CA). .. The isolation of high molecular weight BAC DNAs was confirmed on 1% agarose gels and quantitated by Hoechst fluorometry using a Hoefer TK 100 instrument (Hoefer; South San Francisco, CA).

    Expressing:

    Article Title: The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II
    Article Snippet: .. To obtain bacmids for insect cell expression, plasmids were transformed into chemically competent DH10Bac cells and purified using ZR BAC DNA miniprep kit (Zymo Research). .. Baculoviruses encoding CSB variants, CSA/DDB1, or CUL4A/RBX1 were amplified in three stages (P1, P2, and P3) in Sf9 cells (Expression Systems).

    Transformation Assay:

    Article Title: The cooperative action of CSB, CSA, and UVSSA target TFIIH to DNA damage-stalled RNA polymerase II
    Article Snippet: .. To obtain bacmids for insect cell expression, plasmids were transformed into chemically competent DH10Bac cells and purified using ZR BAC DNA miniprep kit (Zymo Research). .. Baculoviruses encoding CSB variants, CSA/DDB1, or CUL4A/RBX1 were amplified in three stages (P1, P2, and P3) in Sf9 cells (Expression Systems).

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  • 97
    Zymo Research bac dna miniprep kit
    Screen dump of the UCSC Genome Browser (GoldenPath) display showing the <t>BAC</t> ends mapped to the targeted region of chromosome 2: 92,269,115 bp to 92,335,426 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-100H17 (arrow) in a region comprised entirely of satellite <t>DNA,</t> while BAC RP11-469P16 (arrowhead) is predicted to contain a cluster of long interspersed repeated DNA sequences (LINEs)(circled).
    Bac Dna Miniprep Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 97/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bac dna miniprep kit/product/Zymo Research
    Average 97 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    bac dna miniprep kit - by Bioz Stars, 2020-10
    97/100 stars
      Buy from Supplier

    Image Search Results


    Screen dump of the UCSC Genome Browser (GoldenPath) display showing the BAC ends mapped to the targeted region of chromosome 2: 92,269,115 bp to 92,335,426 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-100H17 (arrow) in a region comprised entirely of satellite DNA, while BAC RP11-469P16 (arrowhead) is predicted to contain a cluster of long interspersed repeated DNA sequences (LINEs)(circled).

    Journal: Current Genomics

    Article Title: Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues

    doi: 10.2174/138920212802510510

    Figure Lengend Snippet: Screen dump of the UCSC Genome Browser (GoldenPath) display showing the BAC ends mapped to the targeted region of chromosome 2: 92,269,115 bp to 92,335,426 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-100H17 (arrow) in a region comprised entirely of satellite DNA, while BAC RP11-469P16 (arrowhead) is predicted to contain a cluster of long interspersed repeated DNA sequences (LINEs)(circled).

    Article Snippet: In typical experiments, the BAC DNAs are extracted from overnight cultures following an alkaline lysis protocol [ ] or using a BAC DNA miniprep kit (Zymo Research; Irvine, CA).

    Techniques: BAC Assay, Sequencing

    Screen dump of the UCSC Genome Browser display showing the BAC ends mapped to the region chromosome 4: 49,093,534 bp to 49,183,369 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-360M1 (high-lighted) in a region comprised almost entirely of satellite DNA and completely free of interspersed repeated DNA sequences such as short interspersed repeats (SINEs) or LINEs.

    Journal: Current Genomics

    Article Title: Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues

    doi: 10.2174/138920212802510510

    Figure Lengend Snippet: Screen dump of the UCSC Genome Browser display showing the BAC ends mapped to the region chromosome 4: 49,093,534 bp to 49,183,369 bp. The alignment BAC clone end sequences with the draft sequence of the human genome places BAC RP11-360M1 (high-lighted) in a region comprised almost entirely of satellite DNA and completely free of interspersed repeated DNA sequences such as short interspersed repeats (SINEs) or LINEs.

    Article Snippet: In typical experiments, the BAC DNAs are extracted from overnight cultures following an alkaline lysis protocol [ ] or using a BAC DNA miniprep kit (Zymo Research; Irvine, CA).

    Techniques: BAC Assay, Sequencing

    In situ hybridization analysis of DNA probes prepared from BAC clones. The BAC clones RP11-294C12 and RP11-242E13 hybridized to metaphase spreads prepared from short term cultures of human lymphocytes showed specific hybridization to the target regions on the X (arrowhead) and Y (arrow) chromosome, respectively. A) Schematic representation of the FISH target regions on the X and Y chromosome. B) Hybridization of both probes to metaphase chromosomes. C) Hybridization signals in diploid interphase cell nuclei. (Bars = 10 µm).

    Journal: Current Genomics

    Article Title: Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues

    doi: 10.2174/138920212802510510

    Figure Lengend Snippet: In situ hybridization analysis of DNA probes prepared from BAC clones. The BAC clones RP11-294C12 and RP11-242E13 hybridized to metaphase spreads prepared from short term cultures of human lymphocytes showed specific hybridization to the target regions on the X (arrowhead) and Y (arrow) chromosome, respectively. A) Schematic representation of the FISH target regions on the X and Y chromosome. B) Hybridization of both probes to metaphase chromosomes. C) Hybridization signals in diploid interphase cell nuclei. (Bars = 10 µm).

    Article Snippet: In typical experiments, the BAC DNAs are extracted from overnight cultures following an alkaline lysis protocol [ ] or using a BAC DNA miniprep kit (Zymo Research; Irvine, CA).

    Techniques: In Situ Hybridization, BAC Assay, Clone Assay, Hybridization, Fluorescence In Situ Hybridization

    FISH performance of BAC-derived DNA probes targeting the centromeric heterochromatin of chromosome 2. A-B) A DNA probe prepared from BAC clone RP11-469P16 shows multiple signals in normal interphase cell nuclei ( A ) or on metaphase spreads ( B ). Arrows in B ) point at the target region on chromosome 2. C ) A DNA probe prepared from BAC clone RP11-100H17 binds exclusively to the chromosome 2-specific target region (arrows). (Bars = 10 µm).

    Journal: Current Genomics

    Article Title: Bioinformatic Tools Identify Chromosome-Specific DNA Probes and Facilitate Risk Assessment by Detecting Aneusomies in Extra-embryonic Tissues

    doi: 10.2174/138920212802510510

    Figure Lengend Snippet: FISH performance of BAC-derived DNA probes targeting the centromeric heterochromatin of chromosome 2. A-B) A DNA probe prepared from BAC clone RP11-469P16 shows multiple signals in normal interphase cell nuclei ( A ) or on metaphase spreads ( B ). Arrows in B ) point at the target region on chromosome 2. C ) A DNA probe prepared from BAC clone RP11-100H17 binds exclusively to the chromosome 2-specific target region (arrows). (Bars = 10 µm).

    Article Snippet: In typical experiments, the BAC DNAs are extracted from overnight cultures following an alkaline lysis protocol [ ] or using a BAC DNA miniprep kit (Zymo Research; Irvine, CA).

    Techniques: Fluorescence In Situ Hybridization, BAC Assay, Derivative Assay

    Culture genotype of chromosome 10 in a PTC cell line. Chromosome numbers and signal counts of the chromosome 10-specific DNA probe prepared from BAC RP11-168p20 hybridized to cell line S48TK18A6 (scored by three independent scorers).

    Journal: Journal of Histochemistry and Cytochemistry

    Article Title: Bioinformatics Tools Allow Targeted Selection of Chromosome Enumeration Probes and Aneuploidy Detection

    doi: 10.1369/0022155412470955

    Figure Lengend Snippet: Culture genotype of chromosome 10 in a PTC cell line. Chromosome numbers and signal counts of the chromosome 10-specific DNA probe prepared from BAC RP11-168p20 hybridized to cell line S48TK18A6 (scored by three independent scorers).

    Article Snippet: DNA Probe Preparation The BAC DNAs were extracted from overnight cultures following an alkaline lysis protocol ( ) or using a ZR BAC DNA Miniprep Kit (Zymo Research; Irvine, CA).

    Techniques: BAC Assay

    In situ hybridization results for selected DNA probes. Red shaded areas on the idiograms in (A–B) and (F–G) indicate the hybridization target sites. (A) In situ hybridization using fluorescent probes for the highly repeated satellite III DNA segment (flanked by the PCR primers WYR2 and WYR4) shows bright signals on the long arm of the Y chromosome. (B) Combining biotinylated in situ hybridization probes for the Y chromosome-specific DNA segment (large signal) with probes for X chromosome-specific DNA flanked by the PCR primers WXR1 and WXR2 (small signal) allows chromosome identification based on the size of the signal. (C) A digoxigenin-labeled DNA probe prepared from BAC RP11-348g24 resulted in specific signals on the X chromosome in the presence of a significant amount of cross-hybridization to other chromosomes in metaphase spreads. High level of cross-hybridization was also evident in interphase nuclei. (D) In contrast to the result shown in (C), a probe prepared from BAC RP11-294c12 bound almost exclusively to the centromeric heterochromatin of the human X chromosome. (E) Combining differentially labeled DNA probes in a single hybridization experiment, the Y chromosomal target appears in green, whereas the X chromosomal centromeric repeat DNA is shown in red. (F) In situ hybridization of an autosome-targeting DNA probe prepared from BAC clone RP11-96f8 showed multiple signals and a high level of cross-hybridization in the interphase cell nuclei. (G) The biotinylated probe prepared from BAC RP11-168p20 exhibited strong signals on both homologues of chromosome 10. (H) A combination of three differently labeled probes was hybridized simultaneously. Chromosome 10 signals are shown in red; X chromosomal and Y chromosomal signals are shown in green and blue, respectively. (I–K) The same probe as in (G) (BAC RP11-168p20) was hybridized to the cell line S48TK18A6. Multiple signals indicate chromosomal abnormalities. (I) shows DAPI picture, (J) shows green avidin-FITC signal, and (K) shows the superposition of both. (L–N) A chromosome X probe (BAC clone RP11-294c12) labeled with biotin/avidin-FITC, a Cy-5 labeled chromosome Y probe (RP11-242e13), and a chromosome 10-specific probe prepared from BAC RP11-168p20 (labeled with Spectral Orange-dUTP) were hybridized onto a deparaffinized 12-week placenta tissue section. (L) The chromosome 10 probe (red signals) and bound chromosome X probe (green signals) in this female placental tissue section. (M–N) In our triple probe FISH experiment, the chromosome 10 probe is represented by orange signals, the chromosome X probe by green signals, and the chromosome Y probe by red signals in the male cell nuclei. (Size marker bars indicate 10 µm.)

    Journal: Journal of Histochemistry and Cytochemistry

    Article Title: Bioinformatics Tools Allow Targeted Selection of Chromosome Enumeration Probes and Aneuploidy Detection

    doi: 10.1369/0022155412470955

    Figure Lengend Snippet: In situ hybridization results for selected DNA probes. Red shaded areas on the idiograms in (A–B) and (F–G) indicate the hybridization target sites. (A) In situ hybridization using fluorescent probes for the highly repeated satellite III DNA segment (flanked by the PCR primers WYR2 and WYR4) shows bright signals on the long arm of the Y chromosome. (B) Combining biotinylated in situ hybridization probes for the Y chromosome-specific DNA segment (large signal) with probes for X chromosome-specific DNA flanked by the PCR primers WXR1 and WXR2 (small signal) allows chromosome identification based on the size of the signal. (C) A digoxigenin-labeled DNA probe prepared from BAC RP11-348g24 resulted in specific signals on the X chromosome in the presence of a significant amount of cross-hybridization to other chromosomes in metaphase spreads. High level of cross-hybridization was also evident in interphase nuclei. (D) In contrast to the result shown in (C), a probe prepared from BAC RP11-294c12 bound almost exclusively to the centromeric heterochromatin of the human X chromosome. (E) Combining differentially labeled DNA probes in a single hybridization experiment, the Y chromosomal target appears in green, whereas the X chromosomal centromeric repeat DNA is shown in red. (F) In situ hybridization of an autosome-targeting DNA probe prepared from BAC clone RP11-96f8 showed multiple signals and a high level of cross-hybridization in the interphase cell nuclei. (G) The biotinylated probe prepared from BAC RP11-168p20 exhibited strong signals on both homologues of chromosome 10. (H) A combination of three differently labeled probes was hybridized simultaneously. Chromosome 10 signals are shown in red; X chromosomal and Y chromosomal signals are shown in green and blue, respectively. (I–K) The same probe as in (G) (BAC RP11-168p20) was hybridized to the cell line S48TK18A6. Multiple signals indicate chromosomal abnormalities. (I) shows DAPI picture, (J) shows green avidin-FITC signal, and (K) shows the superposition of both. (L–N) A chromosome X probe (BAC clone RP11-294c12) labeled with biotin/avidin-FITC, a Cy-5 labeled chromosome Y probe (RP11-242e13), and a chromosome 10-specific probe prepared from BAC RP11-168p20 (labeled with Spectral Orange-dUTP) were hybridized onto a deparaffinized 12-week placenta tissue section. (L) The chromosome 10 probe (red signals) and bound chromosome X probe (green signals) in this female placental tissue section. (M–N) In our triple probe FISH experiment, the chromosome 10 probe is represented by orange signals, the chromosome X probe by green signals, and the chromosome Y probe by red signals in the male cell nuclei. (Size marker bars indicate 10 µm.)

    Article Snippet: DNA Probe Preparation The BAC DNAs were extracted from overnight cultures following an alkaline lysis protocol ( ) or using a ZR BAC DNA Miniprep Kit (Zymo Research; Irvine, CA).

    Techniques: In Situ Hybridization, Hybridization, Polymerase Chain Reaction, Labeling, BAC Assay, Avidin-Biotin Assay, Fluorescence In Situ Hybridization, Marker