sequence editing software sequencher Search Results


marathontm cdna amplification kit  (TaKaRa)
96
TaKaRa marathontm cdna amplification kit
Marathontm Cdna Amplification Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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casmini data analysis  (New England Biolabs)
99
New England Biolabs casmini data analysis
Casmini Data Analysis, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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macvector software  (MacVector inc)
90
MacVector inc macvector software
Macvector Software, supplied by MacVector inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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taq dna polymerase  (Thermo Fisher)
99
Thermo Fisher taq dna polymerase
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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assays bca assay kit thermoscientifi c 23250  (Thermo Fisher)
99
Thermo Fisher assays bca assay kit thermoscientifi c 23250
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
Assays Bca Assay Kit Thermoscientifi C 23250, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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vectashield antifade mounting medium  (Vector Laboratories)
99
Vector Laboratories vectashield antifade mounting medium
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
Vectashield Antifade Mounting Medium, supplied by Vector Laboratories, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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9806s recombinant human integrin alpha v beta 1 protein  (Cell Signaling Technology Inc)
99
Cell Signaling Technology Inc 9806s recombinant human integrin alpha v beta 1 protein
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
9806s Recombinant Human Integrin Alpha V Beta 1 Protein, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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precision plus protein dual color standards biorad  (Bio-Rad)
97
Bio-Rad precision plus protein dual color standards biorad
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
Precision Plus Protein Dual Color Standards Biorad, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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44719 software  (Addgene inc)
94
Addgene inc 44719 software
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
44719 Software, supplied by Addgene inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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am7020  (Thermo Fisher)
90
Thermo Fisher am7020
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
Am7020, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ssoadvanced universal sybr green supermix bio rad  (Bio-Rad)
99
Bio-Rad ssoadvanced universal sybr green supermix bio rad
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
Ssoadvanced Universal Sybr Green Supermix Bio Rad, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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dh218 proteinase k neb  (New England Biolabs)
99
New England Biolabs dh218 proteinase k neb
FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free <t>DNA</t> (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, <t>polymerase</t> chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.
Dh218 Proteinase K Neb, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, polymerase chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.

Journal: The Journal of biological chemistry

Article Title: Binding of retinoic acid receptor heterodimers to DNA. A role for histones NH2 termini.

doi: 10.1074/jbc.273.20.12288

Figure Lengend Snippet: FIG. 3. Rotational phasing of the 182-bp RAR-b2 promoter fragment. A, DNase I footprint of the upper strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were incubated for 0, 1, 2, or 5 min or 0, 2, 5, or 10 min, respectively, with 1 unit of DNase I at room temperature. DNAs were extracted and analyzed as described in the legend to Fig. 2. Black dots indicate sites of enhanced DNase I sensitivity of nucleosomal DNA compared with free DNA. Positions of preferential DNase I cleavage were determined at the base pair level using dideoxynucle- otides sequencing reactions (lanes G, A, T, and C). Numbers indicate the sequence position of cleavage sites along the promoter sequence. B, polymerase chain reaction amplification of the 12/2112 DNA segment. DNase I-digested DNA was amplified with a 19-mer oligonucleotide complementary to the upper strand. Fragment sizing was carried out using the Kodak 1D Image Analysis Software and results are indicated on the right. Corresponding cleavage sites by DNase I on the upper strand are indicated on the left. C, DNase I footprint of the lower strand of the RAR-b2 promoter. Free DNA (F) or reconstituted monosomes (R) were cleaved and analyzed as in A. Open circles show less intense, but consistently observed, cleavage sites. Positions of maximal minor groove accessibility (DNase I hypersensitive sites) were deduced from sequencing tracks and are indicated on the left. Experimental data are summarized in Fig. 4.

Article Snippet: Taq DNA polymerase was from Life Technologies, Inc. (Rockville, MD); isopropylthio-b-galactopyranoside, ampicillin, and kanamycin were from Appligene/Oncor (Strasbourg, France).

Techniques: Incubation, Sequencing, Polymerase Chain Reaction, Amplification, Software