cdna amplification Search Results


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  • 99
    Thermo Fisher cdna
    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or <t>cDNA</t> from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ <t>UTR</t> of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .
    Cdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 160058 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    TaKaRa complementary dna cdna amplification
    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or <t>cDNA</t> from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ <t>UTR</t> of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .
    Complementary Dna Cdna Amplification, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher complementary dna cdna template
    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or <t>cDNA</t> from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ <t>UTR</t> of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .
    Complementary Dna Cdna Template, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 33 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Nugen complementary dna cdna amplification
    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or <t>cDNA</t> from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ <t>UTR</t> of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .
    Complementary Dna Cdna Amplification, supplied by Nugen, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Source BioScience plc cdna
    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or <t>cDNA</t> from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ <t>UTR</t> of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .
    Cdna, supplied by Source BioScience plc, used in various techniques. Bioz Stars score: 92/100, based on 270 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Quanta Biosciences qscript complementary dna cdna supermix
    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or <t>cDNA</t> from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ <t>UTR</t> of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .
    Qscript Complementary Dna Cdna Supermix, supplied by Quanta Biosciences, used in various techniques. Bioz Stars score: 92/100, based on 16 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Bio-Rad complementary dna amplification
    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or <t>cDNA</t> from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ <t>UTR</t> of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .
    Complementary Dna Amplification, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 90/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc cdna amplification
    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or <t>cDNA</t> from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ <t>UTR</t> of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .
    Cdna Amplification, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 426 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    TaKaRa complementary dna cdna
    Construction of pFastBac vectors. (A) Toxoplasma gondii IMC gene was PCR-amplified from <t>cDNA</t> synthesized using a Prime Script 1st Strain CDNA Synthesis Kit using total RNA extracted from T . gondii RH. M denotes <t>DNA</t> marker and lane 1 indicates amplified PCR product. (B) Influenza M1 gene was PCR amplified from total RNA extracted from influenza virus (A/PR/8/34). M denotes DNA marker and lane 2 indicates amplified PCR product. (C and D) Toxoplasma gondii IMC gene and influenza M1 gene were cloned in to pFastBac with EcoRI / XhoI and EcoRI / XhoI enzymes, respectively, resulting in T . gondii IMC plasmid (C) and M1 plasmid (D).
    Complementary Dna Cdna, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 7532 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Nugen complementary dna cdna
    Construction of pFastBac vectors. (A) Toxoplasma gondii IMC gene was PCR-amplified from <t>cDNA</t> synthesized using a Prime Script 1st Strain CDNA Synthesis Kit using total RNA extracted from T . gondii RH. M denotes <t>DNA</t> marker and lane 1 indicates amplified PCR product. (B) Influenza M1 gene was PCR amplified from total RNA extracted from influenza virus (A/PR/8/34). M denotes DNA marker and lane 2 indicates amplified PCR product. (C and D) Toxoplasma gondii IMC gene and influenza M1 gene were cloned in to pFastBac with EcoRI / XhoI and EcoRI / XhoI enzymes, respectively, resulting in T . gondii IMC plasmid (C) and M1 plasmid (D).
    Complementary Dna Cdna, supplied by Nugen, used in various techniques. Bioz Stars score: 93/100, based on 149 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Bio-Rad complementary dna cdna
    Alignment of the deep sequenced mitochondrial transcriptome of Chlamydomonas reinhardtii strain cc503. ( A ) A single putative RNA editing site was detected in the cytochrome oxidase b gene at nucleotide 1,182. The mean coverage of the cob gene was 28,371.5 ± 7,598 with a min:max of 816:42,177. ( B ) Sequencing of the cob <t>DNA</t> and <t>cDNA</t> from the cc503 isolate used for the deep sequencing revealed a SNP at that site, therefore no editing had taken place.
    Complementary Dna Cdna, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 94/100, based on 4319 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Illumina Inc complementary dna cdna
    Alignment of the deep sequenced mitochondrial transcriptome of Chlamydomonas reinhardtii strain cc503. ( A ) A single putative RNA editing site was detected in the cytochrome oxidase b gene at nucleotide 1,182. The mean coverage of the cob gene was 28,371.5 ± 7,598 with a min:max of 816:42,177. ( B ) Sequencing of the cob <t>DNA</t> and <t>cDNA</t> from the cc503 isolate used for the deep sequencing revealed a SNP at that site, therefore no editing had taken place.
    Complementary Dna Cdna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 158 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Roche complementary dna cdna
    Amplification results from nested RT-PCR for <t>cDNA</t> of single cells after laser microdissection. A: Amplification results of β-actin-outer primers. B: Amplification results of β-actin-inner primers. M: <t>DNA</t> markers (upper to lower: 2000, 1000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp). 1: PCR positive control; 2: one complete section; 4, 6, 8 and 10 are 200, 100, 10 and 1 cell(s), respectively; 3, 5, 7, 9 and 11 are negative controls of 2, 4, 6, 8 and 10; 12: PCR negative control.
    Complementary Dna Cdna, supplied by Roche, used in various techniques. Bioz Stars score: 94/100, based on 1767 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Addgene inc complementary dna cdna
    Amplification results from nested RT-PCR for <t>cDNA</t> of single cells after laser microdissection. A: Amplification results of β-actin-outer primers. B: Amplification results of β-actin-inner primers. M: <t>DNA</t> markers (upper to lower: 2000, 1000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp). 1: PCR positive control; 2: one complete section; 4, 6, 8 and 10 are 200, 100, 10 and 1 cell(s), respectively; 3, 5, 7, 9 and 11 are negative controls of 2, 4, 6, 8 and 10; 12: PCR negative control.
    Complementary Dna Cdna, supplied by Addgene inc, used in various techniques. Bioz Stars score: 90/100, based on 39 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Promega complementary dna cdna
    Amplification results from nested RT-PCR for <t>cDNA</t> of single cells after laser microdissection. A: Amplification results of β-actin-outer primers. B: Amplification results of β-actin-inner primers. M: <t>DNA</t> markers (upper to lower: 2000, 1000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp). 1: PCR positive control; 2: one complete section; 4, 6, 8 and 10 are 200, 100, 10 and 1 cell(s), respectively; 3, 5, 7, 9 and 11 are negative controls of 2, 4, 6, 8 and 10; 12: PCR negative control.
    Complementary Dna Cdna, supplied by Promega, used in various techniques. Bioz Stars score: 92/100, based on 3228 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Quanta Biosciences complementary dna cdna
    Amplification results from nested RT-PCR for <t>cDNA</t> of single cells after laser microdissection. A: Amplification results of β-actin-outer primers. B: Amplification results of β-actin-inner primers. M: <t>DNA</t> markers (upper to lower: 2000, 1000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp). 1: PCR positive control; 2: one complete section; 4, 6, 8 and 10 are 200, 100, 10 and 1 cell(s), respectively; 3, 5, 7, 9 and 11 are negative controls of 2, 4, 6, 8 and 10; 12: PCR negative control.
    Complementary Dna Cdna, supplied by Quanta Biosciences, used in various techniques. Bioz Stars score: 93/100, based on 726 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Transgenomic complementary dna cdna
    Amplification results from nested RT-PCR for <t>cDNA</t> of single cells after laser microdissection. A: Amplification results of β-actin-outer primers. B: Amplification results of β-actin-inner primers. M: <t>DNA</t> markers (upper to lower: 2000, 1000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp). 1: PCR positive control; 2: one complete section; 4, 6, 8 and 10 are 200, 100, 10 and 1 cell(s), respectively; 3, 5, 7, 9 and 11 are negative controls of 2, 4, 6, 8 and 10; 12: PCR negative control.
    Complementary Dna Cdna, supplied by Transgenomic, used in various techniques. Bioz Stars score: 92/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Toyobo complementary dna cdna
    Enterovirus 71 (EV71) strain infection and replication in rhabdomyosarcoma (RD) cells, mouse neuroblastoma Neuro-2a (N2a) cells and human neuroblastoma (SK-N-SH) cells. ( A ) Images of RD, N2a, and SK-N-SH cells acquired 24 hours post infection (hpi) after infection with 100 50% tissue culture infective dose (TCID50) of three representative EV71 strains, including clinical mild strain Hun11-4, clinical severe strain NX10-36, and clinical fatal strain GD10-45 (magnification 200×). ( B ) Replicative curve of EV71 in RD cells. Total RNA was prepared from infected and uninfected RD cells at 2, 6, 12, 24, 48, and 72 hpi. After reverse transcription, VP-1 specific primers were used to amplify the viral VP1 gene transcript from the complementary <t>DNA</t> <t>(cDNA),</t> confirming viral replication in infected RD cells. ( C ) Replicative curve of EV71 in SK-N-SH cells. Total RNA was prepared from infected and uninfected SK-N-SH cells at 2, 6, 12, 24, 48, and 72 hpi. After reverse transcription, VP-1 specific primers were used to amplify the viral VP1 gene transcript from the cDNA, confirming viral replication in infected SK-N-SH cells.
    Complementary Dna Cdna, supplied by Toyobo, used in various techniques. Bioz Stars score: 92/100, based on 928 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Thermo Fisher human mcm7 complementary dna cdna
    Pb/MCM7i13 transgenic construct. (A) Pb, prostate-specific rat probasin promoter ARR 2 PB; black box, HA tag; white box, Xpress tag; gray boxes, human <t>MCM7</t> coding sequence; red and blue boxes, miR-93/106b and miR-25 genes; yellow box, SV40 poly(A) (SV40 pA); orange box, probe used for Southern analysis of transgenic lines; green arrows, primers used for PCR analysis of transgenic lines and for genotyping. (B) Top: Southern blot analysis. Genomic <t>DNA</t> extracted from tails was digested with Bam HI and hybridized with a probe complementary to the SV40 poly(A) region as shown in (A). The Bam HI–digested Pb/MCM7i13 plasmid was used as positive control (C+). Bottom: PCR analysis. A forward primer complementary to the probasin promoter and a reverse primer complementary to the tag were used, as shown in (A). Empty Pb and Pb/MCM7i13 plasmids were used as negative (C−) and positive (C+) controls. L, 100-bp ladder. Three representative positive (P) and negative (N) mice are shown. (C) Abundance of the transgenic construct measured by real-time PCR in nine different lines. A primer pair specific for human MCM7 coding sequence was used. LE, ME, HE: low, medium, and high expressors, respectively. Human MCM7 .
    Human Mcm7 Complementary Dna Cdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 85/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Agilent technologies strand complementary dna cdna
    Pb/MCM7i13 transgenic construct. (A) Pb, prostate-specific rat probasin promoter ARR 2 PB; black box, HA tag; white box, Xpress tag; gray boxes, human <t>MCM7</t> coding sequence; red and blue boxes, miR-93/106b and miR-25 genes; yellow box, SV40 poly(A) (SV40 pA); orange box, probe used for Southern analysis of transgenic lines; green arrows, primers used for PCR analysis of transgenic lines and for genotyping. (B) Top: Southern blot analysis. Genomic <t>DNA</t> extracted from tails was digested with Bam HI and hybridized with a probe complementary to the SV40 poly(A) region as shown in (A). The Bam HI–digested Pb/MCM7i13 plasmid was used as positive control (C+). Bottom: PCR analysis. A forward primer complementary to the probasin promoter and a reverse primer complementary to the tag were used, as shown in (A). Empty Pb and Pb/MCM7i13 plasmids were used as negative (C−) and positive (C+) controls. L, 100-bp ladder. Three representative positive (P) and negative (N) mice are shown. (C) Abundance of the transgenic construct measured by real-time PCR in nine different lines. A primer pair specific for human MCM7 coding sequence was used. LE, ME, HE: low, medium, and high expressors, respectively. Human MCM7 .
    Strand Complementary Dna Cdna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Bio-Rad complementary dna cdna synthesis
    Pb/MCM7i13 transgenic construct. (A) Pb, prostate-specific rat probasin promoter ARR 2 PB; black box, HA tag; white box, Xpress tag; gray boxes, human <t>MCM7</t> coding sequence; red and blue boxes, miR-93/106b and miR-25 genes; yellow box, SV40 poly(A) (SV40 pA); orange box, probe used for Southern analysis of transgenic lines; green arrows, primers used for PCR analysis of transgenic lines and for genotyping. (B) Top: Southern blot analysis. Genomic <t>DNA</t> extracted from tails was digested with Bam HI and hybridized with a probe complementary to the SV40 poly(A) region as shown in (A). The Bam HI–digested Pb/MCM7i13 plasmid was used as positive control (C+). Bottom: PCR analysis. A forward primer complementary to the probasin promoter and a reverse primer complementary to the tag were used, as shown in (A). Empty Pb and Pb/MCM7i13 plasmids were used as negative (C−) and positive (C+) controls. L, 100-bp ladder. Three representative positive (P) and negative (N) mice are shown. (C) Abundance of the transgenic construct measured by real-time PCR in nine different lines. A primer pair specific for human MCM7 coding sequence was used. LE, ME, HE: low, medium, and high expressors, respectively. Human MCM7 .
    Complementary Dna Cdna Synthesis, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 93/100, based on 443 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    TaKaRa first strand complementary dna cdna amplification
    Pb/MCM7i13 transgenic construct. (A) Pb, prostate-specific rat probasin promoter ARR 2 PB; black box, HA tag; white box, Xpress tag; gray boxes, human <t>MCM7</t> coding sequence; red and blue boxes, miR-93/106b and miR-25 genes; yellow box, SV40 poly(A) (SV40 pA); orange box, probe used for Southern analysis of transgenic lines; green arrows, primers used for PCR analysis of transgenic lines and for genotyping. (B) Top: Southern blot analysis. Genomic <t>DNA</t> extracted from tails was digested with Bam HI and hybridized with a probe complementary to the SV40 poly(A) region as shown in (A). The Bam HI–digested Pb/MCM7i13 plasmid was used as positive control (C+). Bottom: PCR analysis. A forward primer complementary to the probasin promoter and a reverse primer complementary to the tag were used, as shown in (A). Empty Pb and Pb/MCM7i13 plasmids were used as negative (C−) and positive (C+) controls. L, 100-bp ladder. Three representative positive (P) and negative (N) mice are shown. (C) Abundance of the transgenic construct measured by real-time PCR in nine different lines. A primer pair specific for human MCM7 coding sequence was used. LE, ME, HE: low, medium, and high expressors, respectively. Human MCM7 .
    First Strand Complementary Dna Cdna Amplification, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    OriGene length complementary dna cdna
    Pb/MCM7i13 transgenic construct. (A) Pb, prostate-specific rat probasin promoter ARR 2 PB; black box, HA tag; white box, Xpress tag; gray boxes, human <t>MCM7</t> coding sequence; red and blue boxes, miR-93/106b and miR-25 genes; yellow box, SV40 poly(A) (SV40 pA); orange box, probe used for Southern analysis of transgenic lines; green arrows, primers used for PCR analysis of transgenic lines and for genotyping. (B) Top: Southern blot analysis. Genomic <t>DNA</t> extracted from tails was digested with Bam HI and hybridized with a probe complementary to the SV40 poly(A) region as shown in (A). The Bam HI–digested Pb/MCM7i13 plasmid was used as positive control (C+). Bottom: PCR analysis. A forward primer complementary to the probasin promoter and a reverse primer complementary to the tag were used, as shown in (A). Empty Pb and Pb/MCM7i13 plasmids were used as negative (C−) and positive (C+) controls. L, 100-bp ladder. Three representative positive (P) and negative (N) mice are shown. (C) Abundance of the transgenic construct measured by real-time PCR in nine different lines. A primer pair specific for human MCM7 coding sequence was used. LE, ME, HE: low, medium, and high expressors, respectively. Human MCM7 .
    Length Complementary Dna Cdna, supplied by OriGene, used in various techniques. Bioz Stars score: 92/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or cDNA from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ UTR of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .

    Journal: Cell reports

    Article Title: ADAR Regulates RNA Editing, Transcript Stability, and Gene Expression

    doi: 10.1016/j.celrep.2013.10.002

    Figure Lengend Snippet: Validation of A-to-G Editing and RDD Sites by Sanger Sequencing (A) Sequences surrounding editing or RDD sites were amplified by PCR using genomic DNA or cDNA from the same two individuals as templates. The sites validated by Sanger sequencing are highlighted in blue and the corresponding nucleotide changes are labeled. Some samples were sequenced from the reverse strand, and the nucleotides are labeled according to the forward strand. *An example of an editing site in ERO1L that did not meet our inclusion criteria but nonetheless was validated by Sanger sequencing. (B) Hyperedited region in ATM transcript. 3′ UTR of ATM was PCR amplified from cDNA and cloned. Sequences from 137 individual clones are illustrated. Each black dot represents an A-to-G site detected in a clone by Sanger sequencing. See also Figure S1 .

    Article Snippet: The 3′ UTR of ATM was amplified from cDNA of B cells and cloned into TOPO vector (Invitrogen).

    Techniques: Sequencing, Amplification, Polymerase Chain Reaction, Labeling, Clone Assay

    Construction of pFastBac vectors. (A) Toxoplasma gondii IMC gene was PCR-amplified from cDNA synthesized using a Prime Script 1st Strain CDNA Synthesis Kit using total RNA extracted from T . gondii RH. M denotes DNA marker and lane 1 indicates amplified PCR product. (B) Influenza M1 gene was PCR amplified from total RNA extracted from influenza virus (A/PR/8/34). M denotes DNA marker and lane 2 indicates amplified PCR product. (C and D) Toxoplasma gondii IMC gene and influenza M1 gene were cloned in to pFastBac with EcoRI / XhoI and EcoRI / XhoI enzymes, respectively, resulting in T . gondii IMC plasmid (C) and M1 plasmid (D).

    Journal: PLoS ONE

    Article Title: Virus-Like Nanoparticle Vaccine Confers Protection against Toxoplasma gondii

    doi: 10.1371/journal.pone.0161231

    Figure Lengend Snippet: Construction of pFastBac vectors. (A) Toxoplasma gondii IMC gene was PCR-amplified from cDNA synthesized using a Prime Script 1st Strain CDNA Synthesis Kit using total RNA extracted from T . gondii RH. M denotes DNA marker and lane 1 indicates amplified PCR product. (B) Influenza M1 gene was PCR amplified from total RNA extracted from influenza virus (A/PR/8/34). M denotes DNA marker and lane 2 indicates amplified PCR product. (C and D) Toxoplasma gondii IMC gene and influenza M1 gene were cloned in to pFastBac with EcoRI / XhoI and EcoRI / XhoI enzymes, respectively, resulting in T . gondii IMC plasmid (C) and M1 plasmid (D).

    Article Snippet: Complementary DNA (cDNA) was synthesized using a Prime Script 1st Strain CDNA Synthesis Kit (Takara, Japan).

    Techniques: Polymerase Chain Reaction, Amplification, Synthesized, Marker, Clone Assay, Plasmid Preparation

    Stage-specific transcription of PfNSMase in the intraerythrocytic parasite P. falciparum . (A) Northern blotting of asynchronous parasite culture. 10 μg of total RNA prepared from asynchronous cultures of three P. falciparum lines was loaded in each lane. The ethidium bromide-stained gel (lanes 1–3) shows the comparable loadings of RNA. Lane 1 and 4, 3D7; lane 2 and 5, Honduras-1; lane 3 and 6, Dd2. The position of the standard RNA marker (GIBCO BRL) is shown at the left. The stage distribution for each line is indicated: 3D7, 63% ring, 26% trophozoite, 11% schizont; Honduras-1, 71% ring, 22% trophozoite, 7% schizont; and Dd2, 48% ring, 26% trophozoite, 26% schizont. (B) Northern blotting of synchronous parasite culture. 4 μg (lanes 1, 2, 5, and 6) and 10 μg (lanes 3, 4, 7, and 8) of total RNA prepared from different stages of tightly synchronized culture of HB3 line was loaded. The ethidium bromide–stained gel (lanes 1–4) indicates the comparable loadings of RNA from the different stages at two different concentrations. Lanes 1, 3, 5, and 7, ring-rich culture (99% ring, 1% trophozoite, 0% schizont); lanes 2, 4, 6, and 8, trophozoite- and schizont-rich culture (0% ring, 86% trophozoite, 14% schizont). The position of the standard RNA marker is shown at the left. (C) RT-PCR experiment. PCR products obtained from different concentrations of first strand cDNA from various stages of tightly synchronized parasite culture of Honduras-1 line were analyzed in 0.8% agarose gel. Lanes 1 and 2, 3 and 4, 5–9, 10–14, and 15–19 are products obtained from ring, young trophozoite, mature trophozoite, schizont, and segmented-schizont, respectively. Parasite morphology at each stage used is shown on top. Dilution factors of the first strand cDNA solution are as follows: lanes 1, 2, 3, 5, 10, and 15, no dilution; lanes 4, 6, 11, and 16, 10-fold; lanes 7, 12, and 17, 100-fold; lanes 8, 13, and 18, 1,000-fold; lanes 9, 14, and 19, 10,000-fold.

    Journal: The Journal of Experimental Medicine

    Article Title: Plasmodium falciparum Phospholipase C Hydrolyzing Sphingomyelin and Lysocholinephospholipids Is a Possible Target for Malaria Chemotherapy

    doi: 10.1084/jem.20010724

    Figure Lengend Snippet: Stage-specific transcription of PfNSMase in the intraerythrocytic parasite P. falciparum . (A) Northern blotting of asynchronous parasite culture. 10 μg of total RNA prepared from asynchronous cultures of three P. falciparum lines was loaded in each lane. The ethidium bromide-stained gel (lanes 1–3) shows the comparable loadings of RNA. Lane 1 and 4, 3D7; lane 2 and 5, Honduras-1; lane 3 and 6, Dd2. The position of the standard RNA marker (GIBCO BRL) is shown at the left. The stage distribution for each line is indicated: 3D7, 63% ring, 26% trophozoite, 11% schizont; Honduras-1, 71% ring, 22% trophozoite, 7% schizont; and Dd2, 48% ring, 26% trophozoite, 26% schizont. (B) Northern blotting of synchronous parasite culture. 4 μg (lanes 1, 2, 5, and 6) and 10 μg (lanes 3, 4, 7, and 8) of total RNA prepared from different stages of tightly synchronized culture of HB3 line was loaded. The ethidium bromide–stained gel (lanes 1–4) indicates the comparable loadings of RNA from the different stages at two different concentrations. Lanes 1, 3, 5, and 7, ring-rich culture (99% ring, 1% trophozoite, 0% schizont); lanes 2, 4, 6, and 8, trophozoite- and schizont-rich culture (0% ring, 86% trophozoite, 14% schizont). The position of the standard RNA marker is shown at the left. (C) RT-PCR experiment. PCR products obtained from different concentrations of first strand cDNA from various stages of tightly synchronized parasite culture of Honduras-1 line were analyzed in 0.8% agarose gel. Lanes 1 and 2, 3 and 4, 5–9, 10–14, and 15–19 are products obtained from ring, young trophozoite, mature trophozoite, schizont, and segmented-schizont, respectively. Parasite morphology at each stage used is shown on top. Dilution factors of the first strand cDNA solution are as follows: lanes 1, 2, 3, 5, 10, and 15, no dilution; lanes 4, 6, 11, and 16, 10-fold; lanes 7, 12, and 17, 100-fold; lanes 8, 13, and 18, 1,000-fold; lanes 9, 14, and 19, 10,000-fold.

    Article Snippet: First strand cDNA was synthesized from 200 ng total RNA with SMART™ 5′-Rapid Amplification of cDNA Ends (RACE) cDNA Amplification Kit (CLONTECH Laboratories, Inc.) by using the Superscript II reverse transcriptase (GIBCO BRL).

    Techniques: Northern Blot, Staining, Marker, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Agarose Gel Electrophoresis

    Alignment of the deep sequenced mitochondrial transcriptome of Chlamydomonas reinhardtii strain cc503. ( A ) A single putative RNA editing site was detected in the cytochrome oxidase b gene at nucleotide 1,182. The mean coverage of the cob gene was 28,371.5 ± 7,598 with a min:max of 816:42,177. ( B ) Sequencing of the cob DNA and cDNA from the cc503 isolate used for the deep sequencing revealed a SNP at that site, therefore no editing had taken place.

    Journal: Genes

    Article Title: Deep Transcriptome Sequencing of Two Green Algae, Chara vulgaris and Chlamydomonas reinhardtii, Provides No Evidence of Organellar RNA Editing

    doi: 10.3390/genes8020080

    Figure Lengend Snippet: Alignment of the deep sequenced mitochondrial transcriptome of Chlamydomonas reinhardtii strain cc503. ( A ) A single putative RNA editing site was detected in the cytochrome oxidase b gene at nucleotide 1,182. The mean coverage of the cob gene was 28,371.5 ± 7,598 with a min:max of 816:42,177. ( B ) Sequencing of the cob DNA and cDNA from the cc503 isolate used for the deep sequencing revealed a SNP at that site, therefore no editing had taken place.

    Article Snippet: Complementary DNA (cDNA) was produced from DNase treated RNA using Bio-Rad’s iScript cDNA synthesis kit (Hercules, CA, USA).

    Techniques: Sequencing

    Three follow-up experiments attempting to detect three putative RNA editing sites in the C. vulgaris psbI mRNA. ( A ) Chara was grown in nine different environmental conditions: 20 °C, 25 °C, 30 °C and pH 6, 7, 8, in triplicate, and then DNA + RNA were extracted from each. The melt temperatures for genomic DNA (gDNA) and complementary DNA (cDNA) were determined as paired reactions using high resolution melt analysis. Melt temperature differences between gDNA and cDNA derived amplicons were calculated by subtraction. Data presented on these graphs are the averages of nine observations ± standard error (SE). There were qualitative differences in the cDNA–DNA melt temperatures of psbI and the negative control, psbA , at the different incubation temperatures but these differences were statistically insignificant. Different pH also had no significant effect on the cDNA–DNA melt temperatures and two-way analysis of variance detected no interaction between the temperature and pH for either gene; ( B ) RNase H-dependent PCR (rhPCR) was used in an attempt to detect single base changes between the psbI gDNA and cDNA extracted from Chara incubated in different temperatures. This assay was designed to suppress PCR amplification of the genomic sequence but not cDNA made from an edited transcript. The quantitative PCR (qPCR) amplification curves show that gDNA and cDNA amplified with sigmoidal curves with standard PCR but that both gDNA and cDNA were suppressed by the addition of an rhPCR primer despite the presence of RNase H2 in the reactions. This suggests no editing occurred at any of the tested temperatures; ( C ) cDNAs were PCR amplified and sequenced from total RNA extracted from Chara grown at 20 °C, 25 °C, and 30 °C. The sequences all matched the genomic sequence, suggesting no editing had taken place.

    Journal: Genes

    Article Title: Deep Transcriptome Sequencing of Two Green Algae, Chara vulgaris and Chlamydomonas reinhardtii, Provides No Evidence of Organellar RNA Editing

    doi: 10.3390/genes8020080

    Figure Lengend Snippet: Three follow-up experiments attempting to detect three putative RNA editing sites in the C. vulgaris psbI mRNA. ( A ) Chara was grown in nine different environmental conditions: 20 °C, 25 °C, 30 °C and pH 6, 7, 8, in triplicate, and then DNA + RNA were extracted from each. The melt temperatures for genomic DNA (gDNA) and complementary DNA (cDNA) were determined as paired reactions using high resolution melt analysis. Melt temperature differences between gDNA and cDNA derived amplicons were calculated by subtraction. Data presented on these graphs are the averages of nine observations ± standard error (SE). There were qualitative differences in the cDNA–DNA melt temperatures of psbI and the negative control, psbA , at the different incubation temperatures but these differences were statistically insignificant. Different pH also had no significant effect on the cDNA–DNA melt temperatures and two-way analysis of variance detected no interaction between the temperature and pH for either gene; ( B ) RNase H-dependent PCR (rhPCR) was used in an attempt to detect single base changes between the psbI gDNA and cDNA extracted from Chara incubated in different temperatures. This assay was designed to suppress PCR amplification of the genomic sequence but not cDNA made from an edited transcript. The quantitative PCR (qPCR) amplification curves show that gDNA and cDNA amplified with sigmoidal curves with standard PCR but that both gDNA and cDNA were suppressed by the addition of an rhPCR primer despite the presence of RNase H2 in the reactions. This suggests no editing occurred at any of the tested temperatures; ( C ) cDNAs were PCR amplified and sequenced from total RNA extracted from Chara grown at 20 °C, 25 °C, and 30 °C. The sequences all matched the genomic sequence, suggesting no editing had taken place.

    Article Snippet: Complementary DNA (cDNA) was produced from DNase treated RNA using Bio-Rad’s iScript cDNA synthesis kit (Hercules, CA, USA).

    Techniques: Derivative Assay, Negative Control, Incubation, RNase H-dependent PCR, Polymerase Chain Reaction, Amplification, Sequencing, Real-time Polymerase Chain Reaction

    Amplification results from nested RT-PCR for cDNA of single cells after laser microdissection. A: Amplification results of β-actin-outer primers. B: Amplification results of β-actin-inner primers. M: DNA markers (upper to lower: 2000, 1000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp). 1: PCR positive control; 2: one complete section; 4, 6, 8 and 10 are 200, 100, 10 and 1 cell(s), respectively; 3, 5, 7, 9 and 11 are negative controls of 2, 4, 6, 8 and 10; 12: PCR negative control.

    Journal: World Journal of Gastroenterology : WJG

    Article Title: Gene-expression analysis of single cells-nested polymerase chain reaction after laser microdissection

    doi: 10.3748/wjg.v9.i6.1337

    Figure Lengend Snippet: Amplification results from nested RT-PCR for cDNA of single cells after laser microdissection. A: Amplification results of β-actin-outer primers. B: Amplification results of β-actin-inner primers. M: DNA markers (upper to lower: 2000, 1000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp). 1: PCR positive control; 2: one complete section; 4, 6, 8 and 10 are 200, 100, 10 and 1 cell(s), respectively; 3, 5, 7, 9 and 11 are negative controls of 2, 4, 6, 8 and 10; 12: PCR negative control.

    Article Snippet: 12 μL of total RNA was reversely transcribed into complementary DNA (cDNA) using random hexamers according to the manufacturer's instructions (Roche Diagnostics, Rotkreuz, Switzerland)[ ].

    Techniques: Amplification, Reverse Transcription Polymerase Chain Reaction, Laser Capture Microdissection, Polymerase Chain Reaction, Positive Control, Negative Control

    Enterovirus 71 (EV71) strain infection and replication in rhabdomyosarcoma (RD) cells, mouse neuroblastoma Neuro-2a (N2a) cells and human neuroblastoma (SK-N-SH) cells. ( A ) Images of RD, N2a, and SK-N-SH cells acquired 24 hours post infection (hpi) after infection with 100 50% tissue culture infective dose (TCID50) of three representative EV71 strains, including clinical mild strain Hun11-4, clinical severe strain NX10-36, and clinical fatal strain GD10-45 (magnification 200×). ( B ) Replicative curve of EV71 in RD cells. Total RNA was prepared from infected and uninfected RD cells at 2, 6, 12, 24, 48, and 72 hpi. After reverse transcription, VP-1 specific primers were used to amplify the viral VP1 gene transcript from the complementary DNA (cDNA), confirming viral replication in infected RD cells. ( C ) Replicative curve of EV71 in SK-N-SH cells. Total RNA was prepared from infected and uninfected SK-N-SH cells at 2, 6, 12, 24, 48, and 72 hpi. After reverse transcription, VP-1 specific primers were used to amplify the viral VP1 gene transcript from the cDNA, confirming viral replication in infected SK-N-SH cells.

    Journal: Viruses

    Article Title: Neurotropism In Vitro and Mouse Models of Severe and Mild Infection with Clinical Strains of Enterovirus 71

    doi: 10.3390/v9110351

    Figure Lengend Snippet: Enterovirus 71 (EV71) strain infection and replication in rhabdomyosarcoma (RD) cells, mouse neuroblastoma Neuro-2a (N2a) cells and human neuroblastoma (SK-N-SH) cells. ( A ) Images of RD, N2a, and SK-N-SH cells acquired 24 hours post infection (hpi) after infection with 100 50% tissue culture infective dose (TCID50) of three representative EV71 strains, including clinical mild strain Hun11-4, clinical severe strain NX10-36, and clinical fatal strain GD10-45 (magnification 200×). ( B ) Replicative curve of EV71 in RD cells. Total RNA was prepared from infected and uninfected RD cells at 2, 6, 12, 24, 48, and 72 hpi. After reverse transcription, VP-1 specific primers were used to amplify the viral VP1 gene transcript from the complementary DNA (cDNA), confirming viral replication in infected RD cells. ( C ) Replicative curve of EV71 in SK-N-SH cells. Total RNA was prepared from infected and uninfected SK-N-SH cells at 2, 6, 12, 24, 48, and 72 hpi. After reverse transcription, VP-1 specific primers were used to amplify the viral VP1 gene transcript from the cDNA, confirming viral replication in infected SK-N-SH cells.

    Article Snippet: The polymerase chain reaction (PCR) parameters for all primer pairs were as follows: complementary DNA (cDNA) was denatured at 94 °C for 5 min. Amplification was performed using KOD-plus-DNA Polymerase (Toyobo, Tokyo, Japan) with 35 cycles of denaturation for 30 s at 94 °C, primer annealing for 45 s at 56 °C, and elongation for 1 min at 68 °C, followed by extension at 68 °C for 10 min.

    Techniques: Infection

    Pb/MCM7i13 transgenic construct. (A) Pb, prostate-specific rat probasin promoter ARR 2 PB; black box, HA tag; white box, Xpress tag; gray boxes, human MCM7 coding sequence; red and blue boxes, miR-93/106b and miR-25 genes; yellow box, SV40 poly(A) (SV40 pA); orange box, probe used for Southern analysis of transgenic lines; green arrows, primers used for PCR analysis of transgenic lines and for genotyping. (B) Top: Southern blot analysis. Genomic DNA extracted from tails was digested with Bam HI and hybridized with a probe complementary to the SV40 poly(A) region as shown in (A). The Bam HI–digested Pb/MCM7i13 plasmid was used as positive control (C+). Bottom: PCR analysis. A forward primer complementary to the probasin promoter and a reverse primer complementary to the tag were used, as shown in (A). Empty Pb and Pb/MCM7i13 plasmids were used as negative (C−) and positive (C+) controls. L, 100-bp ladder. Three representative positive (P) and negative (N) mice are shown. (C) Abundance of the transgenic construct measured by real-time PCR in nine different lines. A primer pair specific for human MCM7 coding sequence was used. LE, ME, HE: low, medium, and high expressors, respectively. Human MCM7 .

    Journal: Science signaling

    Article Title: Identification of the miR-106b~25 MicroRNA Cluster as a Proto-Oncogenic PTEN-Targeting Intron That Cooperates with Its Host Gene MCM7 in Transformation

    doi: 10.1126/scisignal.2000594

    Figure Lengend Snippet: Pb/MCM7i13 transgenic construct. (A) Pb, prostate-specific rat probasin promoter ARR 2 PB; black box, HA tag; white box, Xpress tag; gray boxes, human MCM7 coding sequence; red and blue boxes, miR-93/106b and miR-25 genes; yellow box, SV40 poly(A) (SV40 pA); orange box, probe used for Southern analysis of transgenic lines; green arrows, primers used for PCR analysis of transgenic lines and for genotyping. (B) Top: Southern blot analysis. Genomic DNA extracted from tails was digested with Bam HI and hybridized with a probe complementary to the SV40 poly(A) region as shown in (A). The Bam HI–digested Pb/MCM7i13 plasmid was used as positive control (C+). Bottom: PCR analysis. A forward primer complementary to the probasin promoter and a reverse primer complementary to the tag were used, as shown in (A). Empty Pb and Pb/MCM7i13 plasmids were used as negative (C−) and positive (C+) controls. L, 100-bp ladder. Three representative positive (P) and negative (N) mice are shown. (C) Abundance of the transgenic construct measured by real-time PCR in nine different lines. A primer pair specific for human MCM7 coding sequence was used. LE, ME, HE: low, medium, and high expressors, respectively. Human MCM7 .

    Article Snippet: The following antibodies and reagents were used: antibodies against Hsp-90 #61041 (Becton Dickinson); PTEN #9559 (WB), pAkt (Ser473 ) #9271 (WB), #3787 (IHC), Akt #9272, pS6 #2211 (Cell Signaling); DICER #CG006 (Clonegene); MSCV-neo (Clontech); siGENOME non-targeting small interfering RNA (siRNA) #2 (si-Luc), si-miR-19a, si-miR-19b, si-miR-22, si-miR-25, si-miR-92a, si-miR-17, si-miR-20a, si-miR-93, si-miR-106b, si-miR-302a, si-miR-372, si-miR-373, si-PTEN, siGLO RISC-free control siRNA miRNA antisense inhibitor negative control #1, miR-19a antisense inhibitor, miR-22 antisense inhibitor, miR-25 antisense inhibitor, miR-93 antisense inhibitor, miR-106b antisense inhibitor, Dharmafect 1 (Dharmacon); miR-17, miR-19a, miR-20a, miR-22, miR-25, miR-93, and miR-106b 3′ digoxigenin (DIG)–labeled LNA ISH probes (Exiqon); lipofectamine 2000, Trizol reagent, deoxyribonuclease I (DNase I) amplification grade, SuperScript II reverse transcriptase, Dulbecco's modified Eagle's medium (DMEM), RPMI 1640, fetal bovine serum (FBS), keratinocyte serum-free medium, epidermal growth factor (EGF), bovine pituitary extract (BPE), antibody against Xpress Tag, pcDNA3.1/His C, geneticin (G418), hygromycin, antibody against PTEN (IHC) #51-2400 (Invitrogen); human MCM7 complementary DNA (cDNA) #MHS1011-75176 (Open Biosystems); pGL3-Control ( Firefly luciferase ), pRL-TK ( Renilla luciferase ), Dual-Luciferase reporter assay (Promega); fraction V bovine serum albumin (BSA), polybrene, insulin, antibody against actin #A3853, anti-FLAG antibody #F3165, puromycin (Sigma); QuantiTect Sybr Green PCRkit (Qiagen); antibody against MCM7 #9966 (Santa Cruz Biotechnology); QuikChange II XL Site-Directed Mutagenesis Kit, Herculase Taq polymerase (Stratagene); Ki67 antibody #VP-K451 (Vector Laboratories).

    Techniques: Transgenic Assay, Construct, Sequencing, Polymerase Chain Reaction, Southern Blot, Plasmid Preparation, Positive Control, Mouse Assay, Real-time Polymerase Chain Reaction