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Characterization of PrP + / SSEA1 – cells isolated from EB at various periods. A: Prevalence of PrP + / SSEA1 + cells derived from EB at the various periods. PrP + cells were sorted from EB at Day 7, 14 and 21 by FACS. The ordinate showed the prevalence of PrP + cells and the abscissa indicated the prevalence of SSEA1 + cells. The upper control board showed the flow cytometry analysis as negative control and the lower control board showed the flow cytometry analysis of PrP + / SSEA1 + cells. B: Colongenic cell assay of cultured PrP + / SSEA1 – cells from EB at day 21. Either PrP + / SSEA1 + or PrP + / SSEA1 – cells of 10,000 cells were isolated from EB at day 21 by FACS and were subsequently cultured for another 10 and 17 days. Upper panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 10 days stained with Giemsa’s dye. Lower panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 17 days stained with Giemsa’s dye. C: Enrichment of cardiac myocytes in PrP + / SSEA1 – cells from EB at day 21. PrP − cells, PrP + cells and PrP + / SSEA1 – cells were sorted from EB at day 21 by FACS and were subjected to RT−PCR using indicating primers. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (−) ] did not show any fragment, indicating no contamination of cDNA by genomic <t>DNA.</t> EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PE, phycoerythrin; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription, SSEA1 – , SSEA1 negative; SSEA1 + , SSEA1 positive.
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1) Product Images from "Prion Protein and Stage Specific Embryo Antigen 1 as Selection Markers to Enrich the Fraction of Murine Embryonic Stem Cell-Derived Cardiomyocytes"

Article Title: Prion Protein and Stage Specific Embryo Antigen 1 as Selection Markers to Enrich the Fraction of Murine Embryonic Stem Cell-Derived Cardiomyocytes

Journal: Yonago Acta Medica

doi:

Characterization of PrP + / SSEA1 – cells isolated from EB at various periods. A: Prevalence of PrP + / SSEA1 + cells derived from EB at the various periods. PrP + cells were sorted from EB at Day 7, 14 and 21 by FACS. The ordinate showed the prevalence of PrP + cells and the abscissa indicated the prevalence of SSEA1 + cells. The upper control board showed the flow cytometry analysis as negative control and the lower control board showed the flow cytometry analysis of PrP + / SSEA1 + cells. B: Colongenic cell assay of cultured PrP + / SSEA1 – cells from EB at day 21. Either PrP + / SSEA1 + or PrP + / SSEA1 – cells of 10,000 cells were isolated from EB at day 21 by FACS and were subsequently cultured for another 10 and 17 days. Upper panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 10 days stained with Giemsa’s dye. Lower panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 17 days stained with Giemsa’s dye. C: Enrichment of cardiac myocytes in PrP + / SSEA1 – cells from EB at day 21. PrP − cells, PrP + cells and PrP + / SSEA1 – cells were sorted from EB at day 21 by FACS and were subjected to RT−PCR using indicating primers. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (−) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PE, phycoerythrin; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription, SSEA1 – , SSEA1 negative; SSEA1 + , SSEA1 positive.
Figure Legend Snippet: Characterization of PrP + / SSEA1 – cells isolated from EB at various periods. A: Prevalence of PrP + / SSEA1 + cells derived from EB at the various periods. PrP + cells were sorted from EB at Day 7, 14 and 21 by FACS. The ordinate showed the prevalence of PrP + cells and the abscissa indicated the prevalence of SSEA1 + cells. The upper control board showed the flow cytometry analysis as negative control and the lower control board showed the flow cytometry analysis of PrP + / SSEA1 + cells. B: Colongenic cell assay of cultured PrP + / SSEA1 – cells from EB at day 21. Either PrP + / SSEA1 + or PrP + / SSEA1 – cells of 10,000 cells were isolated from EB at day 21 by FACS and were subsequently cultured for another 10 and 17 days. Upper panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 10 days stained with Giemsa’s dye. Lower panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 17 days stained with Giemsa’s dye. C: Enrichment of cardiac myocytes in PrP + / SSEA1 – cells from EB at day 21. PrP − cells, PrP + cells and PrP + / SSEA1 – cells were sorted from EB at day 21 by FACS and were subjected to RT−PCR using indicating primers. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (−) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PE, phycoerythrin; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription, SSEA1 – , SSEA1 negative; SSEA1 + , SSEA1 positive.

Techniques Used: Isolation, Derivative Assay, FACS, Flow Cytometry, Cytometry, Negative Control, Cell Culture, Staining, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Fluorescence

mRNA level of pluripotent, ectodermal, endodermal, mesodermal and cardiac cell markers in PrP + cells from EB at day 7, 14 and 21. Cells were isolated by FACS, and then mRNA was extracted from them. Each set corresponds to the transcript amplified using the indicated primers. (+) : PrP + cell fraction, (–) : PrP – cell fraction. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (–) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription.
Figure Legend Snippet: mRNA level of pluripotent, ectodermal, endodermal, mesodermal and cardiac cell markers in PrP + cells from EB at day 7, 14 and 21. Cells were isolated by FACS, and then mRNA was extracted from them. Each set corresponds to the transcript amplified using the indicated primers. (+) : PrP + cell fraction, (–) : PrP – cell fraction. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (–) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription.

Techniques Used: Isolation, FACS, Amplification, Polymerase Chain Reaction, Fluorescence

Changes in mRNA level of pluripotent stem, ectodermal, endodermal, mesodermal and cardiac cell markers expressed in cultured PrP + cells from EB at various period. A: PrP + cells were sorted from EB at day 7 after differentiation by FACS and were cultured for another 7 days, and then mRNA was extracted from them. Each band corresponds to the transcript amplified using the indicated primers. B: PrP + cells were sorted from EB at day 14 by FACS and were subsequently cultured for another 7 days, and then their mRNA was extracted. C: PrP + cells were sorted from EB at day 21 by FACS and were subsequently cultured for another 7 days, and then their mRNA was extracted. AB1 d0: undifferentiated AB1 cells, (+) : PrP + cell fraction, (–) : PrP − cell fraction. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (–) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. d, day; EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription.
Figure Legend Snippet: Changes in mRNA level of pluripotent stem, ectodermal, endodermal, mesodermal and cardiac cell markers expressed in cultured PrP + cells from EB at various period. A: PrP + cells were sorted from EB at day 7 after differentiation by FACS and were cultured for another 7 days, and then mRNA was extracted from them. Each band corresponds to the transcript amplified using the indicated primers. B: PrP + cells were sorted from EB at day 14 by FACS and were subsequently cultured for another 7 days, and then their mRNA was extracted. C: PrP + cells were sorted from EB at day 21 by FACS and were subsequently cultured for another 7 days, and then their mRNA was extracted. AB1 d0: undifferentiated AB1 cells, (+) : PrP + cell fraction, (–) : PrP − cell fraction. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (–) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. d, day; EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription.

Techniques Used: Cell Culture, FACS, Amplification, Polymerase Chain Reaction, Fluorescence

2) Product Images from "Prion Protein and Stage Specific Embryo Antigen 1 as Selection Markers to Enrich the Fraction of Murine Embryonic Stem Cell-Derived Cardiomyocytes"

Article Title: Prion Protein and Stage Specific Embryo Antigen 1 as Selection Markers to Enrich the Fraction of Murine Embryonic Stem Cell-Derived Cardiomyocytes

Journal: Yonago Acta Medica

doi:

Characterization of PrP + / SSEA1 – cells isolated from EB at various periods. A: Prevalence of PrP + / SSEA1 + cells derived from EB at the various periods. PrP + cells were sorted from EB at Day 7, 14 and 21 by FACS. The ordinate showed the prevalence of PrP + cells and the abscissa indicated the prevalence of SSEA1 + cells. The upper control board showed the flow cytometry analysis as negative control and the lower control board showed the flow cytometry analysis of PrP + / SSEA1 + cells. B: Colongenic cell assay of cultured PrP + / SSEA1 – cells from EB at day 21. Either PrP + / SSEA1 + or PrP + / SSEA1 – cells of 10,000 cells were isolated from EB at day 21 by FACS and were subsequently cultured for another 10 and 17 days. Upper panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 10 days stained with Giemsa’s dye. Lower panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 17 days stained with Giemsa’s dye. C: Enrichment of cardiac myocytes in PrP + / SSEA1 – cells from EB at day 21. PrP − cells, PrP + cells and PrP + / SSEA1 – cells were sorted from EB at day 21 by FACS and were subjected to RT−PCR using indicating primers. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (−) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PE, phycoerythrin; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription, SSEA1 – , SSEA1 negative; SSEA1 + , SSEA1 positive.
Figure Legend Snippet: Characterization of PrP + / SSEA1 – cells isolated from EB at various periods. A: Prevalence of PrP + / SSEA1 + cells derived from EB at the various periods. PrP + cells were sorted from EB at Day 7, 14 and 21 by FACS. The ordinate showed the prevalence of PrP + cells and the abscissa indicated the prevalence of SSEA1 + cells. The upper control board showed the flow cytometry analysis as negative control and the lower control board showed the flow cytometry analysis of PrP + / SSEA1 + cells. B: Colongenic cell assay of cultured PrP + / SSEA1 – cells from EB at day 21. Either PrP + / SSEA1 + or PrP + / SSEA1 – cells of 10,000 cells were isolated from EB at day 21 by FACS and were subsequently cultured for another 10 and 17 days. Upper panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 10 days stained with Giemsa’s dye. Lower panels: colonies of cultured PrP + / SSEA1 + or PrP + / SSEA1 – cells from EB at day 21 for another 17 days stained with Giemsa’s dye. C: Enrichment of cardiac myocytes in PrP + / SSEA1 – cells from EB at day 21. PrP − cells, PrP + cells and PrP + / SSEA1 – cells were sorted from EB at day 21 by FACS and were subjected to RT−PCR using indicating primers. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (−) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PE, phycoerythrin; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription, SSEA1 – , SSEA1 negative; SSEA1 + , SSEA1 positive.

Techniques Used: Isolation, Derivative Assay, FACS, Flow Cytometry, Cytometry, Negative Control, Cell Culture, Staining, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Fluorescence

Changes in mRNA level of pluripotent stem, ectodermal, endodermal, mesodermal and cardiac cell markers expressed in cultured PrP + cells from EB at various period. A: PrP + cells were sorted from EB at day 7 after differentiation by FACS and were cultured for another 7 days, and then mRNA was extracted from them. Each band corresponds to the transcript amplified using the indicated primers. B: PrP + cells were sorted from EB at day 14 by FACS and were subsequently cultured for another 7 days, and then their mRNA was extracted. C: PrP + cells were sorted from EB at day 21 by FACS and were subsequently cultured for another 7 days, and then their mRNA was extracted. AB1 d0: undifferentiated AB1 cells, (+) : PrP + cell fraction, (–) : PrP − cell fraction. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (–) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. d, day; EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription.
Figure Legend Snippet: Changes in mRNA level of pluripotent stem, ectodermal, endodermal, mesodermal and cardiac cell markers expressed in cultured PrP + cells from EB at various period. A: PrP + cells were sorted from EB at day 7 after differentiation by FACS and were cultured for another 7 days, and then mRNA was extracted from them. Each band corresponds to the transcript amplified using the indicated primers. B: PrP + cells were sorted from EB at day 14 by FACS and were subsequently cultured for another 7 days, and then their mRNA was extracted. C: PrP + cells were sorted from EB at day 21 by FACS and were subsequently cultured for another 7 days, and then their mRNA was extracted. AB1 d0: undifferentiated AB1 cells, (+) : PrP + cell fraction, (–) : PrP − cell fraction. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (–) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. d, day; EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription.

Techniques Used: Cell Culture, FACS, Amplification, Polymerase Chain Reaction, Fluorescence

mRNA level of pluripotent, ectodermal, endodermal, mesodermal and cardiac cell markers in PrP + cells from EB at day 7, 14 and 21. Cells were isolated by FACS, and then mRNA was extracted from them. Each set corresponds to the transcript amplified using the indicated primers. (+) : PrP + cell fraction, (–) : PrP – cell fraction. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (–) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription.
Figure Legend Snippet: mRNA level of pluripotent, ectodermal, endodermal, mesodermal and cardiac cell markers in PrP + cells from EB at day 7, 14 and 21. Cells were isolated by FACS, and then mRNA was extracted from them. Each set corresponds to the transcript amplified using the indicated primers. (+) : PrP + cell fraction, (–) : PrP – cell fraction. PCR of Gapdh from RNA sample without reverse transcriptase [ Gapdh RT (–) ] did not show any fragment, indicating no contamination of cDNA by genomic DNA. EB, embryoid body; FACS, fluorescence activated cell sorting; mRNA, messenger RNA; PrP − , prion protein negative; PrP + , prion protein positive; RT, reverse transcription.

Techniques Used: Isolation, FACS, Amplification, Polymerase Chain Reaction, Fluorescence

3) Product Images from "The Two-Component Regulators GacS and GacA Positively Regulate a Nonfluorescent Siderophore through the Gac/Rsm Signaling Cascade in High-Siderophore-Yielding Pseudomonas sp. Strain HYS"

Article Title: The Two-Component Regulators GacS and GacA Positively Regulate a Nonfluorescent Siderophore through the Gac/Rsm Signaling Cascade in High-Siderophore-Yielding Pseudomonas sp. Strain HYS

Journal: Journal of Bacteriology

doi: 10.1128/JB.01756-14

RT-PCR of RNA extracted from Pseudomonas sp. HYS with ORF connecting primer pairs (orf1-orf2RT-1 plus orf1-orf2RT-2, orf2-orf3RT-1 plus orf2-orf3RT-2, and orf3-orf4RT-1 plus orf3-orf4RT-2). The different lanes represent different templates: lanes 1, cDNA; lanes 2, genomic DNA as a positive control; lanes 3, RNA without reverse transcription as a negative control; lanes 4, ddH 2 O as a blank control.
Figure Legend Snippet: RT-PCR of RNA extracted from Pseudomonas sp. HYS with ORF connecting primer pairs (orf1-orf2RT-1 plus orf1-orf2RT-2, orf2-orf3RT-1 plus orf2-orf3RT-2, and orf3-orf4RT-1 plus orf3-orf4RT-2). The different lanes represent different templates: lanes 1, cDNA; lanes 2, genomic DNA as a positive control; lanes 3, RNA without reverse transcription as a negative control; lanes 4, ddH 2 O as a blank control.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Positive Control, Negative Control

4) Product Images from "Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons"

Article Title: Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons

Journal: Biotechnology for Biofuels

doi: 10.1186/s13068-018-1323-5

Identification of the co-transcription of structural genes in the CELO1 and CELO2 operon using RT-PCR. cDNA was isolated and RT-PCR was performed as described in the text (for lane 2–8). The RNA and genomic DNA of B. coagulans NL01 was used as negative (for lane 1 and 9) and positive control (for lane 10–16), respectively. The amplified overlapping regions spanned celA – celB (lane 1, 2, and 10), celB – hyp (lane 3 and 11), hyp – celC (lane 4 and 12), celC – pbgl (lane 5 and 13), celB – celA (lane 6, 9, and 14), celA – celX (lane 7 and 15), celX – celC (lane 8 and 16)
Figure Legend Snippet: Identification of the co-transcription of structural genes in the CELO1 and CELO2 operon using RT-PCR. cDNA was isolated and RT-PCR was performed as described in the text (for lane 2–8). The RNA and genomic DNA of B. coagulans NL01 was used as negative (for lane 1 and 9) and positive control (for lane 10–16), respectively. The amplified overlapping regions spanned celA – celB (lane 1, 2, and 10), celB – hyp (lane 3 and 11), hyp – celC (lane 4 and 12), celC – pbgl (lane 5 and 13), celB – celA (lane 6, 9, and 14), celA – celX (lane 7 and 15), celX – celC (lane 8 and 16)

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Isolation, Positive Control, Amplification

5) Product Images from "Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons"

Article Title: Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons

Journal: Biotechnology for Biofuels

doi: 10.1186/s13068-018-1323-5

Identification of the co-transcription of structural genes in the CELO1 and CELO2 operon using RT-PCR. cDNA was isolated and RT-PCR was performed as described in the text (for lane 2–8). The RNA and genomic DNA of B. coagulans NL01 was used as negative (for lane 1 and 9) and positive control (for lane 10–16), respectively. The amplified overlapping regions spanned celA – celB (lane 1, 2, and 10), celB – hyp (lane 3 and 11), hyp – celC (lane 4 and 12), celC – pbgl (lane 5 and 13), celB – celA (lane 6, 9, and 14), celA – celX (lane 7 and 15), celX – celC (lane 8 and 16)
Figure Legend Snippet: Identification of the co-transcription of structural genes in the CELO1 and CELO2 operon using RT-PCR. cDNA was isolated and RT-PCR was performed as described in the text (for lane 2–8). The RNA and genomic DNA of B. coagulans NL01 was used as negative (for lane 1 and 9) and positive control (for lane 10–16), respectively. The amplified overlapping regions spanned celA – celB (lane 1, 2, and 10), celB – hyp (lane 3 and 11), hyp – celC (lane 4 and 12), celC – pbgl (lane 5 and 13), celB – celA (lane 6, 9, and 14), celA – celX (lane 7 and 15), celX – celC (lane 8 and 16)

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Isolation, Positive Control, Amplification

6) Product Images from "Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice"

Article Title: Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice

Journal: International Journal of Genomics

doi: 10.1155/2018/5480617

Generation and identification of OsCTZFP8 -overexpressing rice. (a) Schematic representation of the T-DNA region on the P Ubi : OsCTZFP8 construct. The construct contains the bar gene and a maize ubiquitin (Ubi) promoter. The small double arrow bar represents the Ubi -OsCTZFP8 probe used for Southern blot analysis. (b) Agrobacterium -mediated rice seed transformation. The procedures included induction of callus (A), subculture (B), cocultivation and Basta screening (C), differentiation (D), rooting (E), and planet acclimatization (F). (c) PCR analyses for T 0 transgenic rice using bar gene-specific primers. PC: plasmid DNA; NT: nontransgenic control plant; 1~19: T 0 generation of independent transgenic rice. (d) LibertyLink strip detections of T 0 transgenic rice plants; NT: nontransgenic control plant; 1~10: T 0 transgenic plants; C: control line; T: test line. (e) Southern blot analysis of OsCTZFP8 -overexpressing lines. Hind III-digested genomic DNA from T 1 generation was separated on agarose gel and hybridized with DIG-labeled Ubi -OsCTZFP8 probe; NT: nontransgenic control plants; OE-1~OE-8: overexpressing lines; PC: plasmid DNA. (f) mRNA expression of OsCTZFP8 in overexpressing lines. One-step RT-PCR was performed using total RNA extracted from 2-week-old rice leaves. The expression of OsActin1 was used as an internal control; NT: nontransgenic control plants; OE-1~OE-6: single-copy insertion overexpressing lines. (g) Basta resistance segregation assay. Seeds were germinated on 1/2 MS medium (30 mg/L Basta), and Basta resistance were determined at the 5th day. The experiments were performed in two repetitions; NT: nontransgenic control plants; OE-1~6 and OE-3-2: overexpressing lines.
Figure Legend Snippet: Generation and identification of OsCTZFP8 -overexpressing rice. (a) Schematic representation of the T-DNA region on the P Ubi : OsCTZFP8 construct. The construct contains the bar gene and a maize ubiquitin (Ubi) promoter. The small double arrow bar represents the Ubi -OsCTZFP8 probe used for Southern blot analysis. (b) Agrobacterium -mediated rice seed transformation. The procedures included induction of callus (A), subculture (B), cocultivation and Basta screening (C), differentiation (D), rooting (E), and planet acclimatization (F). (c) PCR analyses for T 0 transgenic rice using bar gene-specific primers. PC: plasmid DNA; NT: nontransgenic control plant; 1~19: T 0 generation of independent transgenic rice. (d) LibertyLink strip detections of T 0 transgenic rice plants; NT: nontransgenic control plant; 1~10: T 0 transgenic plants; C: control line; T: test line. (e) Southern blot analysis of OsCTZFP8 -overexpressing lines. Hind III-digested genomic DNA from T 1 generation was separated on agarose gel and hybridized with DIG-labeled Ubi -OsCTZFP8 probe; NT: nontransgenic control plants; OE-1~OE-8: overexpressing lines; PC: plasmid DNA. (f) mRNA expression of OsCTZFP8 in overexpressing lines. One-step RT-PCR was performed using total RNA extracted from 2-week-old rice leaves. The expression of OsActin1 was used as an internal control; NT: nontransgenic control plants; OE-1~OE-6: single-copy insertion overexpressing lines. (g) Basta resistance segregation assay. Seeds were germinated on 1/2 MS medium (30 mg/L Basta), and Basta resistance were determined at the 5th day. The experiments were performed in two repetitions; NT: nontransgenic control plants; OE-1~6 and OE-3-2: overexpressing lines.

Techniques Used: Construct, Southern Blot, Transformation Assay, Polymerase Chain Reaction, Transgenic Assay, Plasmid Preparation, Stripping Membranes, Agarose Gel Electrophoresis, Labeling, Expressing, Reverse Transcription Polymerase Chain Reaction, Mass Spectrometry

7) Product Images from "Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice"

Article Title: Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice

Journal: International Journal of Genomics

doi: 10.1155/2018/5480617

Generation and identification of OsCTZFP8 -overexpressing rice. (a) Schematic representation of the T-DNA region on the P Ubi : OsCTZFP8 construct. The construct contains the bar gene and a maize ubiquitin (Ubi) promoter. The small double arrow bar represents the Ubi -OsCTZFP8 probe used for Southern blot analysis. (b) Agrobacterium -mediated rice seed transformation. The procedures included induction of callus (A), subculture (B), cocultivation and Basta screening (C), differentiation (D), rooting (E), and planet acclimatization (F). (c) PCR analyses for T 0 transgenic rice using bar gene-specific primers. PC: plasmid DNA; NT: nontransgenic control plant; 1~19: T 0 generation of independent transgenic rice. (d) LibertyLink strip detections of T 0 transgenic rice plants; NT: nontransgenic control plant; 1~10: T 0 transgenic plants; C: control line; T: test line. (e) Southern blot analysis of OsCTZFP8 -overexpressing lines. Hind III-digested genomic DNA from T 1 generation was separated on agarose gel and hybridized with DIG-labeled Ubi -OsCTZFP8 probe; NT: nontransgenic control plants; OE-1~OE-8: overexpressing lines; PC: plasmid DNA. (f) mRNA expression of OsCTZFP8 in overexpressing lines. One-step RT-PCR was performed using total RNA extracted from 2-week-old rice leaves. The expression of OsActin1 was used as an internal control; NT: nontransgenic control plants; OE-1~OE-6: single-copy insertion overexpressing lines. (g) Basta resistance segregation assay. Seeds were germinated on 1/2 MS medium (30 mg/L Basta), and Basta resistance were determined at the 5th day. The experiments were performed in two repetitions; NT: nontransgenic control plants; OE-1~6 and OE-3-2: overexpressing lines.
Figure Legend Snippet: Generation and identification of OsCTZFP8 -overexpressing rice. (a) Schematic representation of the T-DNA region on the P Ubi : OsCTZFP8 construct. The construct contains the bar gene and a maize ubiquitin (Ubi) promoter. The small double arrow bar represents the Ubi -OsCTZFP8 probe used for Southern blot analysis. (b) Agrobacterium -mediated rice seed transformation. The procedures included induction of callus (A), subculture (B), cocultivation and Basta screening (C), differentiation (D), rooting (E), and planet acclimatization (F). (c) PCR analyses for T 0 transgenic rice using bar gene-specific primers. PC: plasmid DNA; NT: nontransgenic control plant; 1~19: T 0 generation of independent transgenic rice. (d) LibertyLink strip detections of T 0 transgenic rice plants; NT: nontransgenic control plant; 1~10: T 0 transgenic plants; C: control line; T: test line. (e) Southern blot analysis of OsCTZFP8 -overexpressing lines. Hind III-digested genomic DNA from T 1 generation was separated on agarose gel and hybridized with DIG-labeled Ubi -OsCTZFP8 probe; NT: nontransgenic control plants; OE-1~OE-8: overexpressing lines; PC: plasmid DNA. (f) mRNA expression of OsCTZFP8 in overexpressing lines. One-step RT-PCR was performed using total RNA extracted from 2-week-old rice leaves. The expression of OsActin1 was used as an internal control; NT: nontransgenic control plants; OE-1~OE-6: single-copy insertion overexpressing lines. (g) Basta resistance segregation assay. Seeds were germinated on 1/2 MS medium (30 mg/L Basta), and Basta resistance were determined at the 5th day. The experiments were performed in two repetitions; NT: nontransgenic control plants; OE-1~6 and OE-3-2: overexpressing lines.

Techniques Used: Construct, Southern Blot, Transformation Assay, Polymerase Chain Reaction, Transgenic Assay, Plasmid Preparation, Stripping Membranes, Agarose Gel Electrophoresis, Labeling, Expressing, Reverse Transcription Polymerase Chain Reaction, Mass Spectrometry

8) Product Images from "Transcriptional quiescence of paternal mtDNA in cyprinid fish embryos"

Article Title: Transcriptional quiescence of paternal mtDNA in cyprinid fish embryos

Journal: Scientific Reports

doi: 10.1038/srep28571

Origin and inheritance of mtDNA in cyprinid fishes. (a ) Goldfish red variety and blunt-snout bream used for reciprocal hybridization. ( b ) Scheme of PCR primers for cytb and tfam, showing primers specific to goldfish (open arrowhead) or blunt-snout bream (grey arrowhead) and common to both species (black arrowheads). For more details see Figs S1 and S2 . ( c , d ) Specificity and sensitivity of mtDNA detection by PCR. Genomic DNA mixtures between goldfish and the blunt-snout bream were prepared at various ratios and used for PCR analysis by using species-specific cytb primers. Notably, an amount as low as 1‰ is easily detectable. ( e ) PCR analysis of mtDNA origins, showing the absence of sperm cytb in the hybrid larvae between female goldfish and male blunt snout bream and the coexistence of maternal and paternal cytb in the zygotes from reciprocal hybridization. Asterisks depict sperm mtDNA. DNA was isolated from 20 pooled zygotes and embryos at each stage from parental species and reciprocal hybridization and analyzed by PCR at representative stages indicated. β-actin was used as a loading control. PCR and gels were run under the same conditions. B, blunt-snout bream; G, goldfish; BG, blunt-snout bream female × goldfish male; GB, goldfish female × blunt-snout bream male.
Figure Legend Snippet: Origin and inheritance of mtDNA in cyprinid fishes. (a ) Goldfish red variety and blunt-snout bream used for reciprocal hybridization. ( b ) Scheme of PCR primers for cytb and tfam, showing primers specific to goldfish (open arrowhead) or blunt-snout bream (grey arrowhead) and common to both species (black arrowheads). For more details see Figs S1 and S2 . ( c , d ) Specificity and sensitivity of mtDNA detection by PCR. Genomic DNA mixtures between goldfish and the blunt-snout bream were prepared at various ratios and used for PCR analysis by using species-specific cytb primers. Notably, an amount as low as 1‰ is easily detectable. ( e ) PCR analysis of mtDNA origins, showing the absence of sperm cytb in the hybrid larvae between female goldfish and male blunt snout bream and the coexistence of maternal and paternal cytb in the zygotes from reciprocal hybridization. Asterisks depict sperm mtDNA. DNA was isolated from 20 pooled zygotes and embryos at each stage from parental species and reciprocal hybridization and analyzed by PCR at representative stages indicated. β-actin was used as a loading control. PCR and gels were run under the same conditions. B, blunt-snout bream; G, goldfish; BG, blunt-snout bream female × goldfish male; GB, goldfish female × blunt-snout bream male.

Techniques Used: Hybridization, Polymerase Chain Reaction, Isolation

9) Product Images from "Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401"

Article Title: Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401

Journal: Frontiers in Cellular and Infection Microbiology

doi: 10.3389/fcimb.2018.00032

H. parasuis can take up heterologous DNA but degrade it after the bacteria was passaged for one generation. The 16S rDNA of different donor genomic DNA to transform wild type H. parasuis SC1401 was examined by PCR. Kan-cassette of homologous derivative SC1401Δ htrA ::kan was examined as a control. Lane 1: Respective genomic DNA (positive control). Lane 2: Pellet. Lane 3: Dnase-treated supernatant. Lane 4: Passaged bacteria. M: DNA ladder (DL5000, TaKaRa, Japan).
Figure Legend Snippet: H. parasuis can take up heterologous DNA but degrade it after the bacteria was passaged for one generation. The 16S rDNA of different donor genomic DNA to transform wild type H. parasuis SC1401 was examined by PCR. Kan-cassette of homologous derivative SC1401Δ htrA ::kan was examined as a control. Lane 1: Respective genomic DNA (positive control). Lane 2: Pellet. Lane 3: Dnase-treated supernatant. Lane 4: Passaged bacteria. M: DNA ladder (DL5000, TaKaRa, Japan).

Techniques Used: Polymerase Chain Reaction, Positive Control

10) Product Images from "Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401"

Article Title: Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401

Journal: Frontiers in Cellular and Infection Microbiology

doi: 10.3389/fcimb.2018.00032

H. parasuis can take up heterologous DNA but degrade it after the bacteria was passaged for one generation. The 16S rDNA of different donor genomic DNA to transform wild type H. parasuis SC1401 was examined by PCR. Kan-cassette of homologous derivative SC1401Δ htrA ::kan was examined as a control. Lane 1: Respective genomic DNA (positive control). Lane 2: Pellet. Lane 3: Dnase-treated supernatant. Lane 4: Passaged bacteria. M: DNA ladder (DL5000, TaKaRa, Japan).
Figure Legend Snippet: H. parasuis can take up heterologous DNA but degrade it after the bacteria was passaged for one generation. The 16S rDNA of different donor genomic DNA to transform wild type H. parasuis SC1401 was examined by PCR. Kan-cassette of homologous derivative SC1401Δ htrA ::kan was examined as a control. Lane 1: Respective genomic DNA (positive control). Lane 2: Pellet. Lane 3: Dnase-treated supernatant. Lane 4: Passaged bacteria. M: DNA ladder (DL5000, TaKaRa, Japan).

Techniques Used: Polymerase Chain Reaction, Positive Control

11) Product Images from "Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation"

Article Title: Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation

Journal: Scientific Reports

doi: 10.1038/srep15892

DNA damage level is higher in the parg1-4 mutant than that in Col-0 plants under genotoxic stress. ( A ) Expression level changes of genes involved in DNA double-strand break repair in roots of Col-0 and parg1-4 seedlings. The data represent the mean values of three replicates ± SD. ( C ) control; ( B ) bleomycin at 20 μg ml −1 . ( B ) Comet assay of the DNA damage levels of Col-0 and parg1-4 seedlings grown on plates with or without (control) 20 μg ml −1 bleomycin for 10 days. The percentage of DNA in comet tails was analyzed and quantified by CASP software ( http://sourceforge.net/projects/casp/ ) and used as an indicator of DNA damage level. 100 nuclei for each treatment were randomly selected and imaged. The bar size represents proportion of nuclei falling into the ranges of damage level indicated by different colors, and the images with percentages beside it indicate the examples of damaged nuclei. ( C ) DNA fragmentation assay showed that genomic DNA is more damaged in parg1-4 than in Col-0.
Figure Legend Snippet: DNA damage level is higher in the parg1-4 mutant than that in Col-0 plants under genotoxic stress. ( A ) Expression level changes of genes involved in DNA double-strand break repair in roots of Col-0 and parg1-4 seedlings. The data represent the mean values of three replicates ± SD. ( C ) control; ( B ) bleomycin at 20 μg ml −1 . ( B ) Comet assay of the DNA damage levels of Col-0 and parg1-4 seedlings grown on plates with or without (control) 20 μg ml −1 bleomycin for 10 days. The percentage of DNA in comet tails was analyzed and quantified by CASP software ( http://sourceforge.net/projects/casp/ ) and used as an indicator of DNA damage level. 100 nuclei for each treatment were randomly selected and imaged. The bar size represents proportion of nuclei falling into the ranges of damage level indicated by different colors, and the images with percentages beside it indicate the examples of damaged nuclei. ( C ) DNA fragmentation assay showed that genomic DNA is more damaged in parg1-4 than in Col-0.

Techniques Used: Mutagenesis, Expressing, Single Cell Gel Electrophoresis, Software, DNA Fragmentation Assay

12) Product Images from "Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis"

Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis

Journal: MicrobiologyOpen

doi: 10.1002/mbo3.928

PCR test result of DNA. Total RNA was reverse transcript to cDNA and test by specific PCR primers. 16S‐F/R targeted to 16S rRNA while rRNA‐I/rRNA‐O targeted to the space between rRNA and tyrS (tyrosyl‐tRNA synthetase) sequences which were not in the same transcript. (a) Samples treated with 0.85% NaCl. (b) Samples treated with CuSO 4 . P, genomic DNA of Clavibacter michiganensis . N, negative control
Figure Legend Snippet: PCR test result of DNA. Total RNA was reverse transcript to cDNA and test by specific PCR primers. 16S‐F/R targeted to 16S rRNA while rRNA‐I/rRNA‐O targeted to the space between rRNA and tyrS (tyrosyl‐tRNA synthetase) sequences which were not in the same transcript. (a) Samples treated with 0.85% NaCl. (b) Samples treated with CuSO 4 . P, genomic DNA of Clavibacter michiganensis . N, negative control

Techniques Used: Polymerase Chain Reaction, Negative Control

13) Product Images from "The Impact of Genome Region of Difference 4 (RD4) on Mycobacterial Virulence and BCG Efficacy"

Article Title: The Impact of Genome Region of Difference 4 (RD4) on Mycobacterial Virulence and BCG Efficacy

Journal: Frontiers in Cellular and Infection Microbiology

doi: 10.3389/fcimb.2017.00239

Molecular characterizations of RD4 knock-in strains of M. bovis BCG and M . marinum . (A) PCR analysis of mycobacterial genomic DNA. Chromosomal DNA from two BCG strains (BCG-Japan, BCG-China) and two M. marinum strains (1218R, 535) transformed with pMV306-Rv1501-1508c or pMV306-Rv1501-1516c were isolated and used as the template for PCR amplifications. PCR primers specific for Rv1507a and Rv1515c were used to amplify these two genes. Rv1507a was detected in all strains harboring Rv1501-1508c or Rv1501-1516c. Rv1515c was detected in strains harboring Rv1501-1516c. Strains transformed with empty vector pMV306 were used as the negative control. (B) RT-PCR analysis of the expression of Rv1501, Rv1507c, and Rv1516c in recombinant strains of BCG-China and M. marinum 535. Lanes 1-6: RNA was isolated from indicated strains and treated with DNase, which was then subjected to reverse transcription PCR analysis; lane 7: the same sample as lane 6 except no RT-PCR was performed. (C,D) Western blot analysis using antisera against Rv1505c. Cell lysates were prepared from indicated strains and subjected to Western blot analysis. The low panel in each figure is the Coomassie blue staining which served as the loading control.
Figure Legend Snippet: Molecular characterizations of RD4 knock-in strains of M. bovis BCG and M . marinum . (A) PCR analysis of mycobacterial genomic DNA. Chromosomal DNA from two BCG strains (BCG-Japan, BCG-China) and two M. marinum strains (1218R, 535) transformed with pMV306-Rv1501-1508c or pMV306-Rv1501-1516c were isolated and used as the template for PCR amplifications. PCR primers specific for Rv1507a and Rv1515c were used to amplify these two genes. Rv1507a was detected in all strains harboring Rv1501-1508c or Rv1501-1516c. Rv1515c was detected in strains harboring Rv1501-1516c. Strains transformed with empty vector pMV306 were used as the negative control. (B) RT-PCR analysis of the expression of Rv1501, Rv1507c, and Rv1516c in recombinant strains of BCG-China and M. marinum 535. Lanes 1-6: RNA was isolated from indicated strains and treated with DNase, which was then subjected to reverse transcription PCR analysis; lane 7: the same sample as lane 6 except no RT-PCR was performed. (C,D) Western blot analysis using antisera against Rv1505c. Cell lysates were prepared from indicated strains and subjected to Western blot analysis. The low panel in each figure is the Coomassie blue staining which served as the loading control.

Techniques Used: Knock-In, Polymerase Chain Reaction, Transformation Assay, Isolation, Plasmid Preparation, Negative Control, Reverse Transcription Polymerase Chain Reaction, Expressing, Recombinant, Western Blot, Staining

14) Product Images from "Arsenic resistance strategy in Pantoea sp. IMH: Organization, function and evolution of ars genes"

Article Title: Arsenic resistance strategy in Pantoea sp. IMH: Organization, function and evolution of ars genes

Journal: Scientific Reports

doi: 10.1038/srep39195

Analysis of co-transcript unit in the ars clusters of Pantoea sp. IMH by RT-PCR. ( a ) Map position of ars genes and the primers for RT-PCR analysis. Primers used and amplified products (numbered) are given below the schematic representation of the genes. (b) Result of RT-PCR reactions with RNA from IMH grown in 1 mM As(V) condition. The numbering on the top of the gels corresponds to the product numbers drawn schematically in the outline given above. M, DNA mark; (+), positive control in which genomic DNA was used as template in the RT-PCR; RT, standard RT-PCR reaction; (−), negative control in which no reverse transcriptase was added to the RT reaction.
Figure Legend Snippet: Analysis of co-transcript unit in the ars clusters of Pantoea sp. IMH by RT-PCR. ( a ) Map position of ars genes and the primers for RT-PCR analysis. Primers used and amplified products (numbered) are given below the schematic representation of the genes. (b) Result of RT-PCR reactions with RNA from IMH grown in 1 mM As(V) condition. The numbering on the top of the gels corresponds to the product numbers drawn schematically in the outline given above. M, DNA mark; (+), positive control in which genomic DNA was used as template in the RT-PCR; RT, standard RT-PCR reaction; (−), negative control in which no reverse transcriptase was added to the RT reaction.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Amplification, Positive Control, Negative Control

15) Product Images from "A Splice Mutation in the PHKG1 Gene Causes High Glycogen Content and Low Meat Quality in Pig Skeletal Muscle"

Article Title: A Splice Mutation in the PHKG1 Gene Causes High Glycogen Content and Low Meat Quality in Pig Skeletal Muscle

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.1004710

Identification of the g.8283C > A splice mutation in the PHKG1 gene. (A) RT-PCR products of the PHKG1 gene on a 2.5% agarose gel, amplified from total RNA from animals with different QTL genotypes ( QQ , Qq and qq ). Two DNA bands of 146 bp and 114 bp with different intensity were observed. (B) Sequence analysis of the RT-PCR products. A 32-bp deletion in exon 10 was detected in QQ and Qq animals. (C) PCR products of the PHKG1 gene on a 2.5% agarose gel, amplified from genomic DNA from animals with different QTL genotypes ( QQ , Qq and qq ). (D) Sequence analysis of the PCR products. A point mutation (g. 8283C > A) was identified in QQ and Qq individuals. (E) PHKG1 genomic sequence from exon 9 to exon 10. Intronic sequence is in black and lower case, and exonic sequence in blue and upper case. The normal splice-acceptor and -donor sequences (lower case) and the cryptic splice-donor sequences (upper case) are underlined with two red nucleotide letters in the center. The C > A mutation is denoted as “M” in red. (F) Sequence analysis of a heterozygote at the g.8283C > A mutation site. In genomic DNA from a heterozygote, the C and A peaks (the position is indicated by “M” and marked by the red bar) were of equal height in sequence of genomic DNA, as expected. Sequence of the cDNA product from the same heterozygote showed a major peak corresponding to the wild-type sequence and a small peak corresponding to the mutant sequence (the +2 position of exon 10 where the nucleotide T belong to the 32-bp deleted portion is marked by the blue bar).
Figure Legend Snippet: Identification of the g.8283C > A splice mutation in the PHKG1 gene. (A) RT-PCR products of the PHKG1 gene on a 2.5% agarose gel, amplified from total RNA from animals with different QTL genotypes ( QQ , Qq and qq ). Two DNA bands of 146 bp and 114 bp with different intensity were observed. (B) Sequence analysis of the RT-PCR products. A 32-bp deletion in exon 10 was detected in QQ and Qq animals. (C) PCR products of the PHKG1 gene on a 2.5% agarose gel, amplified from genomic DNA from animals with different QTL genotypes ( QQ , Qq and qq ). (D) Sequence analysis of the PCR products. A point mutation (g. 8283C > A) was identified in QQ and Qq individuals. (E) PHKG1 genomic sequence from exon 9 to exon 10. Intronic sequence is in black and lower case, and exonic sequence in blue and upper case. The normal splice-acceptor and -donor sequences (lower case) and the cryptic splice-donor sequences (upper case) are underlined with two red nucleotide letters in the center. The C > A mutation is denoted as “M” in red. (F) Sequence analysis of a heterozygote at the g.8283C > A mutation site. In genomic DNA from a heterozygote, the C and A peaks (the position is indicated by “M” and marked by the red bar) were of equal height in sequence of genomic DNA, as expected. Sequence of the cDNA product from the same heterozygote showed a major peak corresponding to the wild-type sequence and a small peak corresponding to the mutant sequence (the +2 position of exon 10 where the nucleotide T belong to the 32-bp deleted portion is marked by the blue bar).

Techniques Used: Mutagenesis, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Amplification, Sequencing, Polymerase Chain Reaction

16) Product Images from "Molecular study on the carAB operon reveals that carB gene is required for swimming and biofilm formation in Xanthomonas citri subsp. citri"

Article Title: Molecular study on the carAB operon reveals that carB gene is required for swimming and biofilm formation in Xanthomonas citri subsp. citri

Journal: BMC Microbiology

doi: 10.1186/s12866-015-0555-9

Schematic representation of the carAB operon and the RT-PCR strategy. a The grey rectangles depicted the open reading frames of the operon and their lengths in base pairs. The arrows represent the sizes and approximate locations in the PCR analysis with primer sets. All forward and reverse primers were gene-specific. b PCR products by using gDNA as template. c and d PCR products from first strand cDNA. The DNA marker was DL5000
Figure Legend Snippet: Schematic representation of the carAB operon and the RT-PCR strategy. a The grey rectangles depicted the open reading frames of the operon and their lengths in base pairs. The arrows represent the sizes and approximate locations in the PCR analysis with primer sets. All forward and reverse primers were gene-specific. b PCR products by using gDNA as template. c and d PCR products from first strand cDNA. The DNA marker was DL5000

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Marker

17) Product Images from "Deletion of Endo-β-1,4-Xylanase VmXyl1 Impacts the Virulence of Valsa mali in Apple Tree"

Article Title: Deletion of Endo-β-1,4-Xylanase VmXyl1 Impacts the Virulence of Valsa mali in Apple Tree

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2018.00663

The electrophoretogram of VmXyl1 cloning process from the Valsa mali . (A) The RT-PCR amplification of the open reading frame of VmXyl1 . The lane M represents DNA marker DL2000. In lane 1, a 1320 bp fragment was obtained using the primer pair VmXyl1 F/ VmXyl1 R with the first-strand cDNA as a template. (B) The PCR amplification of DNA fragment of the VmXyl1 . In lane 2, a 1378 bp fragment was obtained with genomic DNA as the template. (C) The cloning of VmXyl1 by the 3′-RACE. In lane 3, a 231 bp fragment was obtained with the primer pair Inner Primer/IN3RC. (D) The cloning of VmXyl1 by the 5′-RACE with the primer pair NGSP1/UPM. In lane 4, two fragments were obtained in the nested PCR and a 272 bp band was the 5′-end cDNA region of VmXyl1 .
Figure Legend Snippet: The electrophoretogram of VmXyl1 cloning process from the Valsa mali . (A) The RT-PCR amplification of the open reading frame of VmXyl1 . The lane M represents DNA marker DL2000. In lane 1, a 1320 bp fragment was obtained using the primer pair VmXyl1 F/ VmXyl1 R with the first-strand cDNA as a template. (B) The PCR amplification of DNA fragment of the VmXyl1 . In lane 2, a 1378 bp fragment was obtained with genomic DNA as the template. (C) The cloning of VmXyl1 by the 3′-RACE. In lane 3, a 231 bp fragment was obtained with the primer pair Inner Primer/IN3RC. (D) The cloning of VmXyl1 by the 5′-RACE with the primer pair NGSP1/UPM. In lane 4, two fragments were obtained in the nested PCR and a 272 bp band was the 5′-end cDNA region of VmXyl1 .

Techniques Used: Clone Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Marker, Polymerase Chain Reaction, Nested PCR

18) Product Images from "Deletion of Endo-β-1,4-Xylanase VmXyl1 Impacts the Virulence of Valsa mali in Apple Tree"

Article Title: Deletion of Endo-β-1,4-Xylanase VmXyl1 Impacts the Virulence of Valsa mali in Apple Tree

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2018.00663

The electrophoretogram of VmXyl1 cloning process from the Valsa mali . (A) The RT-PCR amplification of the open reading frame of VmXyl1 . The lane M represents DNA marker DL2000. In lane 1, a 1320 bp fragment was obtained using the primer pair VmXyl1 F/ VmXyl1 R with the first-strand cDNA as a template. (B) The PCR amplification of DNA fragment of the VmXyl1 . In lane 2, a 1378 bp fragment was obtained with genomic DNA as the template. (C) The cloning of VmXyl1 by the 3′-RACE. In lane 3, a 231 bp fragment was obtained with the primer pair Inner Primer/IN3RC. (D) The cloning of VmXyl1 by the 5′-RACE with the primer pair NGSP1/UPM. In lane 4, two fragments were obtained in the nested PCR and a 272 bp band was the 5′-end cDNA region of VmXyl1 .
Figure Legend Snippet: The electrophoretogram of VmXyl1 cloning process from the Valsa mali . (A) The RT-PCR amplification of the open reading frame of VmXyl1 . The lane M represents DNA marker DL2000. In lane 1, a 1320 bp fragment was obtained using the primer pair VmXyl1 F/ VmXyl1 R with the first-strand cDNA as a template. (B) The PCR amplification of DNA fragment of the VmXyl1 . In lane 2, a 1378 bp fragment was obtained with genomic DNA as the template. (C) The cloning of VmXyl1 by the 3′-RACE. In lane 3, a 231 bp fragment was obtained with the primer pair Inner Primer/IN3RC. (D) The cloning of VmXyl1 by the 5′-RACE with the primer pair NGSP1/UPM. In lane 4, two fragments were obtained in the nested PCR and a 272 bp band was the 5′-end cDNA region of VmXyl1 .

Techniques Used: Clone Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Marker, Polymerase Chain Reaction, Nested PCR

19) Product Images from "Biological Role of Trichoderma harzianum-Derived Platelet-Activating Factor Acetylhydrolase (PAF-AH) on Stress Response and Antagonism"

Article Title: Biological Role of Trichoderma harzianum-Derived Platelet-Activating Factor Acetylhydrolase (PAF-AH) on Stress Response and Antagonism

Journal: PLoS ONE

doi: 10.1371/journal.pone.0100367

Screening of PAF-AH knockout transformants. (A) Physical map of homologous recombination. (B) Identification of transformants by PCR: 1, fragment of the hygromycin B resistance gene ( hyg ); 2, amplified fragment of PAF-AH from genomic DNA; 3, amplified T-DNA fragments adjusted to the right border of plasmid; 4, fragment amplified with primers PAF-AH-UP-F and Hyg-R. (C) Southern blot to verify T-DNA insertion copies of knockout transformants. The 450 bp fragment amplified from the hyg gene was labeled with 32 P-dCTP as probe 1. (D) Southern blot to confirm PAF-AH was replaced using the 500 bp fragment of PAF-AH as probe 2. WT, wild type strain; P, plasmid; KO15 and KO40: PAF-AH knockout transformants; M: DNA marker.
Figure Legend Snippet: Screening of PAF-AH knockout transformants. (A) Physical map of homologous recombination. (B) Identification of transformants by PCR: 1, fragment of the hygromycin B resistance gene ( hyg ); 2, amplified fragment of PAF-AH from genomic DNA; 3, amplified T-DNA fragments adjusted to the right border of plasmid; 4, fragment amplified with primers PAF-AH-UP-F and Hyg-R. (C) Southern blot to verify T-DNA insertion copies of knockout transformants. The 450 bp fragment amplified from the hyg gene was labeled with 32 P-dCTP as probe 1. (D) Southern blot to confirm PAF-AH was replaced using the 500 bp fragment of PAF-AH as probe 2. WT, wild type strain; P, plasmid; KO15 and KO40: PAF-AH knockout transformants; M: DNA marker.

Techniques Used: Knock-Out, Homologous Recombination, Polymerase Chain Reaction, Amplification, Plasmid Preparation, Southern Blot, Labeling, Marker

20) Product Images from "A Minimal Nitrogen Fixation Gene Cluster from Paenibacillus sp. WLY78 Enables Expression of Active Nitrogenase in Escherichia coli"

Article Title: A Minimal Nitrogen Fixation Gene Cluster from Paenibacillus sp. WLY78 Enables Expression of Active Nitrogenase in Escherichia coli

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.1003865

The nif genes of Paenibacillus sp. WLY78 are organized in an operon as determined by RT-PCR. (A) Outline of the strategy. Primers used and amplified products (numbered) are given below the schematic representation of the genes. (B) Result of RT-PCR reactions with RNA from Paenibacillus sp. WLY78 grown under N 2 -fixing conditions. The numbering on the top of the gels corresponds to the product numbers drawn schematically in the outline given above. RT, standard RT-PCR reaction; ( − ), negative control in which no reverse transcriptase was added to the RT reaction; ( + ), positive control in which genomic DNA was used as template in the RT-PCR.
Figure Legend Snippet: The nif genes of Paenibacillus sp. WLY78 are organized in an operon as determined by RT-PCR. (A) Outline of the strategy. Primers used and amplified products (numbered) are given below the schematic representation of the genes. (B) Result of RT-PCR reactions with RNA from Paenibacillus sp. WLY78 grown under N 2 -fixing conditions. The numbering on the top of the gels corresponds to the product numbers drawn schematically in the outline given above. RT, standard RT-PCR reaction; ( − ), negative control in which no reverse transcriptase was added to the RT reaction; ( + ), positive control in which genomic DNA was used as template in the RT-PCR.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Amplification, Negative Control, Positive Control

21) Product Images from "RfaH Promotes the Ability of the Avian Pathogenic Escherichia coli O2 Strain E058 To Cause Avian Colibacillosis"

Article Title: RfaH Promotes the Ability of the Avian Pathogenic Escherichia coli O2 Strain E058 To Cause Avian Colibacillosis

Journal: Journal of Bacteriology

doi: 10.1128/JB.02074-12

Detection of tatD , rfaH , and ubiD gene expression in E058 and E058Δ rfaH by RT-PCR. The RT-PCRs were performed using the following templates: cDNA derived from total RNA of E058 (lanes 1) and E058Δ rfaH (lanes 4) and genomic DNA from E058
Figure Legend Snippet: Detection of tatD , rfaH , and ubiD gene expression in E058 and E058Δ rfaH by RT-PCR. The RT-PCRs were performed using the following templates: cDNA derived from total RNA of E058 (lanes 1) and E058Δ rfaH (lanes 4) and genomic DNA from E058

Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Derivative Assay

22) Product Images from "RfaH Promotes the Ability of the Avian Pathogenic Escherichia coli O2 Strain E058 To Cause Avian Colibacillosis"

Article Title: RfaH Promotes the Ability of the Avian Pathogenic Escherichia coli O2 Strain E058 To Cause Avian Colibacillosis

Journal: Journal of Bacteriology

doi: 10.1128/JB.02074-12

Detection of tatD , rfaH , and ubiD gene expression in E058 and E058Δ rfaH by RT-PCR. The RT-PCRs were performed using the following templates: cDNA derived from total RNA of E058 (lanes 1) and E058Δ rfaH (lanes 4) and genomic DNA from E058
Figure Legend Snippet: Detection of tatD , rfaH , and ubiD gene expression in E058 and E058Δ rfaH by RT-PCR. The RT-PCRs were performed using the following templates: cDNA derived from total RNA of E058 (lanes 1) and E058Δ rfaH (lanes 4) and genomic DNA from E058

Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Derivative Assay

23) Product Images from "Characterization of Arabidopsis thaliana Hydroxyphenylpyruvate Reductases in the Tyrosine Conversion Pathway"

Article Title: Characterization of Arabidopsis thaliana Hydroxyphenylpyruvate Reductases in the Tyrosine Conversion Pathway

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2018.01305

Characterization of the hppr2 , hppr3 , tat1 , and tat2 mutants. (A) Schematic diagram of the T-DNA insertion in hppr2-1 , hppr3-1 , hppr3-2 , tat1-1 , tat1-2 , tat2-1 , and tat2-2 mutants. Exons and untranslated regions are indicated by gray and white boxes, respectively. (B) Schematic diagram showing the hppr2-c1 mutation, which was generated by CRISPR/Cas9. A 1173-bp fragment was detected in genomic DNA. HPPR2-C-s and HPPR-C-a are the primer pair used to confirm the deletion. (C) PCR analysis of DNA from T2 plants generated from a single T1 plant contained the hppr2-c1 mutation. (D) Quantitative reverse transcription PCR (qRT-PCR) analysis of HPPR2 , HPPR3 , TAT1 , and TAT2 transcript abundance in the wild type (WT) and the T-DNA mutants. Data are means of three biological replicates ± SE.
Figure Legend Snippet: Characterization of the hppr2 , hppr3 , tat1 , and tat2 mutants. (A) Schematic diagram of the T-DNA insertion in hppr2-1 , hppr3-1 , hppr3-2 , tat1-1 , tat1-2 , tat2-1 , and tat2-2 mutants. Exons and untranslated regions are indicated by gray and white boxes, respectively. (B) Schematic diagram showing the hppr2-c1 mutation, which was generated by CRISPR/Cas9. A 1173-bp fragment was detected in genomic DNA. HPPR2-C-s and HPPR-C-a are the primer pair used to confirm the deletion. (C) PCR analysis of DNA from T2 plants generated from a single T1 plant contained the hppr2-c1 mutation. (D) Quantitative reverse transcription PCR (qRT-PCR) analysis of HPPR2 , HPPR3 , TAT1 , and TAT2 transcript abundance in the wild type (WT) and the T-DNA mutants. Data are means of three biological replicates ± SE.

Techniques Used: Mutagenesis, Generated, CRISPR, Polymerase Chain Reaction, Quantitative RT-PCR

24) Product Images from "Characterization of Arabidopsis thaliana Hydroxyphenylpyruvate Reductases in the Tyrosine Conversion Pathway"

Article Title: Characterization of Arabidopsis thaliana Hydroxyphenylpyruvate Reductases in the Tyrosine Conversion Pathway

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2018.01305

Characterization of the hppr2 , hppr3 , tat1 , and tat2 mutants. (A) Schematic diagram of the T-DNA insertion in hppr2-1 , hppr3-1 , hppr3-2 , tat1-1 , tat1-2 , tat2-1 , and tat2-2 mutants. Exons and untranslated regions are indicated by gray and white boxes, respectively. (B) Schematic diagram showing the hppr2-c1 mutation, which was generated by CRISPR/Cas9. A 1173-bp fragment was detected in genomic DNA. HPPR2-C-s and HPPR-C-a are the primer pair used to confirm the deletion. (C) PCR analysis of DNA from T2 plants generated from a single T1 plant contained the hppr2-c1 mutation. (D) Quantitative reverse transcription PCR (qRT-PCR) analysis of HPPR2 , HPPR3 , TAT1 , and TAT2 transcript abundance in the wild type (WT) and the T-DNA mutants. Data are means of three biological replicates ± SE.
Figure Legend Snippet: Characterization of the hppr2 , hppr3 , tat1 , and tat2 mutants. (A) Schematic diagram of the T-DNA insertion in hppr2-1 , hppr3-1 , hppr3-2 , tat1-1 , tat1-2 , tat2-1 , and tat2-2 mutants. Exons and untranslated regions are indicated by gray and white boxes, respectively. (B) Schematic diagram showing the hppr2-c1 mutation, which was generated by CRISPR/Cas9. A 1173-bp fragment was detected in genomic DNA. HPPR2-C-s and HPPR-C-a are the primer pair used to confirm the deletion. (C) PCR analysis of DNA from T2 plants generated from a single T1 plant contained the hppr2-c1 mutation. (D) Quantitative reverse transcription PCR (qRT-PCR) analysis of HPPR2 , HPPR3 , TAT1 , and TAT2 transcript abundance in the wild type (WT) and the T-DNA mutants. Data are means of three biological replicates ± SE.

Techniques Used: Mutagenesis, Generated, CRISPR, Polymerase Chain Reaction, Quantitative RT-PCR

25) Product Images from "Molecular characterization of mutations in white-flowered torenia plants"

Article Title: Molecular characterization of mutations in white-flowered torenia plants

Journal: BMC Plant Biology

doi: 10.1186/1471-2229-14-86

Southern blot analysis of F3H and TORE1 in CrV and CrW. Total genomic DNAs were digested with Hin d III (H), Eco RI (E), and Xba I (X) and transferred to nylon membranes as described in Methods. Membranes were probed with DIG-labeled sequences of F3H (A) , LTR (B) , and gag-pol protein (C) from TORE1 . DNA marker sizes (kbp) are shown.
Figure Legend Snippet: Southern blot analysis of F3H and TORE1 in CrV and CrW. Total genomic DNAs were digested with Hin d III (H), Eco RI (E), and Xba I (X) and transferred to nylon membranes as described in Methods. Membranes were probed with DIG-labeled sequences of F3H (A) , LTR (B) , and gag-pol protein (C) from TORE1 . DNA marker sizes (kbp) are shown.

Techniques Used: Southern Blot, Labeling, Marker

26) Product Images from "A Splice Mutation in the PHKG1 Gene Causes High Glycogen Content and Low Meat Quality in Pig Skeletal Muscle"

Article Title: A Splice Mutation in the PHKG1 Gene Causes High Glycogen Content and Low Meat Quality in Pig Skeletal Muscle

Journal: PLoS Genetics

doi: 10.1371/journal.pgen.1004710

Identification of the g.8283C > A splice mutation in the PHKG1 gene. (A) RT-PCR products of the PHKG1 gene on a 2.5% agarose gel, amplified from total RNA from animals with different QTL genotypes ( QQ , Qq and qq ). Two DNA bands of 146 bp and 114 bp with different intensity were observed. (B) Sequence analysis of the RT-PCR products. A 32-bp deletion in exon 10 was detected in QQ and Qq animals. (C) PCR products of the PHKG1 gene on a 2.5% agarose gel, amplified from genomic DNA from animals with different QTL genotypes ( QQ , Qq and qq ). (D) Sequence analysis of the PCR products. A point mutation (g. 8283C > A) was identified in QQ and Qq individuals. (E) PHKG1 genomic sequence from exon 9 to exon 10. Intronic sequence is in black and lower case, and exonic sequence in blue and upper case. The normal splice-acceptor and -donor sequences (lower case) and the cryptic splice-donor sequences (upper case) are underlined with two red nucleotide letters in the center. The C > A mutation is denoted as “M” in red. (F) Sequence analysis of a heterozygote at the g.8283C > A mutation site. In genomic DNA from a heterozygote, the C and A peaks (the position is indicated by “M” and marked by the red bar) were of equal height in sequence of genomic DNA, as expected. Sequence of the cDNA product from the same heterozygote showed a major peak corresponding to the wild-type sequence and a small peak corresponding to the mutant sequence (the +2 position of exon 10 where the nucleotide T belong to the 32-bp deleted portion is marked by the blue bar).
Figure Legend Snippet: Identification of the g.8283C > A splice mutation in the PHKG1 gene. (A) RT-PCR products of the PHKG1 gene on a 2.5% agarose gel, amplified from total RNA from animals with different QTL genotypes ( QQ , Qq and qq ). Two DNA bands of 146 bp and 114 bp with different intensity were observed. (B) Sequence analysis of the RT-PCR products. A 32-bp deletion in exon 10 was detected in QQ and Qq animals. (C) PCR products of the PHKG1 gene on a 2.5% agarose gel, amplified from genomic DNA from animals with different QTL genotypes ( QQ , Qq and qq ). (D) Sequence analysis of the PCR products. A point mutation (g. 8283C > A) was identified in QQ and Qq individuals. (E) PHKG1 genomic sequence from exon 9 to exon 10. Intronic sequence is in black and lower case, and exonic sequence in blue and upper case. The normal splice-acceptor and -donor sequences (lower case) and the cryptic splice-donor sequences (upper case) are underlined with two red nucleotide letters in the center. The C > A mutation is denoted as “M” in red. (F) Sequence analysis of a heterozygote at the g.8283C > A mutation site. In genomic DNA from a heterozygote, the C and A peaks (the position is indicated by “M” and marked by the red bar) were of equal height in sequence of genomic DNA, as expected. Sequence of the cDNA product from the same heterozygote showed a major peak corresponding to the wild-type sequence and a small peak corresponding to the mutant sequence (the +2 position of exon 10 where the nucleotide T belong to the 32-bp deleted portion is marked by the blue bar).

Techniques Used: Mutagenesis, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Amplification, Sequencing, Polymerase Chain Reaction

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Amplification:

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Positive Control:

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Synthesized:

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Quantitative RT-PCR:

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Real-time Polymerase Chain Reaction:

Article Title: Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401
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Article Title: Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation
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Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis
Article Snippet: Reverse transcription was performed on 2 μl (200 ng) of RNA with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Kusatsu, Shiga, Japan). .. The cDNA was fourfold diluted with EASY Dilution Solution for Real‐Time PCR (Takara, Kusatsu, Shiga, Japan) and stored at −20°C.

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Article Snippet: Paragraph title: cDNA synthesis and qPCR ... Following treatment with gDNA Eraser, 1 μg total RNA was used as the template for first-strand cDNA synthesis with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Japan).

Incubation:

Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis
Article Snippet: Cells were resuspended in 100 μl freshly prepared 1 × TE buffer containing 50 mg/ml lysozyme and incubated at 37°C for 10 min, then the manufacturer's protocol was followed. .. Reverse transcription was performed on 2 μl (200 ng) of RNA with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Kusatsu, Shiga, Japan).

Expressing:

Article Title: Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses
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Transformation Assay:

Article Title: Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401
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SYBR Green Assay:

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Cell Culture:

Article Title: Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401
Article Snippet: RNA samples were isolated from the wild type SC1401 (cultured in TSB++ to obtain an OD600 = 1.46 and on TSA++ for 13 h, respectively), SH0165 (cultured on TSA++ plates for 13 h) using the RNAprep pure Cell/Bacteria Kit (Tiangen, China) according to the manufacturer's instructions. .. Two-step RT-PCR was performed using PrimeScriptTM RT reagent Kit with gDNA Eraser (Takara, Japan).

Article Title: Long noncoding RNA actin filament‐associated protein 1 antisense RNA 1 promotes malignant phenotype through binding with lysine‐specific demethylase 1 and repressing HMG box‐containing protein 1 in non‐small‐cell lung cancer, et al. Long noncoding RNA actin filament‐associated protein 1 antisense RNA 1 promotes malignant phenotype through binding with lysine‐specific demethylase 1 and repressi
Article Snippet: 2.4 RNA extraction and quantitative PCR assays Total RNA was isolated from tissues or cultured cells using TRIzol reagent (Invitrogen Life Technologies). .. After removal of genomic DNA using gDNA Eraser for 2 minutes at 4°C, 1 μg total RNA was reverse transcribed to a final volume of 20 μL master mix with the PrimeScript RT Reagent Kit with gDNA Eraser (TaKaRa, Dalian, China).

Reverse Transcription Polymerase Chain Reaction:

Article Title: Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401
Article Snippet: .. Two-step RT-PCR was performed using PrimeScriptTM RT reagent Kit with gDNA Eraser (Takara, Japan). .. The candidate natural transformation-related or dedicated gene transcripts were then analyzed using quantitative reverse transcription PCR (qRT-PCR) with the reagent of SYBR Premix EX TaqTM II (Tli RNaseH Plus) (Takara, Japan).

Article Title: Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation
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Article Title: The Two-Component Regulators GacS and GacA Positively Regulate a Nonfluorescent Siderophore through the Gac/Rsm Signaling Cascade in High-Siderophore-Yielding Pseudomonas sp. Strain HYS
Article Snippet: Paragraph title: RNA isolation and reverse transcription (RT)-PCR. ... Residual DNA was removed, and the RNA was then reverse transcribed to generate cDNA using a PrimeScript RT Reagent Kit with gDNA Eraser (TaKaRa).

Article Title: Transcriptional quiescence of paternal mtDNA in cyprinid fish embryos
Article Snippet: .. For RT-PCR, first-strand cDNA was synthesized by using the PrimeScriptTM RT reagent Kit with gDNA Eraser (TaKaRa), and PCR was run for 35 cycles (94 °C for 30 s, 58 °C for 30 s and 72 °C for 30 s) in a 25-μl volume containing 10 ng of template cDNA and appropriate primers for cytb and tfam, or for 30 cycles for β-actin as a loading control. .. PCR products were separated on 1.5% agarose gels and documented on the White/UV Transilluminators (UVP, Upland, CA 91786).

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Generated:

Article Title: Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons
Article Snippet: .. The gDNA was erased in advance, and cDNA was generated by PrimeScript™ RT reagent kit with a gDNA eraser (TaKaRa, China). .. Reverse transcription PCR (RT-PCR) was performed in accordance with the standard procedures using 1 μM each specific primer (see Additional file : Table S1).

Sequencing:

Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis
Article Snippet: Reverse transcription was performed on 2 μl (200 ng) of RNA with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Kusatsu, Shiga, Japan). .. The forward primer, rRNA‐I was located between positions 2,253,240 and 2,253,256 and the reverse primer, rRNA‐O was located between positions 2,253,739 and 2,253,755 according to the genome sequence of C . michiganensis strain NCPPB382 (GenBank: AM711867.1) (Gartemann et al., ).

Quantitation Assay:

Article Title: Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice
Article Snippet: One microgram of each RNA sample was reverse transcribed to cDNA using a PrimeScript™ RT Reagent Kit with gDNA Eraser (Takara Bio Inc., Kusatsu, Japan). qRT-PCR was performed with an ABI7500HT instrument (Applied Biosystems, Foster City, USA) using FastStart Universal SYBR Green Master (Roche, Mannheim, Germany). .. The relative quantitation method (ΔΔ CT ) was applied to evaluate the quantitative variation among replicates [ , ].

Isolation:

Article Title: Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401
Article Snippet: RNA samples were isolated from the wild type SC1401 (cultured in TSB++ to obtain an OD600 = 1.46 and on TSA++ for 13 h, respectively), SH0165 (cultured on TSA++ plates for 13 h) using the RNAprep pure Cell/Bacteria Kit (Tiangen, China) according to the manufacturer's instructions. .. Two-step RT-PCR was performed using PrimeScriptTM RT reagent Kit with gDNA Eraser (Takara, Japan).

Article Title: Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation
Article Snippet: Paragraph title: RNA isolation and quantitative RT-PCR (qRT–PCR) ... Complementary DNA (cDNA) was synthesized using PrimeScript RT-PCR Kit with gDNA eraser (Takara, Japan), and then used for qRT-PCR.

Article Title: The Two-Component Regulators GacS and GacA Positively Regulate a Nonfluorescent Siderophore through the Gac/Rsm Signaling Cascade in High-Siderophore-Yielding Pseudomonas sp. Strain HYS
Article Snippet: Paragraph title: RNA isolation and reverse transcription (RT)-PCR. ... Residual DNA was removed, and the RNA was then reverse transcribed to generate cDNA using a PrimeScript RT Reagent Kit with gDNA Eraser (TaKaRa).

Article Title: Prion Protein and Stage Specific Embryo Antigen 1 as Selection Markers to Enrich the Fraction of Murine Embryonic Stem Cell-Derived Cardiomyocytes
Article Snippet: Reverse transcriptase-polymerase chain reaction Total RNA was isolated from EB using an RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. .. RNA samples were treated with DNaseI (Promega Corporation, Fitchburg, WI) to eliminate genomic DNA and cDNA was synthesized using the PrimeScript RT reagent Kit with gDNA Eraser (Takara Bio, Kusatsu, Japan).

Article Title: Long noncoding RNA actin filament‐associated protein 1 antisense RNA 1 promotes malignant phenotype through binding with lysine‐specific demethylase 1 and repressing HMG box‐containing protein 1 in non‐small‐cell lung cancer, et al. Long noncoding RNA actin filament‐associated protein 1 antisense RNA 1 promotes malignant phenotype through binding with lysine‐specific demethylase 1 and repressi
Article Snippet: 2.4 RNA extraction and quantitative PCR assays Total RNA was isolated from tissues or cultured cells using TRIzol reagent (Invitrogen Life Technologies). .. After removal of genomic DNA using gDNA Eraser for 2 minutes at 4°C, 1 μg total RNA was reverse transcribed to a final volume of 20 μL master mix with the PrimeScript RT Reagent Kit with gDNA Eraser (TaKaRa, Dalian, China).

Article Title: Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice
Article Snippet: Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) Analysis For qRT-PCR analysis, total RNA was isolated from abiotic stress-treated rice shoots and roots using a MiniBEST Universal RNA Extraction Kit (Takara Bio Inc., Kusatsu, Japan) according to the manufacturer's instructions. .. One microgram of each RNA sample was reverse transcribed to cDNA using a PrimeScript™ RT Reagent Kit with gDNA Eraser (Takara Bio Inc., Kusatsu, Japan). qRT-PCR was performed with an ABI7500HT instrument (Applied Biosystems, Foster City, USA) using FastStart Universal SYBR Green Master (Roche, Mannheim, Germany).

Article Title: Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons
Article Snippet: Paragraph title: RNA isolation, cDNA generation, and RT-PCR ... The gDNA was erased in advance, and cDNA was generated by PrimeScript™ RT reagent kit with a gDNA eraser (TaKaRa, China).

Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis
Article Snippet: Paragraph title: RNA isolation and cDNA synthesis ... Reverse transcription was performed on 2 μl (200 ng) of RNA with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Kusatsu, Shiga, Japan).

Polymerase Chain Reaction:

Article Title: Basic Characterization of Natural Transformation in a Highly Transformable Haemophilus parasuis Strain SC1401
Article Snippet: Two-step RT-PCR was performed using PrimeScriptTM RT reagent Kit with gDNA Eraser (Takara, Japan). .. The candidate natural transformation-related or dedicated gene transcripts were then analyzed using quantitative reverse transcription PCR (qRT-PCR) with the reagent of SYBR Premix EX TaqTM II (Tli RNaseH Plus) (Takara, Japan).

Article Title: Arabidopsis PARG1 is the key factor promoting cell survival among the enzymes regulating post-translational poly(ADP-ribosyl)ation
Article Snippet: Complementary DNA (cDNA) was synthesized using PrimeScript RT-PCR Kit with gDNA eraser (Takara, Japan), and then used for qRT-PCR. .. PCR were performed with SyBR Premix Ex TaqTM II (TaKaRa, Japan) in a Real One Plus Real-Time PCR System (Applied Biosystem, USA), following the manufacturer’s instructions.

Article Title: Prion Protein and Stage Specific Embryo Antigen 1 as Selection Markers to Enrich the Fraction of Murine Embryonic Stem Cell-Derived Cardiomyocytes
Article Snippet: RNA samples were treated with DNaseI (Promega Corporation, Fitchburg, WI) to eliminate genomic DNA and cDNA was synthesized using the PrimeScript RT reagent Kit with gDNA Eraser (Takara Bio, Kusatsu, Japan). .. PCR amplifications were performed using Emerald Amp Max polymerase (Takara Bio) with primers listed in .

Article Title: Transcriptional quiescence of paternal mtDNA in cyprinid fish embryos
Article Snippet: .. For RT-PCR, first-strand cDNA was synthesized by using the PrimeScriptTM RT reagent Kit with gDNA Eraser (TaKaRa), and PCR was run for 35 cycles (94 °C for 30 s, 58 °C for 30 s and 72 °C for 30 s) in a 25-μl volume containing 10 ng of template cDNA and appropriate primers for cytb and tfam, or for 30 cycles for β-actin as a loading control. .. PCR products were separated on 1.5% agarose gels and documented on the White/UV Transilluminators (UVP, Upland, CA 91786).

Article Title: Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons
Article Snippet: The gDNA was erased in advance, and cDNA was generated by PrimeScript™ RT reagent kit with a gDNA eraser (TaKaRa, China). .. Reverse transcription PCR (RT-PCR) was performed in accordance with the standard procedures using 1 μM each specific primer (see Additional file : Table S1).

Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis
Article Snippet: Reverse transcription was performed on 2 μl (200 ng) of RNA with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Kusatsu, Shiga, Japan). .. All cDNA samples were tested by conventional PCR using the primer pair rRNA‐I (5′‐CATCACAGCCAGCCATC‐3′)/rRNA‐O (5′‐ACCACCGTTATCCAGGC‐3′) to confirm the absence of genomic DNA (gDNA).

Electrophoresis:

Article Title: Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons
Article Snippet: The integrity of the RNA was guaranteed by electrophoresis of total RNA in a 1.5% agarose gel. .. The gDNA was erased in advance, and cDNA was generated by PrimeScript™ RT reagent kit with a gDNA eraser (TaKaRa, China).

RNA Extraction:

Article Title: Long noncoding RNA actin filament‐associated protein 1 antisense RNA 1 promotes malignant phenotype through binding with lysine‐specific demethylase 1 and repressing HMG box‐containing protein 1 in non‐small‐cell lung cancer, et al. Long noncoding RNA actin filament‐associated protein 1 antisense RNA 1 promotes malignant phenotype through binding with lysine‐specific demethylase 1 and repressi
Article Snippet: Paragraph title: RNA extraction and quantitative PCR assays ... After removal of genomic DNA using gDNA Eraser for 2 minutes at 4°C, 1 μg total RNA was reverse transcribed to a final volume of 20 μL master mix with the PrimeScript RT Reagent Kit with gDNA Eraser (TaKaRa, Dalian, China).

Article Title: Overexpression of a New Zinc Finger Protein Transcription Factor OsCTZFP8 Improves Cold Tolerance in Rice
Article Snippet: Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) Analysis For qRT-PCR analysis, total RNA was isolated from abiotic stress-treated rice shoots and roots using a MiniBEST Universal RNA Extraction Kit (Takara Bio Inc., Kusatsu, Japan) according to the manufacturer's instructions. .. One microgram of each RNA sample was reverse transcribed to cDNA using a PrimeScript™ RT Reagent Kit with gDNA Eraser (Takara Bio Inc., Kusatsu, Japan). qRT-PCR was performed with an ABI7500HT instrument (Applied Biosystems, Foster City, USA) using FastStart Universal SYBR Green Master (Roche, Mannheim, Germany).

Agarose Gel Electrophoresis:

Article Title: Simultaneous consumption of cellobiose and xylose by Bacillus coagulans to circumvent glucose repression and identification of its cellobiose-assimilating operons
Article Snippet: The integrity of the RNA was guaranteed by electrophoresis of total RNA in a 1.5% agarose gel. .. The gDNA was erased in advance, and cDNA was generated by PrimeScript™ RT reagent kit with a gDNA eraser (TaKaRa, China).

Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis
Article Snippet: Total RNA concentration and purity were determined using a NanoDrop 2000 (Thermo Fisher Scientific), and RNA integrity was tested by running 1% (w/v) native agarose gel in 1 × TAE buffer under 6 V/cm for 15 min. Two bands will be observed on the gel after EB staining, the intensity of 23S rRNA band should be twice as strong as the 16S rRNA band if the integrity of RNA sample is good. .. Reverse transcription was performed on 2 μl (200 ng) of RNA with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Kusatsu, Shiga, Japan).

Random Hexamer Labeling:

Article Title: Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses
Article Snippet: Following treatment with gDNA Eraser, 1 μg total RNA was used as the template for first-strand cDNA synthesis with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Japan). .. Reverse transcription was completed with oligo(dT) and random hexamer primers.

Concentration Assay:

Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis
Article Snippet: The concentration of all RNA samples was adjusted to 100 ng/μl and used for following experiment. .. Reverse transcription was performed on 2 μl (200 ng) of RNA with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Kusatsu, Shiga, Japan).

Staining:

Article Title: Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis, et al. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis
Article Snippet: Total RNA concentration and purity were determined using a NanoDrop 2000 (Thermo Fisher Scientific), and RNA integrity was tested by running 1% (w/v) native agarose gel in 1 × TAE buffer under 6 V/cm for 15 min. Two bands will be observed on the gel after EB staining, the intensity of 23S rRNA band should be twice as strong as the 16S rRNA band if the integrity of RNA sample is good. .. Reverse transcription was performed on 2 μl (200 ng) of RNA with the PrimeScript RT Reagent Kit with gDNA Eraser (Takara, Kusatsu, Shiga, Japan).

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  • 90
    TaKaRa gdna eraser
    Gdna Eraser, supplied by TaKaRa, used in various techniques. Bioz Stars score: 90/100, based on 690 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 690 article reviews
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    gdna eraser - by Bioz Stars, 2020-01
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