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    RsaI
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    RsaI 5 000 units
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    r0167l
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    Category:
    Restriction Enzymes
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    New England Biolabs rsa i
    RsaI
    RsaI 5 000 units
    https://www.bioz.com/result/rsa i/product/New England Biolabs
    Average 99 stars, based on 163 article reviews
    Price from $9.99 to $1999.99
    rsa i - by Bioz Stars, 2020-08
    99/100 stars

    Images

    1) Product Images from "Growth factor receptors as regulators of hematopoiesis"

    Article Title: Growth factor receptors as regulators of hematopoiesis

    Journal: Blood

    doi: 10.1182/blood-2006-01-012278

    F36VFGFR1 supports the survival of long-term repopulating HSCs during growth factor deprivation. Marrow cells (5 × 10 5 ) transduced with the F36VFGFR1 vector were transplanted into lethally irradiated recipients either immediately following transduction (A) or after 1 (B) or 5 days (C) of culture in the presence (solid symbols) or absence (open symbols) of 100 nM AP20187. Mice that were given transplants of cultured cells received all the progeny generated in cultures initiated with 5 × 10 5 transduced cells at day 0. Each line depicts results from a single mouse. One mouse (6281) that was given transplants of cells cultured for 5 days in AP20187 was killed at day 174 after transplantation and 5 × 10 6 marrow cells from this mouse were transplanted into 2 lethally irradiated secondary recipients (symbols × and +). E indicates erythroid; P, platelets, G, granulocytes; M, monocytes; B, B cells; and T, T cells. (C; inserts) LAM-PCR using Rsa I confirms common provirus insertion patterns in the granulocytes (G), monocytes (M), B cells (B), and T cells (T) of mouse 6281. MW indicates DNA ladder. Similar results were obtained using 2 other restriction enzymes, Tsp509 I and Hae III. Sequencing of LAM-PCR products from mouse 6281 (panel D) revealed provirus insertion sites at the indicated positions in chromosomes 4 and 16, and their presence in the indicated lineages was confirmed by PCR using using an LTR primer, a host genomic primer, and 38 cycles of amplification. A second independent experiment performed in serum-free conditions showed a similar trend at 64 days after transplantation.
    Figure Legend Snippet: F36VFGFR1 supports the survival of long-term repopulating HSCs during growth factor deprivation. Marrow cells (5 × 10 5 ) transduced with the F36VFGFR1 vector were transplanted into lethally irradiated recipients either immediately following transduction (A) or after 1 (B) or 5 days (C) of culture in the presence (solid symbols) or absence (open symbols) of 100 nM AP20187. Mice that were given transplants of cultured cells received all the progeny generated in cultures initiated with 5 × 10 5 transduced cells at day 0. Each line depicts results from a single mouse. One mouse (6281) that was given transplants of cells cultured for 5 days in AP20187 was killed at day 174 after transplantation and 5 × 10 6 marrow cells from this mouse were transplanted into 2 lethally irradiated secondary recipients (symbols × and +). E indicates erythroid; P, platelets, G, granulocytes; M, monocytes; B, B cells; and T, T cells. (C; inserts) LAM-PCR using Rsa I confirms common provirus insertion patterns in the granulocytes (G), monocytes (M), B cells (B), and T cells (T) of mouse 6281. MW indicates DNA ladder. Similar results were obtained using 2 other restriction enzymes, Tsp509 I and Hae III. Sequencing of LAM-PCR products from mouse 6281 (panel D) revealed provirus insertion sites at the indicated positions in chromosomes 4 and 16, and their presence in the indicated lineages was confirmed by PCR using using an LTR primer, a host genomic primer, and 38 cycles of amplification. A second independent experiment performed in serum-free conditions showed a similar trend at 64 days after transplantation.

    Techniques Used: Transduction, Plasmid Preparation, Irradiation, Mouse Assay, Cell Culture, Generated, Transplantation Assay, Laser Capture Microdissection, Polymerase Chain Reaction, Sequencing, Amplification

    2) Product Images from "Molecular appraisal of intestinal parasitic infection in transplant recipients"

    Article Title: Molecular appraisal of intestinal parasitic infection in transplant recipients

    Journal: The Indian Journal of Medical Research

    doi: 10.4103/0971-5916.195041

    Restriction fragment length polymorphism assay using Rsa I RE for Cryptosporidium oocyst wall protein gene. Lane 1 - 100 bp DNA ladder, lanes 2, 3, 4 - Cryptosporidium hominis isolates ( Rsa I - 284, 129, 106 bp).
    Figure Legend Snippet: Restriction fragment length polymorphism assay using Rsa I RE for Cryptosporidium oocyst wall protein gene. Lane 1 - 100 bp DNA ladder, lanes 2, 3, 4 - Cryptosporidium hominis isolates ( Rsa I - 284, 129, 106 bp).

    Techniques Used: Polymorphism Assay

    Restriction fragment length polymorphism assay using Rsa I RE for Cpgp40 /15 gene. Lane 1 - Ie isolates (424, 159, 134, 129, 106 bp), lanes 2, 4 - Ia (391, 241, 159, 143 bp), lane 3 - IIc (356, 256, 143 bp), lane 5 - 100 bp DNA ladder.
    Figure Legend Snippet: Restriction fragment length polymorphism assay using Rsa I RE for Cpgp40 /15 gene. Lane 1 - Ie isolates (424, 159, 134, 129, 106 bp), lanes 2, 4 - Ia (391, 241, 159, 143 bp), lane 3 - IIc (356, 256, 143 bp), lane 5 - 100 bp DNA ladder.

    Techniques Used: Polymorphism Assay, IA

    3) Product Images from "Telomere Length Assessment in Human Archival Tissues "

    Article Title: Telomere Length Assessment in Human Archival Tissues

    Journal: The American Journal of Pathology

    doi:

    TEL-FISH quantitation results. A: Box and whisker plot of relative telomere signals from four LNCaP sublines each possessing distinctly different telomere lengths ( n = 10 to 12 cells measured per subline). The boxed region encloses the 25th through 75th percentiles, with the horizontal line indicating the median. Whiskers include the 5th to 95th percentiles, open circles represent outliers. B: TRF-Southern blot of LNCaP sublines (numbered 1 to 4). Genomic DNA was digested with Rsa I and Msp I, blotted, and probed with a radiolabeled telomere-specific oligonucleotide primer. Molecular weight markers (M) are labeled in Kbp. C: Relative mean telomere fluorescence signals for each LNCaP subline ( large circles ) plus additional cell lines ( diamonds ) plotted against mean telomere length calculated from TRF-Southern data collected on the same cells. Cell lines (all human-derived) included the prostate cancer (LNCaP, PC-3, and DU145)-, leukemia (HL-60)-, and colon cancer (HCT116)-derived lines. The trend line indicates linear regression results.
    Figure Legend Snippet: TEL-FISH quantitation results. A: Box and whisker plot of relative telomere signals from four LNCaP sublines each possessing distinctly different telomere lengths ( n = 10 to 12 cells measured per subline). The boxed region encloses the 25th through 75th percentiles, with the horizontal line indicating the median. Whiskers include the 5th to 95th percentiles, open circles represent outliers. B: TRF-Southern blot of LNCaP sublines (numbered 1 to 4). Genomic DNA was digested with Rsa I and Msp I, blotted, and probed with a radiolabeled telomere-specific oligonucleotide primer. Molecular weight markers (M) are labeled in Kbp. C: Relative mean telomere fluorescence signals for each LNCaP subline ( large circles ) plus additional cell lines ( diamonds ) plotted against mean telomere length calculated from TRF-Southern data collected on the same cells. Cell lines (all human-derived) included the prostate cancer (LNCaP, PC-3, and DU145)-, leukemia (HL-60)-, and colon cancer (HCT116)-derived lines. The trend line indicates linear regression results.

    Techniques Used: Fluorescence In Situ Hybridization, Quantitation Assay, Whisker Assay, Southern Blot, Molecular Weight, Labeling, Fluorescence, Derivative Assay

    4) Product Images from "Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis"

    Article Title: Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis

    Journal: Applied and Environmental Microbiology

    doi:

    Rsa I TRF profiles of 16S rDNA amplified directly from S0, S1, C0, and C1 soil DNA samples.
    Figure Legend Snippet: Rsa I TRF profiles of 16S rDNA amplified directly from S0, S1, C0, and C1 soil DNA samples.

    Techniques Used: Amplification

    Detection of a 16S rDNA clone (5-kb plasmid from clone S075) in a background of 1 ng of C0 soil DNA. (A) Rsa I TRF profile of 16S rDNA amplified from 0.01 pg of S075 plasmid DNA. (B) Rsa I TRf profile of 16S rDNA amplified from a mixture of 0.01 pg of plasmid S075 and 1 ng of C0 soil DNA. (C) Rsa I TRf profile of 16S rDNA amplified from a mixture of 0.001 pg of plasmid S075 and 1 ng of C0 soil DNA. (D) Rsa I TRF profile of 16S rDNA amplified from 1 ng of C0 soil DNA.
    Figure Legend Snippet: Detection of a 16S rDNA clone (5-kb plasmid from clone S075) in a background of 1 ng of C0 soil DNA. (A) Rsa I TRF profile of 16S rDNA amplified from 0.01 pg of S075 plasmid DNA. (B) Rsa I TRf profile of 16S rDNA amplified from a mixture of 0.01 pg of plasmid S075 and 1 ng of C0 soil DNA. (C) Rsa I TRf profile of 16S rDNA amplified from a mixture of 0.001 pg of plasmid S075 and 1 ng of C0 soil DNA. (D) Rsa I TRF profile of 16S rDNA amplified from 1 ng of C0 soil DNA.

    Techniques Used: Plasmid Preparation, Amplification

    5) Product Images from "Distribution of BoLA-DRB3 Allelic Frequencies and Identification of Two New Alleles in Iranian Buffalo Breed"

    Article Title: Distribution of BoLA-DRB3 Allelic Frequencies and Identification of Two New Alleles in Iranian Buffalo Breed

    Journal: The Scientific World Journal

    doi: 10.1100/2012/863024

    Electrophoresis in 8% polyacrylamide gel of exon 2 amplification products of gene BoLA-DRB3 digested by endonucleases Rsa I (b), Hae III (a), and BstYI (c). Msp I fragments of plasmid pUC19 are used as a molecular marker. The length of fragments composing Rsa I, Hae III, or Bst YI DNA patterns is shown on pictures.
    Figure Legend Snippet: Electrophoresis in 8% polyacrylamide gel of exon 2 amplification products of gene BoLA-DRB3 digested by endonucleases Rsa I (b), Hae III (a), and BstYI (c). Msp I fragments of plasmid pUC19 are used as a molecular marker. The length of fragments composing Rsa I, Hae III, or Bst YI DNA patterns is shown on pictures.

    Techniques Used: Electrophoresis, Amplification, Plasmid Preparation, Marker

    6) Product Images from "Molecular appraisal of intestinal parasitic infection in transplant recipients"

    Article Title: Molecular appraisal of intestinal parasitic infection in transplant recipients

    Journal: The Indian Journal of Medical Research

    doi: 10.4103/0971-5916.195041

    Restriction fragment length polymorphism assay using Rsa I RE for Cryptosporidium oocyst wall protein gene. Lane 1 - 100 bp DNA ladder, lanes 2, 3, 4 - Cryptosporidium hominis isolates ( Rsa I - 284, 129, 106 bp).
    Figure Legend Snippet: Restriction fragment length polymorphism assay using Rsa I RE for Cryptosporidium oocyst wall protein gene. Lane 1 - 100 bp DNA ladder, lanes 2, 3, 4 - Cryptosporidium hominis isolates ( Rsa I - 284, 129, 106 bp).

    Techniques Used: Polymorphism Assay

    Restriction fragment length polymorphism assay using Rsa I RE for Cpgp40 /15 gene. Lane 1 - Ie isolates (424, 159, 134, 129, 106 bp), lanes 2, 4 - Ia (391, 241, 159, 143 bp), lane 3 - IIc (356, 256, 143 bp), lane 5 - 100 bp DNA ladder.
    Figure Legend Snippet: Restriction fragment length polymorphism assay using Rsa I RE for Cpgp40 /15 gene. Lane 1 - Ie isolates (424, 159, 134, 129, 106 bp), lanes 2, 4 - Ia (391, 241, 159, 143 bp), lane 3 - IIc (356, 256, 143 bp), lane 5 - 100 bp DNA ladder.

    Techniques Used: Polymorphism Assay, IA

    7) Product Images from "Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India"

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India

    Journal: Indian journal of virology : an official organ of Indian Virological Society

    doi: 10.1007/s13337-011-0023-6

    Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria
    Figure Legend Snippet: Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria

    Techniques Used: Polymerase Chain Reaction, Amplification

    Actual RFLP analyses of 1.25 kb of 16S rDNA nested-PCR products of TP phytoplasma (amplified using primer pair R16F2n/R16R2) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM,
    Figure Legend Snippet: Actual RFLP analyses of 1.25 kb of 16S rDNA nested-PCR products of TP phytoplasma (amplified using primer pair R16F2n/R16R2) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM,

    Techniques Used: Nested PCR, Amplification

    8) Product Images from "Biodiversity and ITS-RFLP Characterisation of Aspergillus Section Nigri Isolates in Grapes from Four Traditional Grape-Producing Areas in Greece"

    Article Title: Biodiversity and ITS-RFLP Characterisation of Aspergillus Section Nigri Isolates in Grapes from Four Traditional Grape-Producing Areas in Greece

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0093923

    Restriction digestion patterns of sequenced ribosomal 5.8S-ITS region amplicons. Restriction digestion patterns (designated as A , B , C and D ) of five sequenced ribosomal 5.8S-ITS DNA amplicons from five different Aspergilli grape isolates (presented as isolate designations), after digestion with the restriction endonucleases Hha I , Hinf I and Rsa I . Each isolate is a representative of the five different Aspergillus species characterized in this study. L : DNA ladder.
    Figure Legend Snippet: Restriction digestion patterns of sequenced ribosomal 5.8S-ITS region amplicons. Restriction digestion patterns (designated as A , B , C and D ) of five sequenced ribosomal 5.8S-ITS DNA amplicons from five different Aspergilli grape isolates (presented as isolate designations), after digestion with the restriction endonucleases Hha I , Hinf I and Rsa I . Each isolate is a representative of the five different Aspergillus species characterized in this study. L : DNA ladder.

    Techniques Used:

    Ribosomal 5.8S-ITS region restriction digestion patterns of Aspergillus reference strains. Restriction digestion patterns (designated as A and B ) of ribosomal 5.8S-ITS DNA amplicons from Aspergillus reference strains, after digestion with the restriction endonucleases Hinf I , Hha I and Rsa I . Ac : Aspergillus carbonarius , An : Aspergillus niger , At : Aspergillus tubingensis , Aw : Aspergillus westerdijkiae , Ao : Aspergillus ochraceus , L : Low molecular weight DNA ladder (molecular sizes are 766, 500, 350, 300, 250, 200, 150, 100, 75, 50 and 25 bp respectively).
    Figure Legend Snippet: Ribosomal 5.8S-ITS region restriction digestion patterns of Aspergillus reference strains. Restriction digestion patterns (designated as A and B ) of ribosomal 5.8S-ITS DNA amplicons from Aspergillus reference strains, after digestion with the restriction endonucleases Hinf I , Hha I and Rsa I . Ac : Aspergillus carbonarius , An : Aspergillus niger , At : Aspergillus tubingensis , Aw : Aspergillus westerdijkiae , Ao : Aspergillus ochraceus , L : Low molecular weight DNA ladder (molecular sizes are 766, 500, 350, 300, 250, 200, 150, 100, 75, 50 and 25 bp respectively).

    Techniques Used: Molecular Weight

    9) Product Images from "Novel Cryptosporidium Genotypes in Sporadic Cryptosporidiosis Cases: First Report of Human Infections with a Cervine Genotype"

    Article Title: Novel Cryptosporidium Genotypes in Sporadic Cryptosporidiosis Cases: First Report of Human Infections with a Cervine Genotype

    Journal: Emerging Infectious Diseases

    doi: 10.3201/eid0803.010194

    Restriction profiles obtained after digestion of polymerase chain reaction products from the Cryptosporidium oocyst wall protein locus with Rsa I. Lanes 1- 3-, 100-, 50-, and 10-bp ladder molecular weight markers; lanes 4 and 6, bovine genotype 2 isolates; lanes 7 and 8, human genotype 1 isolates; lane 9, cervine genotype isolate MH205; and lane 10, C. meleagridis isolate CS33
    Figure Legend Snippet: Restriction profiles obtained after digestion of polymerase chain reaction products from the Cryptosporidium oocyst wall protein locus with Rsa I. Lanes 1- 3-, 100-, 50-, and 10-bp ladder molecular weight markers; lanes 4 and 6, bovine genotype 2 isolates; lanes 7 and 8, human genotype 1 isolates; lane 9, cervine genotype isolate MH205; and lane 10, C. meleagridis isolate CS33

    Techniques Used: Polymerase Chain Reaction, Molecular Weight

    10) Product Images from "Development and validation of a T7 based linear amplification for genomic DNA"

    Article Title: Development and validation of a T7 based linear amplification for genomic DNA

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-4-19

    Hierarchical clustering of replicate datasets generated by direct labeling, IVT and R-PCR. Each thin bar represents a single datapoint. Red bars correspond to enrichment in the Cy5-labeled Alu I probe, while green bars correspond to enrichment in the Cy3-labeled Rsa I probe. The dendrograms (top) indicate clustering relationships among the sample replicates. The lengths of the branches represent the degree of similarity between the samples (shorter indicates higher similarity). Purple stripes to the right of the diagram highlight discordant areas (log ratios with opposite signs) in the R-PCR replicates relative to the direct labeling and IVT samples.
    Figure Legend Snippet: Hierarchical clustering of replicate datasets generated by direct labeling, IVT and R-PCR. Each thin bar represents a single datapoint. Red bars correspond to enrichment in the Cy5-labeled Alu I probe, while green bars correspond to enrichment in the Cy3-labeled Rsa I probe. The dendrograms (top) indicate clustering relationships among the sample replicates. The lengths of the branches represent the degree of similarity between the samples (shorter indicates higher similarity). Purple stripes to the right of the diagram highlight discordant areas (log ratios with opposite signs) in the R-PCR replicates relative to the direct labeling and IVT samples.

    Techniques Used: Generated, Labeling, Polymerase Chain Reaction

    11) Product Images from "Hermansky-Pudlak Syndrome Type 3 in Ashkenazi Jews and Other Non-Puerto Rican Patients with Hypopigmentation and Platelet Storage-Pool Deficiency"

    Article Title: Hermansky-Pudlak Syndrome Type 3 in Ashkenazi Jews and Other Non-Puerto Rican Patients with Hypopigmentation and Platelet Storage-Pool Deficiency

    Journal: American Journal of Human Genetics

    doi:

    Ashkenazi Jewish mutation in HPS3 . A, PCR amplification of a 908-bp HPS3 cDNA fragment, showing homozygous and heterozygous skipping of exon 5 (714-bp band). B, PCR amplification of exon 5 genomic DNA (328-bp) followed by Rsa I restiction enzyme digestion. The 1303+1G→A splice-site mutation deletes an Rsa I restriction site. Normal genomic DNA is cut into 251-bp, 42-bp, and 35-bp bands; homozygously mutated genomic DNA is cut into 251-bp and 77-bp bands. Patients 44, 89, and 100 exhibit homozygous 1303+1G→A mutations. Patients 26 and 86 carry the mutation in the heterozygous state. Patients 34, 90, and 91 do not have this mutation.
    Figure Legend Snippet: Ashkenazi Jewish mutation in HPS3 . A, PCR amplification of a 908-bp HPS3 cDNA fragment, showing homozygous and heterozygous skipping of exon 5 (714-bp band). B, PCR amplification of exon 5 genomic DNA (328-bp) followed by Rsa I restiction enzyme digestion. The 1303+1G→A splice-site mutation deletes an Rsa I restriction site. Normal genomic DNA is cut into 251-bp, 42-bp, and 35-bp bands; homozygously mutated genomic DNA is cut into 251-bp and 77-bp bands. Patients 44, 89, and 100 exhibit homozygous 1303+1G→A mutations. Patients 26 and 86 carry the mutation in the heterozygous state. Patients 34, 90, and 91 do not have this mutation.

    Techniques Used: Mutagenesis, Polymerase Chain Reaction, Amplification

    12) Product Images from "Global remodeling of nucleosome positions in C. elegans"

    Article Title: Global remodeling of nucleosome positions in C. elegans

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-14-284

    Nucleosome organization in exons and introns. A) Barplot of exon and intron nucleosome occupancies. The mean normalized nucleosome occupancy in introns and exons for each dataset is plotted. Error bars show the standard error. B) Barplot of predicted exon and intron nucleosome occupancies. Same as (A), but using normalized nucleosome occupancy profiles predicted by N = 2 position-independent models fit on the indicated datasets. C) In vitro nucleosome occupancy in exons and introns grouped by GC content. Exons and introns were divided into three equally sized groups of high, medium, and low GC content. Introns were aligned on their center, and exons were aligned to their 3’ ends (left) and 5’ ends (right). Mean normalized nucleosome occupancy in each group is plotted against the distance from the center for introns, and the distance from either the 3’ or the 5’ boundary for exons. Averages x bases upstream of the 3’ boundary or downstream of the 5’ boundary are calculated only among exons of length ≥ x . The average intron nucleosome occupancy a distance x from the intron center is calculated only among introns of length ≥ 2x . Dashed curves show standard errors of the mean. The nucleosome occupancy profile is from the Rsa I in vitro assay. D) In vivo nucleosome occupancy in exons and introns grouped by GC content. Same as (C), but using in vivo data from Valouev et al. [ 39 ]. E) Exon and intron nucleosome occupancy grouped by gene expression levels. Same as (A), except that exons and introns are from the genes with high and low expression levels. Expression levels were inferred from SAGE data. All tagged genes were ranked by the abundance of SAGE tags, with high and low expression groups corresponding to the top and bottom 10%, respectively (see Methods).
    Figure Legend Snippet: Nucleosome organization in exons and introns. A) Barplot of exon and intron nucleosome occupancies. The mean normalized nucleosome occupancy in introns and exons for each dataset is plotted. Error bars show the standard error. B) Barplot of predicted exon and intron nucleosome occupancies. Same as (A), but using normalized nucleosome occupancy profiles predicted by N = 2 position-independent models fit on the indicated datasets. C) In vitro nucleosome occupancy in exons and introns grouped by GC content. Exons and introns were divided into three equally sized groups of high, medium, and low GC content. Introns were aligned on their center, and exons were aligned to their 3’ ends (left) and 5’ ends (right). Mean normalized nucleosome occupancy in each group is plotted against the distance from the center for introns, and the distance from either the 3’ or the 5’ boundary for exons. Averages x bases upstream of the 3’ boundary or downstream of the 5’ boundary are calculated only among exons of length ≥ x . The average intron nucleosome occupancy a distance x from the intron center is calculated only among introns of length ≥ 2x . Dashed curves show standard errors of the mean. The nucleosome occupancy profile is from the Rsa I in vitro assay. D) In vivo nucleosome occupancy in exons and introns grouped by GC content. Same as (C), but using in vivo data from Valouev et al. [ 39 ]. E) Exon and intron nucleosome occupancy grouped by gene expression levels. Same as (A), except that exons and introns are from the genes with high and low expression levels. Expression levels were inferred from SAGE data. All tagged genes were ranked by the abundance of SAGE tags, with high and low expression groups corresponding to the top and bottom 10%, respectively (see Methods).

    Techniques Used: In Vitro, In Vivo, Expressing

    The role of dinucleotide periodicities in well-positioned nucleosomes. A) Dinucleotide frequencies in well-positioned in vitro nucleosomes. Each curve shows a relative dinucleotide frequency at a given position (with respect to the nucleosome dyad) for the set of well-placed nucleosomes selected from the Rsa I in vitro assay (see Methods). Dinucleotide counts used to calculate the frequencies include both forward and reverse strands for each well-placed nucleosome. We define the relative frequency of a group of dinucleotides as the sum of frequencies of all dinucleotides in that group at a given position, divided by the sum of genome-wide frequencies for the same group of dinucleotides. The groups plotted (with a 3-bp moving average) are AA/AT/TA/TT, CC/CG/GC/GG, and mixed dinucleotides (one A or T and one G or C nucleotide). B) Dinucleotide frequencies in well-positioned in vivo nucleosomes. Same as (A) but using well-placed nucleosomes from the Valouev et al. dataset [ 39 ]. C) Predicting well-positioned nucleosomes in vitro . Each curve shows a probability enrichment predicted by a given model at a given distance from well-placed nucleosomes. Probability enrichment is defined as the predicted probability at a given position, divided by the genome-wide mean of the predicted probability profile. Probability enrichment is averaged over all well-placed nucleosomes in the Rsa I in vitro assay; the resulting curves are smoothed with a 7-bp moving average. The two models shown, N = 2 position-independent (magenta) and spatially resolved (green), were fit on the Rsa I in vitro data. D ) Predicting well-positioned nucleosomes in vivo . Same as (C) but with models fit on, and well-placed nucleosomes selected from the Valouev et al. dataset [ 39 ].
    Figure Legend Snippet: The role of dinucleotide periodicities in well-positioned nucleosomes. A) Dinucleotide frequencies in well-positioned in vitro nucleosomes. Each curve shows a relative dinucleotide frequency at a given position (with respect to the nucleosome dyad) for the set of well-placed nucleosomes selected from the Rsa I in vitro assay (see Methods). Dinucleotide counts used to calculate the frequencies include both forward and reverse strands for each well-placed nucleosome. We define the relative frequency of a group of dinucleotides as the sum of frequencies of all dinucleotides in that group at a given position, divided by the sum of genome-wide frequencies for the same group of dinucleotides. The groups plotted (with a 3-bp moving average) are AA/AT/TA/TT, CC/CG/GC/GG, and mixed dinucleotides (one A or T and one G or C nucleotide). B) Dinucleotide frequencies in well-positioned in vivo nucleosomes. Same as (A) but using well-placed nucleosomes from the Valouev et al. dataset [ 39 ]. C) Predicting well-positioned nucleosomes in vitro . Each curve shows a probability enrichment predicted by a given model at a given distance from well-placed nucleosomes. Probability enrichment is defined as the predicted probability at a given position, divided by the genome-wide mean of the predicted probability profile. Probability enrichment is averaged over all well-placed nucleosomes in the Rsa I in vitro assay; the resulting curves are smoothed with a 7-bp moving average. The two models shown, N = 2 position-independent (magenta) and spatially resolved (green), were fit on the Rsa I in vitro data. D ) Predicting well-positioned nucleosomes in vivo . Same as (C) but with models fit on, and well-placed nucleosomes selected from the Valouev et al. dataset [ 39 ].

    Techniques Used: In Vitro, Genome Wide, In Vivo

    Overlap between well-positioned nucleosomes in different datasets. A) Each curve shows the average number of reads observed in the indicated dataset within D bp of all well-placed nucleosomes from the Rsa I in vitro assay. B) Same as (A), but with respect to well-placed nucleosomes in the Hinc II in vitro assay. C) Same as (A), but with respect to well-placed nucleosomes in Valouev et al. in vivo dataset [ 39 ]. D) Same as (A), but with respect to well-placed nucleosomes in Gu Fire in vivo dataset [ 38 ]. Note that in each panel, the vertical scale of each curve is normalized to match the total read-coverage of the dataset from which the well-placed nucleosomes are drawn. Sequence read cutoffs and filtering procedures used to define well-positioned nucleosomes are described in Methods.
    Figure Legend Snippet: Overlap between well-positioned nucleosomes in different datasets. A) Each curve shows the average number of reads observed in the indicated dataset within D bp of all well-placed nucleosomes from the Rsa I in vitro assay. B) Same as (A), but with respect to well-placed nucleosomes in the Hinc II in vitro assay. C) Same as (A), but with respect to well-placed nucleosomes in Valouev et al. in vivo dataset [ 39 ]. D) Same as (A), but with respect to well-placed nucleosomes in Gu Fire in vivo dataset [ 38 ]. Note that in each panel, the vertical scale of each curve is normalized to match the total read-coverage of the dataset from which the well-placed nucleosomes are drawn. Sequence read cutoffs and filtering procedures used to define well-positioned nucleosomes are described in Methods.

    Techniques Used: In Vitro, In Vivo, Sequencing

    13) Product Images from "Polymorphism of the Prolactin Gene and Its Relationship with Milk Production in Gir and Kankrej Cattle"

    Article Title: Polymorphism of the Prolactin Gene and Its Relationship with Milk Production in Gir and Kankrej Cattle

    Journal: Journal of Natural Science, Biology, and Medicine

    doi: 10.4103/jnsbm.JNSBM_303_16

    Electrophoretic pattern of Rsa I digested polymerase chain reaction product of representative samples on 3% agarose, in Lane 1, two fragments with 82 and 74 bp (BB genotype), in Lane 5, 12, and 14 one uncut fragment with 156 bp, in Lane 2, 3, 4, 6, 7, 8, 9, 10, 11, 13 three fragments with 156, 82 and 74 bp (AB genotype), in Lane 15-polymerase chain reaction product, in Lane 16 low-range DNA ladder (100 bp)
    Figure Legend Snippet: Electrophoretic pattern of Rsa I digested polymerase chain reaction product of representative samples on 3% agarose, in Lane 1, two fragments with 82 and 74 bp (BB genotype), in Lane 5, 12, and 14 one uncut fragment with 156 bp, in Lane 2, 3, 4, 6, 7, 8, 9, 10, 11, 13 three fragments with 156, 82 and 74 bp (AB genotype), in Lane 15-polymerase chain reaction product, in Lane 16 low-range DNA ladder (100 bp)

    Techniques Used: Polymerase Chain Reaction

    14) Product Images from "DNA-PKcs is critical for telomere capping"

    Article Title: DNA-PKcs is critical for telomere capping

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi: 10.1073/pnas.261574698

    DNA-PKcs-deficient MEFs exhibit similar telomere lengths and telomerase activities when compared with wild-type MEFs. ( A ) Southern analysis of MEFs. Early passage MEFs from independently isolated littermates were prepared from wild-type (lanes 7 and 8), DNA-PKcs+/− (lanes 1, 2, 5, and 6), and DNA-PKcs−/− (lanes 3 and 4). Gel plugs containing genomic DNAs were digested with Rsa I and Hin fI (odd number lanes) or undigested (even number lanes), fractionated by pulse-field gel electrophoresis, and hybridized with the telomeric specific [TTAGGG] 3 probe. The approximate sizes of the products (kb) are indicated based on molecular weight markers. The Southern hybridization signal observed with the [TTAGGG] 3 probe under these conditions was sensitive to BAL-31 exonuclease digestion, suggesting that this is telomeric DNA (data not shown). ( B ) PCR analysis for genotyping. Using the specific primer pairs (see Materials and Methods ), wild-type and targeted alleles were amplified as products of 450 bp and 360 bp, respectively. Lanes 2 and 4 show the DNA-PKcs+/− pattern, lane 3 shows the DNA-PKcs−/− pattern, and lane 5 shows the wild-type pattern. Lane 1 contains a size marker. ( C ) Telomerase activity in DNA-PKcs-deficient MEFs. TRAP assay was performed after 30 PCR cycles on cell extracts (10, 10 2 , and 10 3 cells) prepared from DNA-PKcs−/− (lanes 1–3), DNA-PKcs+/− (lanes 4–6), and wild-type (lanes 7–9) MEFs. In lanes 10–12, a serial dilution of HeLa cell lysate was run as a positive control for quantitating relative telomerase activity levels. Lane 13 contains a negative control without cell lysate. IC denotes a standard internal control for PCR efficiency.
    Figure Legend Snippet: DNA-PKcs-deficient MEFs exhibit similar telomere lengths and telomerase activities when compared with wild-type MEFs. ( A ) Southern analysis of MEFs. Early passage MEFs from independently isolated littermates were prepared from wild-type (lanes 7 and 8), DNA-PKcs+/− (lanes 1, 2, 5, and 6), and DNA-PKcs−/− (lanes 3 and 4). Gel plugs containing genomic DNAs were digested with Rsa I and Hin fI (odd number lanes) or undigested (even number lanes), fractionated by pulse-field gel electrophoresis, and hybridized with the telomeric specific [TTAGGG] 3 probe. The approximate sizes of the products (kb) are indicated based on molecular weight markers. The Southern hybridization signal observed with the [TTAGGG] 3 probe under these conditions was sensitive to BAL-31 exonuclease digestion, suggesting that this is telomeric DNA (data not shown). ( B ) PCR analysis for genotyping. Using the specific primer pairs (see Materials and Methods ), wild-type and targeted alleles were amplified as products of 450 bp and 360 bp, respectively. Lanes 2 and 4 show the DNA-PKcs+/− pattern, lane 3 shows the DNA-PKcs−/− pattern, and lane 5 shows the wild-type pattern. Lane 1 contains a size marker. ( C ) Telomerase activity in DNA-PKcs-deficient MEFs. TRAP assay was performed after 30 PCR cycles on cell extracts (10, 10 2 , and 10 3 cells) prepared from DNA-PKcs−/− (lanes 1–3), DNA-PKcs+/− (lanes 4–6), and wild-type (lanes 7–9) MEFs. In lanes 10–12, a serial dilution of HeLa cell lysate was run as a positive control for quantitating relative telomerase activity levels. Lane 13 contains a negative control without cell lysate. IC denotes a standard internal control for PCR efficiency.

    Techniques Used: Isolation, Nucleic Acid Electrophoresis, Molecular Weight, Hybridization, Polymerase Chain Reaction, Amplification, Marker, Activity Assay, TRAP Assay, Serial Dilution, Positive Control, Negative Control

    15) Product Images from "Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat"

    Article Title: Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.67.10.4414-4425.2001

    ARDRA of distinct strains of the most abundant bacterial populations isolated from wheat rhizospheres in this study. All bacteria were cultured on 1/3× KMB +++ . ARDRA of 16S sequences was performed using Msp I and Rsa I. Restriction digests of 16S sequences amplified from the most abundant cultured bacteria obtained from the 1998 (lanes 1 through 5) and 1999 (lanes 6 through 12) growth chamber experiments are shown, as are digests of sequences obtained from bacteria with the capacity to inhibit G . graminis var. tritici in vitro (lanes 13 through 15). The ARDRA group designation for each strain is indicated at the bottom of the figure. The five ARDRA groups identified in the1998 samples are represented by isolates U5 (lane 1), dI14 (lane 2), U3 (lane 3), dU1 (lane 4), and U1 (lane 5). The seven ARDRA groups identified in the 1999 samples are represented by strains C201A (lane 6), C201 (lane 7), C2+6 (lane 8), C2+4 (lane 9), E1+1 (lane 10), E102 (lane 11), and C204B (lane 12). In addition, representative strains with the ability to inhibit the take-all pathogen are also displayed: strain dI1 (lane 13), strain E206 (lane 14), and phlD + strain MtV1 (lane 15). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.
    Figure Legend Snippet: ARDRA of distinct strains of the most abundant bacterial populations isolated from wheat rhizospheres in this study. All bacteria were cultured on 1/3× KMB +++ . ARDRA of 16S sequences was performed using Msp I and Rsa I. Restriction digests of 16S sequences amplified from the most abundant cultured bacteria obtained from the 1998 (lanes 1 through 5) and 1999 (lanes 6 through 12) growth chamber experiments are shown, as are digests of sequences obtained from bacteria with the capacity to inhibit G . graminis var. tritici in vitro (lanes 13 through 15). The ARDRA group designation for each strain is indicated at the bottom of the figure. The five ARDRA groups identified in the1998 samples are represented by isolates U5 (lane 1), dI14 (lane 2), U3 (lane 3), dU1 (lane 4), and U1 (lane 5). The seven ARDRA groups identified in the 1999 samples are represented by strains C201A (lane 6), C201 (lane 7), C2+6 (lane 8), C2+4 (lane 9), E1+1 (lane 10), E102 (lane 11), and C204B (lane 12). In addition, representative strains with the ability to inhibit the take-all pathogen are also displayed: strain dI1 (lane 13), strain E206 (lane 14), and phlD + strain MtV1 (lane 15). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Techniques Used: Isolation, Cell Culture, Amplification, In Vitro

    FT-ARDRA of bacterial communities inhabiting the rhizospheres of healthy and diseased wheat grown in growth chambers. The analysis shown was perfomed on rhizosphere washes of diseased (D) and healthy (H) plants grown in soil A which had been collected from Mount Vernon, Wash., following harvest in 1998. The T-RFLP profiles were generated from amplified 16S sequences digested with either Msp I or Rsa I. In each panel, overlaid chromatographic traces from four independent samples are displayed. The data for two serial dilutions (3 and 4) of rhizosphere washes from each condition (D and H) are shown. Signals corresponding to TRFs that increased significantly in the rhizospheres of diseased plants in all of the 1998 and 1999 growth chamber experiments are indicated by black arrows, while those specific to this 1998 experiment are indicated by grey arrows. The size of each TRF in base pairs is indicated by the horizontal scale at the top the GeneScan results display, and the abundance of each is correlated with the peak area given in arbitrary fluorescence units on the vertical scale.
    Figure Legend Snippet: FT-ARDRA of bacterial communities inhabiting the rhizospheres of healthy and diseased wheat grown in growth chambers. The analysis shown was perfomed on rhizosphere washes of diseased (D) and healthy (H) plants grown in soil A which had been collected from Mount Vernon, Wash., following harvest in 1998. The T-RFLP profiles were generated from amplified 16S sequences digested with either Msp I or Rsa I. In each panel, overlaid chromatographic traces from four independent samples are displayed. The data for two serial dilutions (3 and 4) of rhizosphere washes from each condition (D and H) are shown. Signals corresponding to TRFs that increased significantly in the rhizospheres of diseased plants in all of the 1998 and 1999 growth chamber experiments are indicated by black arrows, while those specific to this 1998 experiment are indicated by grey arrows. The size of each TRF in base pairs is indicated by the horizontal scale at the top the GeneScan results display, and the abundance of each is correlated with the peak area given in arbitrary fluorescence units on the vertical scale.

    Techniques Used: Generated, Amplification, Fluorescence

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    Polymerase Chain Reaction:

    Article Title: Use of stable isotope-labelled cells to identify active grazers of picocyanobacteria in ocean surface waters
    Article Snippet: .. PCR products were digested with the restriction endonucleases HhaI and RsaI (New England Biolabs, Ipswich, MA, USA). ..

    Article Title: Molecular appraisal of intestinal parasitic infection in transplant recipients
    Article Snippet: .. Small subunit ribosomal RNA (SSUrRNA ), Cryptosporidium oocyst wall protein (COWP ), dihydrofolate reductase (DHFR ) using previously described primers and PCR conditions were used for genotyping, and RFLP was performed using restriction enzymes Ssp I and Ase I (New England Biolabs, USA) for SSUrRNA gene ( ) and Rsa I (New England Biolabs, USA) for COWP gene ( ). .. Cryptosporidium glycoprotein (Cpgp40/15 ) locus was amplified using previously described primers and PCR conditions for subgenotyping Cryptosporidium species and RFLP was done using Rsa I (New England Biolabs) restriction enzyme ( ).

    Amplification:

    Article Title: Assessment of Microbial Diversity in Four Southwestern United States Soils by 16S rRNA Gene Terminal Restriction Fragment Analysis
    Article Snippet: .. Fluorescent amplification products were ethanol precipitated and resuspended in 25 μl of sterile, distilled water, and 8 μl was digested with 5 U of Rsa I (New England Biolabs, Beverly, Mass.) in 12-μl reaction mixtures. .. Following restriction digestion, 1 μl of each digest was dried, suspended in 1.75 μl of loading buffer containing 0.25 μl of Genescan 2500 TAMRA size standard (ABI), a 5:1 mixture of deionized formamide-blue dextran, and 25 mM EDTA, and then denatured at 94°C for 2 min. Fragments were separated by electrophoresis in denaturing 4% polyacrylamide gels with an ABI 377 DNA sequencer.

    Agarose Gel Electrophoresis:

    Article Title: Development and Evaluation of a Real-Time PCR Assay for Detection of Klebsiella pneumoniae Carbapenemase Genes ▿
    Article Snippet: .. The following cycling conditions were used: 95o for 2 min, followed by 35 cycles of 94°C for 2 s, 62°C for 10 s, and 72°C for 15 s. The amplicons from KPC-positive samples were then digested at 48°C for 1 h in RsaI and BstNI (New England Biolabs, Ipswitch, MA) using NEB buffer 2 (New England Biolabs) and electrophoresed on a 2% agarose gel to differentiate bla KPC-1 , bla KPC-2 , and bla KPC-3 . ..

    Methylation:

    Article Title: Interplay between Cellular Methyl Metabolism and Adaptive Efflux during Oncogenic Transformation from Chronic Arsenic Exposure in Human Cells *Interplay between Cellular Methyl Metabolism and Adaptive Efflux during Oncogenic Transformation from Chronic Arsenic Exposure in Human Cells * S⃞
    Article Snippet: .. Restriction Enzyme Digestions of Genomic DNA —One μg of DNA from control and arsenic-treated cells at 4 weeks of arsenic exposure was separately digested with either 10 units of RsaI, 10 units each of RsaI and the methylation-sensitive restriction enzyme HpaII, or 10 units each of RsaI and MspI (New England BioLabs, Ipswich, MA) at 37 °C for 16 h. This was followed by heat inactivation of the enzymes at 65 °C for 20 min. .. HpaII does not cut DNA if the internal cytosine of its restriction site (CCGG) is methylated.

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    New England Biolabs rsa i
    F36VFGFR1 supports the survival of long-term repopulating HSCs during growth factor deprivation. Marrow cells (5 × 10 5 ) transduced with the F36VFGFR1 vector were transplanted into lethally irradiated recipients either immediately following transduction (A) or after 1 (B) or 5 days (C) of culture in the presence (solid symbols) or absence (open symbols) of 100 nM AP20187. Mice that were given transplants of cultured cells received all the progeny generated in cultures initiated with 5 × 10 5 transduced cells at day 0. Each line depicts results from a single mouse. One mouse (6281) that was given transplants of cells cultured for 5 days in AP20187 was killed at day 174 after transplantation and 5 × 10 6 marrow cells from this mouse were transplanted into 2 lethally irradiated secondary recipients (symbols × and +). E indicates erythroid; P, platelets, G, granulocytes; M, monocytes; B, B cells; and T, T cells. (C; inserts) LAM-PCR using <t>Rsa</t> I confirms common provirus insertion patterns in the granulocytes (G), monocytes (M), B cells (B), and T cells (T) of mouse 6281. MW indicates DNA ladder. Similar results were obtained using 2 other restriction enzymes, <t>Tsp509</t> I and Hae III. Sequencing of LAM-PCR products from mouse 6281 (panel D) revealed provirus insertion sites at the indicated positions in chromosomes 4 and 16, and their presence in the indicated lineages was confirmed by PCR using using an LTR primer, a host genomic primer, and 38 cycles of amplification. A second independent experiment performed in serum-free conditions showed a similar trend at 64 days after transplantation.
    Rsa I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 163 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs rsa i restriction enzyme
    The Slx4-Rtt107 complex modulates long-range DSB resection. ( A ) Schematic illustration of MAT locus in JKM179 strains showing positions of HO-cut site, SspI restriction sites and the RNA probe used. ( B ) ssDNA visualization using RNA probe as described in ( A ) in indicated mutants after inducing HO in nocodazole arrested cells. ( C ) Resection products analysis by densitometry. Plotted values are the mean values ± SEM from two independent experiments performed as in ( B ). ( D ) Schematic illustration of DSB resection at the indicated <t>Rsa</t> I sites, 5 kb and 10 kb distal from the irreparable HO cut at the MAT locus on chromosome III. ( E – G ) DSB resection analysis by qPCR in nocodazole-arrested JKM179 derivative strains. Plotted values are the mean of at least two independent experiments ± SEM. Where indicated, significance was determined by single-tailed Student's t test (*for P
    Rsa I Restriction Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    F36VFGFR1 supports the survival of long-term repopulating HSCs during growth factor deprivation. Marrow cells (5 × 10 5 ) transduced with the F36VFGFR1 vector were transplanted into lethally irradiated recipients either immediately following transduction (A) or after 1 (B) or 5 days (C) of culture in the presence (solid symbols) or absence (open symbols) of 100 nM AP20187. Mice that were given transplants of cultured cells received all the progeny generated in cultures initiated with 5 × 10 5 transduced cells at day 0. Each line depicts results from a single mouse. One mouse (6281) that was given transplants of cells cultured for 5 days in AP20187 was killed at day 174 after transplantation and 5 × 10 6 marrow cells from this mouse were transplanted into 2 lethally irradiated secondary recipients (symbols × and +). E indicates erythroid; P, platelets, G, granulocytes; M, monocytes; B, B cells; and T, T cells. (C; inserts) LAM-PCR using Rsa I confirms common provirus insertion patterns in the granulocytes (G), monocytes (M), B cells (B), and T cells (T) of mouse 6281. MW indicates DNA ladder. Similar results were obtained using 2 other restriction enzymes, Tsp509 I and Hae III. Sequencing of LAM-PCR products from mouse 6281 (panel D) revealed provirus insertion sites at the indicated positions in chromosomes 4 and 16, and their presence in the indicated lineages was confirmed by PCR using using an LTR primer, a host genomic primer, and 38 cycles of amplification. A second independent experiment performed in serum-free conditions showed a similar trend at 64 days after transplantation.

    Journal: Blood

    Article Title: Growth factor receptors as regulators of hematopoiesis

    doi: 10.1182/blood-2006-01-012278

    Figure Lengend Snippet: F36VFGFR1 supports the survival of long-term repopulating HSCs during growth factor deprivation. Marrow cells (5 × 10 5 ) transduced with the F36VFGFR1 vector were transplanted into lethally irradiated recipients either immediately following transduction (A) or after 1 (B) or 5 days (C) of culture in the presence (solid symbols) or absence (open symbols) of 100 nM AP20187. Mice that were given transplants of cultured cells received all the progeny generated in cultures initiated with 5 × 10 5 transduced cells at day 0. Each line depicts results from a single mouse. One mouse (6281) that was given transplants of cells cultured for 5 days in AP20187 was killed at day 174 after transplantation and 5 × 10 6 marrow cells from this mouse were transplanted into 2 lethally irradiated secondary recipients (symbols × and +). E indicates erythroid; P, platelets, G, granulocytes; M, monocytes; B, B cells; and T, T cells. (C; inserts) LAM-PCR using Rsa I confirms common provirus insertion patterns in the granulocytes (G), monocytes (M), B cells (B), and T cells (T) of mouse 6281. MW indicates DNA ladder. Similar results were obtained using 2 other restriction enzymes, Tsp509 I and Hae III. Sequencing of LAM-PCR products from mouse 6281 (panel D) revealed provirus insertion sites at the indicated positions in chromosomes 4 and 16, and their presence in the indicated lineages was confirmed by PCR using using an LTR primer, a host genomic primer, and 38 cycles of amplification. A second independent experiment performed in serum-free conditions showed a similar trend at 64 days after transplantation.

    Article Snippet: Products were divided into 3 equal arms and digested with Tsp509 I, Hae III, or Rsa I (New England BioLabs).

    Techniques: Transduction, Plasmid Preparation, Irradiation, Mouse Assay, Cell Culture, Generated, Transplantation Assay, Laser Capture Microdissection, Polymerase Chain Reaction, Sequencing, Amplification

    Restriction fragment length polymorphism assay using Rsa I RE for Cryptosporidium oocyst wall protein gene. Lane 1 - 100 bp DNA ladder, lanes 2, 3, 4 - Cryptosporidium hominis isolates ( Rsa I - 284, 129, 106 bp).

    Journal: The Indian Journal of Medical Research

    Article Title: Molecular appraisal of intestinal parasitic infection in transplant recipients

    doi: 10.4103/0971-5916.195041

    Figure Lengend Snippet: Restriction fragment length polymorphism assay using Rsa I RE for Cryptosporidium oocyst wall protein gene. Lane 1 - 100 bp DNA ladder, lanes 2, 3, 4 - Cryptosporidium hominis isolates ( Rsa I - 284, 129, 106 bp).

    Article Snippet: Small subunit ribosomal RNA (SSUrRNA ), Cryptosporidium oocyst wall protein (COWP ), dihydrofolate reductase (DHFR ) using previously described primers and PCR conditions were used for genotyping, and RFLP was performed using restriction enzymes Ssp I and Ase I (New England Biolabs, USA) for SSUrRNA gene ( ) and Rsa I (New England Biolabs, USA) for COWP gene ( ).

    Techniques: Polymorphism Assay

    Restriction fragment length polymorphism assay using Rsa I RE for Cpgp40 /15 gene. Lane 1 - Ie isolates (424, 159, 134, 129, 106 bp), lanes 2, 4 - Ia (391, 241, 159, 143 bp), lane 3 - IIc (356, 256, 143 bp), lane 5 - 100 bp DNA ladder.

    Journal: The Indian Journal of Medical Research

    Article Title: Molecular appraisal of intestinal parasitic infection in transplant recipients

    doi: 10.4103/0971-5916.195041

    Figure Lengend Snippet: Restriction fragment length polymorphism assay using Rsa I RE for Cpgp40 /15 gene. Lane 1 - Ie isolates (424, 159, 134, 129, 106 bp), lanes 2, 4 - Ia (391, 241, 159, 143 bp), lane 3 - IIc (356, 256, 143 bp), lane 5 - 100 bp DNA ladder.

    Article Snippet: Small subunit ribosomal RNA (SSUrRNA ), Cryptosporidium oocyst wall protein (COWP ), dihydrofolate reductase (DHFR ) using previously described primers and PCR conditions were used for genotyping, and RFLP was performed using restriction enzymes Ssp I and Ase I (New England Biolabs, USA) for SSUrRNA gene ( ) and Rsa I (New England Biolabs, USA) for COWP gene ( ).

    Techniques: Polymorphism Assay, IA

    TEL-FISH quantitation results. A: Box and whisker plot of relative telomere signals from four LNCaP sublines each possessing distinctly different telomere lengths ( n = 10 to 12 cells measured per subline). The boxed region encloses the 25th through 75th percentiles, with the horizontal line indicating the median. Whiskers include the 5th to 95th percentiles, open circles represent outliers. B: TRF-Southern blot of LNCaP sublines (numbered 1 to 4). Genomic DNA was digested with Rsa I and Msp I, blotted, and probed with a radiolabeled telomere-specific oligonucleotide primer. Molecular weight markers (M) are labeled in Kbp. C: Relative mean telomere fluorescence signals for each LNCaP subline ( large circles ) plus additional cell lines ( diamonds ) plotted against mean telomere length calculated from TRF-Southern data collected on the same cells. Cell lines (all human-derived) included the prostate cancer (LNCaP, PC-3, and DU145)-, leukemia (HL-60)-, and colon cancer (HCT116)-derived lines. The trend line indicates linear regression results.

    Journal: The American Journal of Pathology

    Article Title: Telomere Length Assessment in Human Archival Tissues

    doi:

    Figure Lengend Snippet: TEL-FISH quantitation results. A: Box and whisker plot of relative telomere signals from four LNCaP sublines each possessing distinctly different telomere lengths ( n = 10 to 12 cells measured per subline). The boxed region encloses the 25th through 75th percentiles, with the horizontal line indicating the median. Whiskers include the 5th to 95th percentiles, open circles represent outliers. B: TRF-Southern blot of LNCaP sublines (numbered 1 to 4). Genomic DNA was digested with Rsa I and Msp I, blotted, and probed with a radiolabeled telomere-specific oligonucleotide primer. Molecular weight markers (M) are labeled in Kbp. C: Relative mean telomere fluorescence signals for each LNCaP subline ( large circles ) plus additional cell lines ( diamonds ) plotted against mean telomere length calculated from TRF-Southern data collected on the same cells. Cell lines (all human-derived) included the prostate cancer (LNCaP, PC-3, and DU145)-, leukemia (HL-60)-, and colon cancer (HCT116)-derived lines. The trend line indicates linear regression results.

    Article Snippet: Restriction enzymes Msp I (catalog no. 106S) and Rsa I (catalog no. 167S) were obtained from New England Biolabs, Beverly, MA.

    Techniques: Fluorescence In Situ Hybridization, Quantitation Assay, Whisker Assay, Southern Blot, Molecular Weight, Labeling, Fluorescence, Derivative Assay

    The Slx4-Rtt107 complex modulates long-range DSB resection. ( A ) Schematic illustration of MAT locus in JKM179 strains showing positions of HO-cut site, SspI restriction sites and the RNA probe used. ( B ) ssDNA visualization using RNA probe as described in ( A ) in indicated mutants after inducing HO in nocodazole arrested cells. ( C ) Resection products analysis by densitometry. Plotted values are the mean values ± SEM from two independent experiments performed as in ( B ). ( D ) Schematic illustration of DSB resection at the indicated Rsa I sites, 5 kb and 10 kb distal from the irreparable HO cut at the MAT locus on chromosome III. ( E – G ) DSB resection analysis by qPCR in nocodazole-arrested JKM179 derivative strains. Plotted values are the mean of at least two independent experiments ± SEM. Where indicated, significance was determined by single-tailed Student's t test (*for P

    Journal: Nucleic Acids Research

    Article Title: Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaks

    doi: 10.1093/nar/gkv1080

    Figure Lengend Snippet: The Slx4-Rtt107 complex modulates long-range DSB resection. ( A ) Schematic illustration of MAT locus in JKM179 strains showing positions of HO-cut site, SspI restriction sites and the RNA probe used. ( B ) ssDNA visualization using RNA probe as described in ( A ) in indicated mutants after inducing HO in nocodazole arrested cells. ( C ) Resection products analysis by densitometry. Plotted values are the mean values ± SEM from two independent experiments performed as in ( B ). ( D ) Schematic illustration of DSB resection at the indicated Rsa I sites, 5 kb and 10 kb distal from the irreparable HO cut at the MAT locus on chromosome III. ( E – G ) DSB resection analysis by qPCR in nocodazole-arrested JKM179 derivative strains. Plotted values are the mean of at least two independent experiments ± SEM. Where indicated, significance was determined by single-tailed Student's t test (*for P

    Article Snippet: The DNA was digested with the Rsa I restriction enzyme (NEB), which cuts inside the amplicons at 5 kb and 10 kb from the HO-cut site, but not in the PRE1 control region on chromosome V.

    Techniques: Real-time Polymerase Chain Reaction