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    AclI
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    AclI 1 500 units
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    R0598L
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    Restriction Enzymes
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    1 500 units
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    New England Biolabs acli
    AclI
    AclI 1 500 units
    https://www.bioz.com/result/acli/product/New England Biolabs
    Average 96 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    acli - by Bioz Stars, 2021-06
    96/100 stars

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    1) Product Images from "EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates"

    Article Title: EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates

    Journal: RNA

    doi: 10.1261/rna.048785.114

    Analysis of Drosophila histone mRNAs. ( A , B ) RNA from Drosophila ovary dH2a ( A ) and dH3 ( B ) was analyzed by EnD-Seq using a strategy to amplify the histone mRNAs selectively. Essentially all the 3′ ends mapped to the 3′ side of the stem in the stem–loop. The graphs represent the distribution of all recovered 3′ ends (with or without nontemplated tails) for each developmental stage. The inset shows the expansion of the distribution of 3′ ends from nucleotides −4 to −10 covering the 3′ side of the stem. ( C ) Pie charts showing nucleotide composition of single nucleotide tails in embryo ( top ) and ovary ( bottom ). ( D , E ) Distribution of 3′ ends and nontemplated tails in 3–6 h Drosophila embryos for ( D ) dH2a and ( E ) dH3. Note that the pattern of tail addition matches the ovary genes in ( A ) and ( B ) but the nucleotide composition is different. ( F ) Distribution of tail lengths for tails longer than 2 nt in the ovary RNA mapping between nucleotides 4 and 10 in the 3′ end of the stem. The tails > 2 nt in the ovary were predominantly oligo(A). The tails of 1 or 2 nt in the embryo at nucleotides 4–10 were predominantly U's, and there were very few tails longer than 2 nt. ( G ) Chart showing the distribution of tail length between mRNA positions −4 and −10. Note that there are very few long tails. ( H ) S1 nuclease mapping of ovary histone mRNAs. Total RNA from ovaries was fractionated into poly(A + ) and poly(A − ) fractions on oligo(dT) cellulose. Total RNA, and equal proportions of the poly(A − ) and poly(A + ) RNA, were subjected to S1 nuclease mapping using the histone H2a gene labeled at the 3′ end of the AclI site as a probe. The S1 resistant fragments were resolved on a 6% polyacrylamine-7M urea gel and detected by autoradiography. A diagram of the S1 assay is shown on the left . The arrow indicates the fragment protected by the full-length mRNA. ( I ) RT-PCR analysis of the histone H2a mRNA. cDNA primed with oligo(dT) fused to an anchor primer was synthesized from 1 μg of total RNA from adult males, ovaries, 0–1 h embryos, and 3–6 h embryos, and then amplified using a primer near the 5′ end of the H2a mRNA. An amplicon of full-length H2a mRNA would be ∼500 nt long. Several amplicons were cloned and the majority had A-tails added in the 3′ end of the stem, consistent with the high-throughput sequencing data.
    Figure Legend Snippet: Analysis of Drosophila histone mRNAs. ( A , B ) RNA from Drosophila ovary dH2a ( A ) and dH3 ( B ) was analyzed by EnD-Seq using a strategy to amplify the histone mRNAs selectively. Essentially all the 3′ ends mapped to the 3′ side of the stem in the stem–loop. The graphs represent the distribution of all recovered 3′ ends (with or without nontemplated tails) for each developmental stage. The inset shows the expansion of the distribution of 3′ ends from nucleotides −4 to −10 covering the 3′ side of the stem. ( C ) Pie charts showing nucleotide composition of single nucleotide tails in embryo ( top ) and ovary ( bottom ). ( D , E ) Distribution of 3′ ends and nontemplated tails in 3–6 h Drosophila embryos for ( D ) dH2a and ( E ) dH3. Note that the pattern of tail addition matches the ovary genes in ( A ) and ( B ) but the nucleotide composition is different. ( F ) Distribution of tail lengths for tails longer than 2 nt in the ovary RNA mapping between nucleotides 4 and 10 in the 3′ end of the stem. The tails > 2 nt in the ovary were predominantly oligo(A). The tails of 1 or 2 nt in the embryo at nucleotides 4–10 were predominantly U's, and there were very few tails longer than 2 nt. ( G ) Chart showing the distribution of tail length between mRNA positions −4 and −10. Note that there are very few long tails. ( H ) S1 nuclease mapping of ovary histone mRNAs. Total RNA from ovaries was fractionated into poly(A + ) and poly(A − ) fractions on oligo(dT) cellulose. Total RNA, and equal proportions of the poly(A − ) and poly(A + ) RNA, were subjected to S1 nuclease mapping using the histone H2a gene labeled at the 3′ end of the AclI site as a probe. The S1 resistant fragments were resolved on a 6% polyacrylamine-7M urea gel and detected by autoradiography. A diagram of the S1 assay is shown on the left . The arrow indicates the fragment protected by the full-length mRNA. ( I ) RT-PCR analysis of the histone H2a mRNA. cDNA primed with oligo(dT) fused to an anchor primer was synthesized from 1 μg of total RNA from adult males, ovaries, 0–1 h embryos, and 3–6 h embryos, and then amplified using a primer near the 5′ end of the H2a mRNA. An amplicon of full-length H2a mRNA would be ∼500 nt long. Several amplicons were cloned and the majority had A-tails added in the 3′ end of the stem, consistent with the high-throughput sequencing data.

    Techniques Used: Labeling, Autoradiography, Reverse Transcription Polymerase Chain Reaction, Synthesized, Amplification, Clone Assay, Next-Generation Sequencing

    Related Articles

    DNA Sequencing:

    Article Title: Geographic separation and genetic differentiation of populations are not coupled with niche differentiation in threatened Kaiser’s spotted newt (Neurergus kaiseri)
    Article Snippet: Genomic DNA was extracted using the Macherey-Nagel NucleoSpin Tissue kit following the manufacturer’s instructions. .. We performed double-digest Restriction Site Associated DNA sequencing (ddRADseq ) preparing the library as follows : 1 μg of DNA from each individual was double-digested using the PstI-HF and AclI restriction enzymes (NewEngland Biolabs) and modified Illumina adaptors with unique barcodes for each individual were ligated to obtained DNA fragments. .. Samples were multiplexed (pooled) and a Pippin Prep was used to select for fragments with a size around a tight range of 383 bp, based on the fragment length distribution identified using a 2200 TapeStation instrument (Agilent Technologies).

    Modification:

    Article Title: Geographic separation and genetic differentiation of populations are not coupled with niche differentiation in threatened Kaiser’s spotted newt (Neurergus kaiseri)
    Article Snippet: Genomic DNA was extracted using the Macherey-Nagel NucleoSpin Tissue kit following the manufacturer’s instructions. .. We performed double-digest Restriction Site Associated DNA sequencing (ddRADseq ) preparing the library as follows : 1 μg of DNA from each individual was double-digested using the PstI-HF and AclI restriction enzymes (NewEngland Biolabs) and modified Illumina adaptors with unique barcodes for each individual were ligated to obtained DNA fragments. .. Samples were multiplexed (pooled) and a Pippin Prep was used to select for fragments with a size around a tight range of 383 bp, based on the fragment length distribution identified using a 2200 TapeStation instrument (Agilent Technologies).

    Article Title: Polarly localized receptor-like kinases PXC2 and IRK act redundantly during Arabidopsis root development in the radial axis
    Article Snippet: Plasmids were amplified in ccdB-resistant E. coli and plasmids prepped with a Bio Basic Plasmid DNA Miniprep kit. .. 34uL of the modified dpGreenBarT and unmodified pGII0125 were digested with 1ul each FspI and AclI in CutSmart buffer (NEB) for 1hr at 37°C. ..

    Polymerase Chain Reaction:

    Article Title: Two Distinct Genetic Elements Are Responsible for erm(TR)-Mediated Erythromycin Resistance in Tetracycline-Susceptible and Tetracycline-Resistant Strains of Streptococcus pyogenes ▿ ▿ †
    Article Snippet: Inverse PCR ( ) was carried out to analyze unknown DNA regions. .. Genomic DNA digested with endonucleases MunI, HindIII (Roche Applied Science, Basel, Switzerland), BanI, Hpy188I, or AclI (New England Biolabs, Ipswich, MA) was ligated and used as the template in the PCR assays. .. Overlapping fragments of the erm (TR)-carrying elements were obtained by PCR assays and primer walking techniques using suitable primer pairs.

    Article Title: CX3CR1 Receptor Polymorphisms, Th1 Cell Recruitment, and Acute Myocardial Infarction Outcome: Looking for a Link
    Article Snippet: Amplification reactions were performed using 35 cycles of 95°C, 69°C, and 72°C for 30 seconds each, preceded by a single cycle of 95°C for 3 minutes and followed by a single cycle of 72°C for 10 minutes. .. In order to type the alleles at codons 249 and 280, 5 μ L of PCR reaction was digested, respectively, with Acl I (New England Biolabs, Beverly, MA) or BsbmB1 (New England Biolabs, Beverly, MA) in 20 μ L of reaction as previously described [ ]. .. In order to evaluate the efficiency of endonucleases enzymes, control DNA with Acl I and Bst 4CI restriction sites was used, and DNA was loaded at different times on agarose gel.

    Article Title: Molecular evidence of iron limitation and availability in the global diazotroph Trichodesmium
    Article Snippet: The PCR cyling conditions were: 50 °C for 2 min, 95 °C for 10 min; 40 cycles of 95 °C for 15 s, 55 °C for 1 min; followed by a final extension at 60 °C for 5 min. For the Hae III restriction digest, 5 μl of PCR product was incubated with 25 units of Hae III (New England Biolabs, Ipswich, MA, USA) and 1 × NEB4 buffer in a final volume of 47.5 μl for 3 h at 37 °C, followed by 20 min at 80 °C. .. For the Acl I restriction digest, 5 μl of PCR product was incubated with 7.5 units of Acl I (New England Biolabs) and 1 × NEB4 buffer in a final volume of 45 μl for 3 h at 37 °C. .. Uncut and cut PCR products were run side by side on a 1.5% agarose gel and imaged using GeneSnap imaging software on a ChemiGenius2 gel documentation system (Synoptics Ltd, Cambridge, UK).

    Generated:

    Article Title: EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates
    Article Snippet: .. Briefly, the probe was generated by end labeling H2a DNA digested with AclI with α-32 P-dCTP and Klenow Polymerase (NEB). .. After release from the TOPO TA vector (Invitrogen) by digestion with HindIII (NEB), the probe was gel purified and hybridized with the indicated RNA sample at either at 40°C overnight.

    End Labeling:

    Article Title: EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates
    Article Snippet: .. Briefly, the probe was generated by end labeling H2a DNA digested with AclI with α-32 P-dCTP and Klenow Polymerase (NEB). .. After release from the TOPO TA vector (Invitrogen) by digestion with HindIII (NEB), the probe was gel purified and hybridized with the indicated RNA sample at either at 40°C overnight.

    Stable Transfection:

    Article Title: Rad51 Promoter-Targeted Gene Therapy Is Effective for In Vivo Visualization and Treatment of Cancer
    Article Snippet: Cells were grown on treated polystyrene cell culture dishes (Corning) at 37 °C in 3% O2 , 5% CO2 , and 97% relative humidity in HERA Cell 240 incubators. .. HeLa cells stably expressing firefly luciferase, termed HeLa-Luc, were made by transfecting HeLa cells at 50% confluence with 2 µg of Acl I (New England Biolabs, Ipswich, MA) linearized pCDNA3-Lucferase (Addgene plasmid 18964, William G. Kaelin) using Fugene 6 transfection agent (Roche). .. Twenty-four hours after transfection, cells were selected for antibiotic resistance by replacing the media with new media containing Geneticin at a final concentrating of 2 mg/ml.

    Expressing:

    Article Title: Rad51 Promoter-Targeted Gene Therapy Is Effective for In Vivo Visualization and Treatment of Cancer
    Article Snippet: Cells were grown on treated polystyrene cell culture dishes (Corning) at 37 °C in 3% O2 , 5% CO2 , and 97% relative humidity in HERA Cell 240 incubators. .. HeLa cells stably expressing firefly luciferase, termed HeLa-Luc, were made by transfecting HeLa cells at 50% confluence with 2 µg of Acl I (New England Biolabs, Ipswich, MA) linearized pCDNA3-Lucferase (Addgene plasmid 18964, William G. Kaelin) using Fugene 6 transfection agent (Roche). .. Twenty-four hours after transfection, cells were selected for antibiotic resistance by replacing the media with new media containing Geneticin at a final concentrating of 2 mg/ml.

    Luciferase:

    Article Title: Rad51 Promoter-Targeted Gene Therapy Is Effective for In Vivo Visualization and Treatment of Cancer
    Article Snippet: Cells were grown on treated polystyrene cell culture dishes (Corning) at 37 °C in 3% O2 , 5% CO2 , and 97% relative humidity in HERA Cell 240 incubators. .. HeLa cells stably expressing firefly luciferase, termed HeLa-Luc, were made by transfecting HeLa cells at 50% confluence with 2 µg of Acl I (New England Biolabs, Ipswich, MA) linearized pCDNA3-Lucferase (Addgene plasmid 18964, William G. Kaelin) using Fugene 6 transfection agent (Roche). .. Twenty-four hours after transfection, cells were selected for antibiotic resistance by replacing the media with new media containing Geneticin at a final concentrating of 2 mg/ml.

    Plasmid Preparation:

    Article Title: Rad51 Promoter-Targeted Gene Therapy Is Effective for In Vivo Visualization and Treatment of Cancer
    Article Snippet: Cells were grown on treated polystyrene cell culture dishes (Corning) at 37 °C in 3% O2 , 5% CO2 , and 97% relative humidity in HERA Cell 240 incubators. .. HeLa cells stably expressing firefly luciferase, termed HeLa-Luc, were made by transfecting HeLa cells at 50% confluence with 2 µg of Acl I (New England Biolabs, Ipswich, MA) linearized pCDNA3-Lucferase (Addgene plasmid 18964, William G. Kaelin) using Fugene 6 transfection agent (Roche). .. Twenty-four hours after transfection, cells were selected for antibiotic resistance by replacing the media with new media containing Geneticin at a final concentrating of 2 mg/ml.

    Transfection:

    Article Title: Rad51 Promoter-Targeted Gene Therapy Is Effective for In Vivo Visualization and Treatment of Cancer
    Article Snippet: Cells were grown on treated polystyrene cell culture dishes (Corning) at 37 °C in 3% O2 , 5% CO2 , and 97% relative humidity in HERA Cell 240 incubators. .. HeLa cells stably expressing firefly luciferase, termed HeLa-Luc, were made by transfecting HeLa cells at 50% confluence with 2 µg of Acl I (New England Biolabs, Ipswich, MA) linearized pCDNA3-Lucferase (Addgene plasmid 18964, William G. Kaelin) using Fugene 6 transfection agent (Roche). .. Twenty-four hours after transfection, cells were selected for antibiotic resistance by replacing the media with new media containing Geneticin at a final concentrating of 2 mg/ml.

    Incubation:

    Article Title: Molecular evidence of iron limitation and availability in the global diazotroph Trichodesmium
    Article Snippet: The PCR cyling conditions were: 50 °C for 2 min, 95 °C for 10 min; 40 cycles of 95 °C for 15 s, 55 °C for 1 min; followed by a final extension at 60 °C for 5 min. For the Hae III restriction digest, 5 μl of PCR product was incubated with 25 units of Hae III (New England Biolabs, Ipswich, MA, USA) and 1 × NEB4 buffer in a final volume of 47.5 μl for 3 h at 37 °C, followed by 20 min at 80 °C. .. For the Acl I restriction digest, 5 μl of PCR product was incubated with 7.5 units of Acl I (New England Biolabs) and 1 × NEB4 buffer in a final volume of 45 μl for 3 h at 37 °C. .. Uncut and cut PCR products were run side by side on a 1.5% agarose gel and imaged using GeneSnap imaging software on a ChemiGenius2 gel documentation system (Synoptics Ltd, Cambridge, UK).

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    New England Biolabs acli
    Analysis of Drosophila histone mRNAs. ( A , B ) RNA from Drosophila ovary dH2a ( A ) and dH3 ( B ) was analyzed by EnD-Seq using a strategy to amplify the histone mRNAs selectively. Essentially all the 3′ ends mapped to the 3′ side of the stem in the stem–loop. The graphs represent the distribution of all recovered 3′ ends (with or without nontemplated tails) for each developmental stage. The inset shows the expansion of the distribution of 3′ ends from nucleotides −4 to −10 covering the 3′ side of the stem. ( C ) Pie charts showing nucleotide composition of single nucleotide tails in embryo ( top ) and ovary ( bottom ). ( D , E ) Distribution of 3′ ends and nontemplated tails in 3–6 h Drosophila embryos for ( D ) dH2a and ( E ) dH3. Note that the pattern of tail addition matches the ovary genes in ( A ) and ( B ) but the nucleotide composition is different. ( F ) Distribution of tail lengths for tails longer than 2 nt in the ovary RNA mapping between nucleotides 4 and 10 in the 3′ end of the stem. The tails > 2 nt in the ovary were predominantly oligo(A). The tails of 1 or 2 nt in the embryo at nucleotides 4–10 were predominantly U's, and there were very few tails longer than 2 nt. ( G ) Chart showing the distribution of tail length between mRNA positions −4 and −10. Note that there are very few long tails. ( H ) S1 nuclease mapping of ovary histone mRNAs. Total RNA from ovaries was fractionated into poly(A + ) and poly(A − ) fractions on oligo(dT) cellulose. Total RNA, and equal proportions of the poly(A − ) and poly(A + ) RNA, were subjected to S1 nuclease mapping using the histone <t>H2a</t> gene labeled at the 3′ end of the <t>AclI</t> site as a probe. The S1 resistant fragments were resolved on a 6% polyacrylamine-7M urea gel and detected by autoradiography. A diagram of the S1 assay is shown on the left . The arrow indicates the fragment protected by the full-length mRNA. ( I ) RT-PCR analysis of the histone H2a mRNA. cDNA primed with oligo(dT) fused to an anchor primer was synthesized from 1 μg of total RNA from adult males, ovaries, 0–1 h embryos, and 3–6 h embryos, and then amplified using a primer near the 5′ end of the H2a mRNA. An amplicon of full-length H2a mRNA would be ∼500 nt long. Several amplicons were cloned and the majority had A-tails added in the 3′ end of the stem, consistent with the high-throughput sequencing data.
    Acli, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Analysis of Drosophila histone mRNAs. ( A , B ) RNA from Drosophila ovary dH2a ( A ) and dH3 ( B ) was analyzed by EnD-Seq using a strategy to amplify the histone mRNAs selectively. Essentially all the 3′ ends mapped to the 3′ side of the stem in the stem–loop. The graphs represent the distribution of all recovered 3′ ends (with or without nontemplated tails) for each developmental stage. The inset shows the expansion of the distribution of 3′ ends from nucleotides −4 to −10 covering the 3′ side of the stem. ( C ) Pie charts showing nucleotide composition of single nucleotide tails in embryo ( top ) and ovary ( bottom ). ( D , E ) Distribution of 3′ ends and nontemplated tails in 3–6 h Drosophila embryos for ( D ) dH2a and ( E ) dH3. Note that the pattern of tail addition matches the ovary genes in ( A ) and ( B ) but the nucleotide composition is different. ( F ) Distribution of tail lengths for tails longer than 2 nt in the ovary RNA mapping between nucleotides 4 and 10 in the 3′ end of the stem. The tails > 2 nt in the ovary were predominantly oligo(A). The tails of 1 or 2 nt in the embryo at nucleotides 4–10 were predominantly U's, and there were very few tails longer than 2 nt. ( G ) Chart showing the distribution of tail length between mRNA positions −4 and −10. Note that there are very few long tails. ( H ) S1 nuclease mapping of ovary histone mRNAs. Total RNA from ovaries was fractionated into poly(A + ) and poly(A − ) fractions on oligo(dT) cellulose. Total RNA, and equal proportions of the poly(A − ) and poly(A + ) RNA, were subjected to S1 nuclease mapping using the histone H2a gene labeled at the 3′ end of the AclI site as a probe. The S1 resistant fragments were resolved on a 6% polyacrylamine-7M urea gel and detected by autoradiography. A diagram of the S1 assay is shown on the left . The arrow indicates the fragment protected by the full-length mRNA. ( I ) RT-PCR analysis of the histone H2a mRNA. cDNA primed with oligo(dT) fused to an anchor primer was synthesized from 1 μg of total RNA from adult males, ovaries, 0–1 h embryos, and 3–6 h embryos, and then amplified using a primer near the 5′ end of the H2a mRNA. An amplicon of full-length H2a mRNA would be ∼500 nt long. Several amplicons were cloned and the majority had A-tails added in the 3′ end of the stem, consistent with the high-throughput sequencing data.

    Journal: RNA

    Article Title: EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates

    doi: 10.1261/rna.048785.114

    Figure Lengend Snippet: Analysis of Drosophila histone mRNAs. ( A , B ) RNA from Drosophila ovary dH2a ( A ) and dH3 ( B ) was analyzed by EnD-Seq using a strategy to amplify the histone mRNAs selectively. Essentially all the 3′ ends mapped to the 3′ side of the stem in the stem–loop. The graphs represent the distribution of all recovered 3′ ends (with or without nontemplated tails) for each developmental stage. The inset shows the expansion of the distribution of 3′ ends from nucleotides −4 to −10 covering the 3′ side of the stem. ( C ) Pie charts showing nucleotide composition of single nucleotide tails in embryo ( top ) and ovary ( bottom ). ( D , E ) Distribution of 3′ ends and nontemplated tails in 3–6 h Drosophila embryos for ( D ) dH2a and ( E ) dH3. Note that the pattern of tail addition matches the ovary genes in ( A ) and ( B ) but the nucleotide composition is different. ( F ) Distribution of tail lengths for tails longer than 2 nt in the ovary RNA mapping between nucleotides 4 and 10 in the 3′ end of the stem. The tails > 2 nt in the ovary were predominantly oligo(A). The tails of 1 or 2 nt in the embryo at nucleotides 4–10 were predominantly U's, and there were very few tails longer than 2 nt. ( G ) Chart showing the distribution of tail length between mRNA positions −4 and −10. Note that there are very few long tails. ( H ) S1 nuclease mapping of ovary histone mRNAs. Total RNA from ovaries was fractionated into poly(A + ) and poly(A − ) fractions on oligo(dT) cellulose. Total RNA, and equal proportions of the poly(A − ) and poly(A + ) RNA, were subjected to S1 nuclease mapping using the histone H2a gene labeled at the 3′ end of the AclI site as a probe. The S1 resistant fragments were resolved on a 6% polyacrylamine-7M urea gel and detected by autoradiography. A diagram of the S1 assay is shown on the left . The arrow indicates the fragment protected by the full-length mRNA. ( I ) RT-PCR analysis of the histone H2a mRNA. cDNA primed with oligo(dT) fused to an anchor primer was synthesized from 1 μg of total RNA from adult males, ovaries, 0–1 h embryos, and 3–6 h embryos, and then amplified using a primer near the 5′ end of the H2a mRNA. An amplicon of full-length H2a mRNA would be ∼500 nt long. Several amplicons were cloned and the majority had A-tails added in the 3′ end of the stem, consistent with the high-throughput sequencing data.

    Article Snippet: Briefly, the probe was generated by end labeling H2a DNA digested with AclI with α-32 P-dCTP and Klenow Polymerase (NEB).

    Techniques: Labeling, Autoradiography, Reverse Transcription Polymerase Chain Reaction, Synthesized, Amplification, Clone Assay, Next-Generation Sequencing