pcr dna marker  (worthington biochemical)

Journal: bioRxiv

Article Title: Experimental and Bioinformatic upgrade for genome-wide mapping of nucleosomes in Trypanosoma cruzi

doi: 10.1101/2021.07.02.450927

Figure Lengend Snippet: Titration of T. cruzi chromatin with MNase. Chromatin digested with increasing amounts of MNase analyzed in a 2% agarose gel (lanes 1-9). An example of the level of digestion of choice is highlighted in lane 9. PCR DNA marker (NEB) was loaded in lane 10.

Article Snippet: 3.4 Selecting the best mononucleosomal sample to proceed withTo determine the extent of digestion 10 μl of each MNase-digested sample was analyzed in a 2% agarose gel next to the PCR DNA Marker (New England Biolabs, Ipswich, Massachusetts, U.S.A.).

Techniques: Titration, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Marker

Journal: bioRxiv

Article Title: Experimental and Bioinformatic upgrade for genome-wide mapping of nucleosomes in Trypanosoma cruzi

doi: 10.1101/2021.07.02.450927

Figure Lengend Snippet: Mononucleosome sample and total number of paired-reads. (A) Chromatin digestions from the CL Brener replicate 1 experiment analyzed in a 2% agarose gel. The sample loaded in lane 4 was used for the experiment. PCR DNA (NEB) marker was loaded in lane 1. (B) Total number of paired-reads obtained in each replicate experiment.

Article Snippet: 3.4 Selecting the best mononucleosomal sample to proceed withTo determine the extent of digestion 10 μl of each MNase-digested sample was analyzed in a 2% agarose gel next to the PCR DNA Marker (New England Biolabs, Ipswich, Massachusetts, U.S.A.).

Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Marker

Journal: Drug Delivery and Translational Research

Article Title: Covalently tethered transforming growth factor beta in PEG hydrogels promotes chondrogenic differentiation of encapsulated human mesenchymal stem cells

doi: 10.1007/s13346-012-0090-2

Figure Lengend Snippet: Viability of hMSCs encapsulated in tethered TGF β hydrogels. DNA content of cell-laden hydrogels was assayed over 14 days of culture, and used as a general correlative measure of cell viability. Hydrogels cultured in growth medium (used as a negative control for chondrogenesis) maintained initial cell counts, as did those incorporating 1-nM tethered TGF β . Chondrogenic media samples (positive control) exhibited an increase in DNA of approximately twofold, while TGF β tethered at 10 or 100 nM demonstrated similar increases in DNA content, suggesting high levels of viability of the encapsulated hMSCs. Results are presented as mean ± s.e.m. ( n = 3)

Article Snippet: DNA quantification of encapsulated hMSCs Immediately following photoencapsulation, cell-laden hydrogels (n = 3) were placed into an enzymatic digest buffer (125 μg/mL papain (Worthington Biochemical), 10 mM cysteine) overnight at 60 °C, then frozen prior to analysis.

Techniques: Cell Culture, Negative Control, Positive Control

Journal: Molecular and Cellular Biology

Article Title: Role of the Promoter in Maintaining Transcriptionally Active Chromatin Structure and DNA Methylation Patterns In Vivo

doi: 10.1128/MCB.23.12.4150-4161.2003

Figure Lengend Snippet: Analysis of DNase I hypersensitivity. HT-1080 (male human fibrosarcoma) cells and Δ3B (HT-1080 cells carrying the promoter mutation) cells were treated with 0, 10, 20, 30, 40, 50, 60, 70, 80, 90, and 100 μg of DNase I/ml. Southern blot analysis was performed on DNA digested with Eco RI and was hybridized to the HPRT promoter probe HPRT A. “HS site” indicates the positions of HPRT -hypersensitive sites; “globin” indicates the hybridization band detected by the control human β-globin probe.

Article Snippet: It is possible that the steeper slope detected by this probe is indicative of an intrinsically higher accessibility of the 5′flanking region to DNase I (or preferential DNase I cleavage of the underlying DNA sequence).

Techniques: Mutagenesis, Southern Blot, Hybridization

Journal: Molecular and Cellular Biology

Article Title: Role of the Promoter in Maintaining Transcriptionally Active Chromatin Structure and DNA Methylation Patterns In Vivo

doi: 10.1128/MCB.23.12.4150-4161.2003

Figure Lengend Snippet: Physical map of the human HPRT gene. The thick horizontal line represents the HPRT gene. Open horizontal boxes represent exons, and “ATG” indicates the translation initiation site. The bent arrow represents the major transcription initiation sites, and a putative initiator element is shaded. The gray box indicates the position of probe “HPRT A.” The bracket above the line indicates the position of the 5′ flanking DNase I-hypersensitive site. The positions of CpG-dinucleotides within the gene are shown as vertical lines below the gene map. Numbers indicate the position of CpGs relative to the translation initiation site. The horizontal bracket below the line indicates the region deleted in Δ2B and Δ3B cells.

Article Snippet: It is possible that the steeper slope detected by this probe is indicative of an intrinsically higher accessibility of the 5′flanking region to DNase I (or preferential DNase I cleavage of the underlying DNA sequence).

Techniques:

Journal: Nucleic Acids Research

Article Title: 3?-Exonuclease resistance of DNA oligodeoxynucleotides containing O6-[4-oxo-4-(3-pyridyl)butyl]guanine

doi:

Figure Lengend Snippet: MALDI-TOF mass spectra of SVPDE digests of modified DNA 16mers d(AACAGCCATATGXCCC): ( A ) X = O 6 -POB-dG, time-controlled digest; ( B ) X = O 6 -POB-dG, complete digest conditions; ( C ) O 6 -Me-dG-containing oligomers, controlled digest conditions. Arrows indicate the portion of the sequence represented in the spectra, and doubly charged ions are marked with #.

Article Snippet: SVPDE and E.coli DNA polymerase I were purchased from Worthington Biochemicals (Lakewood, NJ).

Techniques: Modification, Sequencing