Preparation of cDNA followed the procedure described in Mortazavi et al.2 (link), with minor modifications as described below. Prior to fragmentation, a 7 uL aliquot (∼ 500 pgs total mass) containing known concentrations of 7 “spiked in” control transcripts from A. thaliana and the lambda phage genome were added to a 100 ng aliquot of mRNA from each time point. This mixture was then fragmented to an average length of 200 nts by metal ion/heat catalyzed hydrolysis. The hydrolysis was performed in a 25 uL volume at 94°C for 90 seconds. The 5X hydrolyis buffer components are: 200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate. After removal of hydrolysis ions by G50 Sephadex filtration (USA Scientific catalog # 1415-1602), the fragmented mRNA was random primed with hexamers and reverse-transcribed using the Super Script II cDNA synthesis kit (Invitrogen catalog # 11917010). After second strand synthesis, the cDNA went through end-repair and ligation reactions according to the Illumina ChIP-Seq genomic DNA preparation kit protocol (Illumina catalog # IP102-1001), using the paired end adapters and amplification primers (Illumina Catalog # PE102-1004). Ligation of the adapters adds 94 bases to the length of the cDNA molecules.
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Bacteriophage lambda
Bacteriophage lambda
Bacteriophage lambda is a well-studied bacterial virus that infects Escherichia coli.
It is a temperate phage, meaning it can either enter a lytic cycle, leading to host cell lysis and progeny virion release, or a lysogenic cycle, where the phage genome integrates into the host chromosome.
Bacteriaphage lambda serves as a model system for understanding viral genetics, regulation of gene expression, and host-pathogen interactions.
Researchers can leverage PubCompare.ai's innovative AI-powered platform to locate optimal research protocols from literature, pre-prints, and patents, and identify the best approaches for their experiments on this important model organism.
By leveraging AI-driven comparisons, scientists can enhance the reproducibility and streamlie their research on bacteriopphage lambda.
It is a temperate phage, meaning it can either enter a lytic cycle, leading to host cell lysis and progeny virion release, or a lysogenic cycle, where the phage genome integrates into the host chromosome.
Bacteriaphage lambda serves as a model system for understanding viral genetics, regulation of gene expression, and host-pathogen interactions.
Researchers can leverage PubCompare.ai's innovative AI-powered platform to locate optimal research protocols from literature, pre-prints, and patents, and identify the best approaches for their experiments on this important model organism.
By leveraging AI-driven comparisons, scientists can enhance the reproducibility and streamlie their research on bacteriopphage lambda.
Most cited protocols related to «Bacteriophage lambda»
Acetate
Anabolism
Bacteriophage lambda
Buffers
Chromatin Immunoprecipitation Sequencing
DNA, Complementary
DNA Chips
Filtration
Genome
Hydrolysis
Ions
Ligation
magnesium acetate
Metals
Oligonucleotide Primers
Potassium Acetate
RNA, Messenger
sephadex
Tromethamine
The plasmid pBL was constructed by insertion of a 70-bp chemically synthesized multiple cloning site into the 2.5-kb PCR-generated plasmid backbone of pBluescript II KS(+) (Stratagene) and deletion of the LacZα ORF by conventional cloning. The plasmid pBL-DL was constructed by insertion of a 1-kb PCR fragment from pGEM®-luc (Promega) into the NotI/SalI sites of pBL by SLiCE. The suicide plasmid pGT1 was constructed by SLiCE-mediated insertion of a 830-bp PCR-amplified fragment spanning the 3′ region of the E. coli DH10B cynX gene and an araC-pBAD-redα/EM7-redβ/Tn5-gam expression cassette isolated from plasmid pBAD24 (8 (link)) and lambda phage DNA (NEB) into the SmaI site of plasmid pEL04 (9 (link)). pGT1 also contains a temperature-sensitive replicon and a chloramphenicol selection marker.
Ara-C
Bacteriophage lambda
Chloramphenicol
Deletion Mutation
Escherichia coli
Genes
HMN (Hereditary Motor Neuropathy) Proximal Type I
KS 5-2
Plasmids
Promega
prostaglandin M
Replicon
Vertebral Column
All DNA samples were mixed in TBE buffer (Medicago, 10 x TBE tablets) diluted in milli-Q water to the desired ionic strength. The oxygen scavenger β-mercaptoethanol (Sigma-Aldrich) was added to the buffer (3% v/v) to suppress photonicking of the DNA. YOYO-1 was purchased from Invitrogen and DNA from phage lambda (λ-DNA, 48.5 kb) was purchased from New England Biolabs.
The nanofluidic chips were fabricated in fused silica according to methods described elsewhere (6 (link)), with a cross-section of ∼100 × 150 nm2 and a length of ∼500 µm. All experiments were conducted in a nanofluidic chip consisting of pairs of microchannels that are spanned by nanochannels. The DNA sample solution was loaded into one of the microchannels of the chip and transferred to the nanochannel array by pressure. By applying pressure over two connected microchannels, the DNA was subsequently injected into the nanochannels. The DNA was imaged using an epi-fluorescence microscope (Zeiss AxioObserver.Z1) equipped with a Photometrics Evolve EMCCD camera and a 100× oil immersion TIRF objective (NA = 1.46) from Zeiss. Stacks of 200 images were recorded for each molecule, using the AxioVision software, with an exposure time of 100 ms per image at maximum speed, corresponding to approximately seven frames per second. Data analysis was performed with the freeware ImageJ (www.imagej.com ) and a custom-written MatLab based software. For each molecule, kymographs (timetraces) were first extracted. Subsequently, each line in the kymograph—corresponding to one frame in the original time series—was fitted with a convolution of a box function and an error function (6 (link)). This gives the position and extension of the molecule in each frame that is used to align the kymograph as well as obtaining average intensities and fluctuations.
The fluorescence intensity was normalized to a distinct upper limit in fluorescence intensity identified from measurements. This upper limit is assumed to correspond to the fluorescence intensity of fully intercalated DNA, ∼1 YOYO molecule every 4 bp (21 (link),22 (link)). Extrapolation of the extension of native DNA was obtained by a linear fit of the first eight binned values for each ionic strength. The straight lines inFigure 3 B were calculated from the extrapolated extension of the native DNA, again assuming a maximal intercalation of one YOYO every 4 bp and adding the resulting increase in contour length of 0.51 nm per YOYO molecule (22 (link)), taking the relative extension of the native DNA compared with the full contour length into account.
The nanofluidic chips were fabricated in fused silica according to methods described elsewhere (6 (link)), with a cross-section of ∼100 × 150 nm2 and a length of ∼500 µm. All experiments were conducted in a nanofluidic chip consisting of pairs of microchannels that are spanned by nanochannels. The DNA sample solution was loaded into one of the microchannels of the chip and transferred to the nanochannel array by pressure. By applying pressure over two connected microchannels, the DNA was subsequently injected into the nanochannels. The DNA was imaged using an epi-fluorescence microscope (Zeiss AxioObserver.Z1) equipped with a Photometrics Evolve EMCCD camera and a 100× oil immersion TIRF objective (NA = 1.46) from Zeiss. Stacks of 200 images were recorded for each molecule, using the AxioVision software, with an exposure time of 100 ms per image at maximum speed, corresponding to approximately seven frames per second. Data analysis was performed with the freeware ImageJ (
The fluorescence intensity was normalized to a distinct upper limit in fluorescence intensity identified from measurements. This upper limit is assumed to correspond to the fluorescence intensity of fully intercalated DNA, ∼1 YOYO molecule every 4 bp (21 (link),22 (link)). Extrapolation of the extension of native DNA was obtained by a linear fit of the first eight binned values for each ionic strength. The straight lines in
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1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidine)quinolinium, tetraiodide
2-Mercaptoethanol
Bacteriophage lambda
Buffers
DNA Chips
Fluorescence
Gas Scavengers
Kymography
Medicago
Microscopy, Fluorescence
Oxygen
Pressure
Reading Frames
Silicon Dioxide
Submersion
Tris-borate-EDTA buffer
All sequencing runs were single-ended and 100 nucleotides (nt) in length, and performed on the Illumina HiSeq 2000 platform. Based on the qPCR quantification, 3×108 copies of double-stranded DNA from the PBAT library were sequenced per lane on HiSeq 2000, as previously described [15] (link). Cluster generation and sequencing were performed in single-read mode using the TruSeq SR Cluster Kit v3-cBot-HS (Illumina) and the TruSeq SBS Kit v3-HS (Illumina) according to the manufacturer's protocols. Sequenced reads were processed using the standard Illumina base caller (v.1.8.2). We truncated raw reads to 92 nt to remove lower quality bases near the end of the reads and any remaining adapter sequences incorporated in the read. The resulting reads were aligned to the reference genome (mouse mm9) using Bismark alignment software v.0.6.3 [49] (link) with a maximum of two mismatches, and only uniquely aligned reads were retained. We estimated bisulfite conversion rates using reads that uniquely aligned to the lambda phage genome. For strand-independent analysis of CG methylation, counts from the two cytosines in a CG and its reverse complement were combined. We subsequently evaluated only CG sites with at least 6× coverage and non-CG sites with at least 4× coverage, and discarded cytosines with more than 100× coverage. CG islands, RefSeq genes, and repeat sequences for the mm9 genome were downloaded from the UCSC Genome Browser [50] (link). The logo plot images were generated with WebLogo [51] (link).
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Bacteriophage lambda
CpG Islands
Cytosine
DNA, Double-Stranded
DNA Library
Genes
Genome
hydrogen sulfite
Methylation
Mice, House
Nucleotides
Repetitive Region
Double-stranded lambda phage DNA was purchased from Takara (Shiga, Japan). Concatemers of lambda DNA were prepared with T4 DNA ligase (Takara, Shiga, Japan) by incubating in ligation buffer for 1 h at 25°C. To biotinylate one end of the concatemeric DNA, a biotin-labeled oligonucleotide with the sequence 5′-GGGCGGCGACCT-biotin-3′ (Sigma-Aldrich), which is hybridized at the right cos site of lambda phage DNA, was added to the concatemeric DNA solution at a DNA:oligonucleotide ratio of 1:2 and incubated for 10 min at room temperature with T4 DNA ligase. After ligation of the biotin-labeled oligonucleotide, the concatemeric biotinylated DNA was isolated by 1% agarose gel electrophoresis in 1× TAE and extracted from gel slices by electro-elution.
Bacteriophage lambda
Biotin
Buffers
DNA, A-Form
DNA, Concatenated
DNA, Double-Stranded
Electrophoresis, Agar Gel
Ligation
Oligonucleotides
T4 DNA Ligase
Most recents protocols related to «Bacteriophage lambda»
Nanopore sequence data was filtered to remove the control lambda-phage and sequences shorter than 1,000 bases using the nanopack tool suite [v1.0.1] (De Coster et al. 2018 (link)). Trimmomatic [v0.32] (Bolger et al. 2014 (link)) was used to remove adapters, trim low-quality bases, and filter out reads shorter than 85 bp. The filtered nanopore data were assembled into contigs using wtdbg2 [v2.4] (Ruan and Li 2020 (link)). The contigs were polished using two iterations of racon [v1.4.0] (Vaser et al. 2017 (link)) with minimap2 [v2.17] (Li 2018 (link)) mapping the nanopore reads. The contigs were further polished with Illumina paired-end read data using pilon [v1.23] (Walker et al. 2014 (link)) with bwa [v0.7.10] (Li 2013 ) mapping the Illumina paired reads. The resulting contigs were scaffolded using Bionano Solve [Solve3.4.1_09262019] using the optical mapping data generated from the Saphyr run. SALSA [v2.3] (Ghurye et al. 2019 (link)) was used to produce super-scaffolds using the Hi-C library and the Bionano scaffolded sequences. Those scaffolds larger than 10Mb were linked and oriented based on the Onychostoma macrolepis genome (Sun et al. 2020 (link)), the chromosome assembly most similar to L. rohita available on NCBI, using RagTag [v1.1.1] (Alonge et al. 2022 (link)).
RepeatModeler [v2.0.1] (Flynn et al. 2020 (link)) and RepeatMasker [v4.1.1] (Smit et al. 2013 ) were used to create a species-specific repeat database, and this database was subsequently used by RepeatMasker to mask those repeats in the genome. All available RNA-seq libraries for L. rohita (comprising brain, pituitary, gonad, liver, pooled, and whole body tissues for both sexes;Supplementary Table 1 ) were downloaded from NCBI and mapped to the masked genome using hisat2 [v2.1.0] (Kim et al. 2019 (link)). These alignments were used in both the mikado [v2.0rc2] (Venturini et al. 2018 (link)) and braker2 [v2.1.5] (Brůna et al. 2021 (link)) pipelines. Mikado uses putative transcripts assembled from the RNA-seq alignments generated via stringtie [v2.1.2] (Kovaka et al. 2019 (link)), cufflinks [v2.2.1] (Trapnell et al. 2012 (link)), and trinity [v2.11.0] (Grabherr et al. 2011 (link)) along with the junction site prediction from portcullis [v1.2.2] (Mapleson et al. 2018 (link)), the alignments of the putative transcripts with UniprotKB Swiss-Prot [v2021.03] (The UniProt Consortium 2021 (link)), and the ORFs from prodigal [v2.6.3] (Hyatt et al. 2010 (link)) to select the best representative transcript for each locus. Braker2 uses those RNA-seq alignments and the gene prediction from GeneMark-ES [v4.61] (Borodovsky and Lomsadze 2011 (link)) to train a species-specific Augustus [v3.3.3] (Stanke et al. 2006 (link)) model. Maker2 [v2.31.10] (Holt and Yandell 2011 (link)) predicts genes based on the new Augustus, GeneMark, and SNAP models derived from Braker2 along with the Mikado predicted transcripts as an external ab-initio source, modifying the predictions based on the available RNA and protein evidence from the Cyprinidae family in the NCBI RefSeq database. Any predicted genes with an annotation edit distance (AED) above 0.47 were removed from further analysis. The remaining genes were functionally annotated using InterProScan [v5.47-82.0] (Jones et al. 2014 (link)) and BLAST + [v2.9.0] (Camacho et al. 2009 (link)) alignments against the UniprotKB Swiss-Prot database. BUSCO [v5.2.2] (Manni et al. 2021 (link)) was used to verify the completeness of both the genome and annotations against the actinopterygii_odb10 database. Lastly, genes spanning large gaps or completely contained within another gene on the opposite strand were removed using a custom Perl script (https://github.com/IGBB/rohu-genome/ ).
RepeatModeler [v2.0.1] (Flynn et al. 2020 (link)) and RepeatMasker [v4.1.1] (Smit et al. 2013 ) were used to create a species-specific repeat database, and this database was subsequently used by RepeatMasker to mask those repeats in the genome. All available RNA-seq libraries for L. rohita (comprising brain, pituitary, gonad, liver, pooled, and whole body tissues for both sexes;
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Bacteriophage lambda
Brain
Chromosomes
Cyprinidae
DNA Library
Gender
Gene Annotation
Genes
Genome
Gonads
Liver
Open Reading Frames
Proteins
RNA-Seq
Tissues
Vision
Walkers
High-molecular-weight DNA extracted from all enrichment cultures was combined in equimolar amounts and used to prepare two metagenomic fosmid libraries, IS_Lib1 (Cavascura enrichments) and IS_Lib2 (Maronti enrichments) using the CopyControl fosmid library pCC2FOS production kit (Epicentre Technologies, Madison, WI, USA). DNA was end-repaired to generate blunt-ended 5′-phosphorylated fragments according to the manufacturer’s instructions. Subsequently, DNA fragments in the range of 30 to 40 kbp were resolved by gel electrophoresis (2 V cm−1 overnight at 4°C) and recovered from 1% low-melting-point agarose gel using GELase 50× buffer and GELase enzyme (Epicentre). Nucleic acid fragments were then ligated to the linearized CopyControl pCC2FOS vector following the manufacturer’s instructions. After the in vitro packaging into the phage lambda (MaxPlax lambda packaging extract, Epicentre), the transfected phage T1-resistant EPI300-T1RE. coli cells were spread on Luria-Bertani (LB) agar medium containing 12.5 μg mL−1 chloramphenicol and incubated at 37°C overnight to determine the titer of the phage particles. The resulting libraries had estimated titers of 14 × 104 and 1 × 104 nonredundant fosmid clones in the IS_Lib1 and IS_Lib2 libraries, respectively. For long-term storage, E. coli colonies were washed from the agar surface using liquid LB medium containing 20% (vol/vol) sterile glycerol, and the aliquots were stored at −80°C.
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Agar
Bacteriophage lambda
Bacteriophages
Buffers
Cells
Chloramphenicol
Clone Cells
Cloning Vectors
DNA Library
Electrophoresis
Enzymes
Escherichia coli
GELase
Glycerin
Metagenome
Nucleic Acids
Sepharose
Sterility, Reproductive
For metaphase spread preparation, mitoses were mechanically collected by blowing the medium on the dish surface. Chromosome preparations were performed with the standard air-drying procedure and were used for karyotype analysis or fluorescence in situ hybridization (FISH).
Whole genomic DNA from Przewalski’s horse fibroblasts was extracted according to standard procedures. BAC clones (CHOR1241-17G8, coordinates in EquCab2.0: chr5:37,011,456–37,167,308; CHOR1241-25H7 coordinates in EquCab2.0: chr5: 98,031,303–98,224,666) and lambda phage 37cen and 2PI clones [16 (link),53 (link)] were extracted from 10 mL bacterial cultures with the Quantum Prep Plasmid miniprep kit (BioRad, Milan, Italy), according to supplier instructions. All probes were labeled by nick translation with Cy3-dUTP (Enzo Life Sciences, Milan, Italy) or Alexa488-dUTP (Life Technologies, Monza, Italy) as previously described [64 (link)]. FISH was performed as previously described [68 (link)].
Chromosomes were counterstained by DAPI. Digital grayscale images for fluorescence signals were acquired with a fluorescence microscope (Zeiss Axio Scope.A1, Zeiss, Göttingen, Germany) equipped with a cooled CCD camera (Teledyne Photometrics, Birmingham, UK). Pseudocoloring and merging of images were performed using the IPLab 3.5.5 Imaging Software (Scanalytics Inc., Fairfax, VA, USA). Chromosomes were identified by DAPI banding according to the published karyotypes [49 (link),50 (link)].
Whole genomic DNA from Przewalski’s horse fibroblasts was extracted according to standard procedures. BAC clones (CHOR1241-17G8, coordinates in EquCab2.0: chr5:37,011,456–37,167,308; CHOR1241-25H7 coordinates in EquCab2.0: chr5: 98,031,303–98,224,666) and lambda phage 37cen and 2PI clones [16 (link),53 (link)] were extracted from 10 mL bacterial cultures with the Quantum Prep Plasmid miniprep kit (BioRad, Milan, Italy), according to supplier instructions. All probes were labeled by nick translation with Cy3-dUTP (Enzo Life Sciences, Milan, Italy) or Alexa488-dUTP (Life Technologies, Monza, Italy) as previously described [64 (link)]. FISH was performed as previously described [68 (link)].
Chromosomes were counterstained by DAPI. Digital grayscale images for fluorescence signals were acquired with a fluorescence microscope (Zeiss Axio Scope.A1, Zeiss, Göttingen, Germany) equipped with a cooled CCD camera (Teledyne Photometrics, Birmingham, UK). Pseudocoloring and merging of images were performed using the IPLab 3.5.5 Imaging Software (Scanalytics Inc., Fairfax, VA, USA). Chromosomes were identified by DAPI banding according to the published karyotypes [49 (link),50 (link)].
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3'-deoxy-5-(cyanine dye 3)uridine 5'-trisphosphate
Bacteria
Bacteriophage lambda
Chromosomes
Clone Cells
DAPI
deoxyuridine triphosphate
Equus przewalskii
Fibroblasts
Fluorescence
Fluorescent in Situ Hybridization
Genome
Hyperostosis, Diffuse Idiopathic Skeletal
Karyotyping
Metaphase
Microscopy, Fluorescence
Mitosis
Plasmids
Codon optimised NDI1 sequences, designed to encode specific amino acid changes to reduce immunogenicity profiles and a minimal polyadenylation signal, were synthesised by GeneArt, Inc. (Invitrogen, Paisley, UK) and cloned into pAAV-MCS (Agilent Technologies, CA, USA) downstream of a CMV promoter. The lead construct, pAAV-ophNdi1, contained 329 synonymous codon modifications and an I82V amino acid substitution (patent no. 10220102). An additional construct, pAAV-ophNdi1-HA, was created by cloning ophNdi1 with a C-terminal HA tag (synthesized by GeneArt®, Thermo Fischer Scientific, MA, USA) into pAAV-MCS. To enhance AAV packaging efficiency, 4.4 kb of bacteriophage lambda DNA [46 (link)] was inserted into the plasmid backbone of pAAV-ophNdi1 and the antibiotic resistance gene substituted for kanamycin. Cloning was verified by DNA sequencing. pAAV-Ndi1 and pAAV-CAG-EGFP vectors were cloned as previously described in [39 (link),47 (link)], respectively.
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Amino Acids
Amino Acid Substitution
Antibiotic Resistance, Microbial
Antigens
Bacteriophage lambda
Cloning Vectors
Codon
Genes
Kanamycin
Nephrogenic Diabetes Insipidus, Type I
Plasmids
Polyadenylation
Vertebral Column
DHMs were fabricated by the step-wise spotting of DNA and histone droplets into wells of standard 96-well microplates. To increase the binding efficiency of DHMs, untreated 96-well microplates (CLS3370; Corning, Corning, NY, USA) were coated with 0.001% poly-L-lysine (P4707; Sigma-Aldrich, St. Louis, MO, USA) for 10 min and rinsed once with water. Once dry, the DNA layer was prepared by combining a solution of 0.1 mg/mL lambda-phage methylated DNA (D9768; Sigma-Aldrich, St. Louis, MO, USA) with a 400 mM trehalose solution (T-104-4; Pfanstiehl, Waukegan, IL, USA) at a 1:1 ratio. Suspending the soluble DNA within a trehalose phase added stability, localization, and uniformity to the final structures. The trehalose phase could be washed off prior to testing, leaving only the chromatin fibers in each well. As a note, histones could not be pre-mixed with the DNA solution as they instantly formed fibers and therefore could not be dispensed with liquid-handling techniques.
A sub-microliter droplet, 0.6 μL, of the DNA–trehalose solution was dispensed into each well. The droplets were vitrified for 24 h in a vacuum desiccator. A 0.6 μL droplet containing a 0.5 mg/mL histone solution (H9250; Sigma-Aldrich, St. Louis, MO, USA) was then deposited over the vitrified DNA spot and dried for another 24 h in a vacuum desiccator. The concentration of DNA and histone solutions, as well as the volume, can be modified to vary the resulting morphology and compaction of the DHM chromatin structure. The binding of histones to DNA strands resulted in a defined sub-millimeter mesh of condensed chromatin fibers within the boundaries of the initial droplet area. Once fabricated, the resulting vitrified fibrous DNA structures were stable at room temperature until use.
A sub-microliter droplet, 0.6 μL, of the DNA–trehalose solution was dispensed into each well. The droplets were vitrified for 24 h in a vacuum desiccator. A 0.6 μL droplet containing a 0.5 mg/mL histone solution (H9250; Sigma-Aldrich, St. Louis, MO, USA) was then deposited over the vitrified DNA spot and dried for another 24 h in a vacuum desiccator. The concentration of DNA and histone solutions, as well as the volume, can be modified to vary the resulting morphology and compaction of the DHM chromatin structure. The binding of histones to DNA strands resulted in a defined sub-millimeter mesh of condensed chromatin fibers within the boundaries of the initial droplet area. Once fabricated, the resulting vitrified fibrous DNA structures were stable at room temperature until use.
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Bacteriophage lambda
Chromatin
Dihydrostreptomycin
Fibrosis
Histones
Lysine
Poly A
Trehalose
Vacuum
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The HiSeq 2500 is a high-throughput DNA sequencing system designed for a wide range of applications, including whole-genome sequencing, targeted sequencing, and transcriptome analysis. The system utilizes Illumina's proprietary sequencing-by-synthesis technology to generate high-quality sequencing data with speed and accuracy.
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Unmethylated lambda phage DNA is a laboratory reagent that consists of purified DNA from the lambda bacteriophage. It has not been methylated and retains the natural DNA structure of the phage. This DNA can be used as a control or reference material in various molecular biology applications.
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The Quant-iT PicoGreen dsDNA Assay Kit is a fluorescence-based method for quantifying double-stranded DNA (dsDNA). The kit contains a proprietary fluorescent dye that binds specifically to dsDNA, allowing for sensitive and accurate measurement of DNA concentration in samples.
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The DNeasy PowerSoil Kit is a laboratory product designed for the isolation and purification of DNA from soil and other environmental samples. It provides a standardized method for extracting high-quality genomic DNA from a wide range of soil types.
Sourced in United States, United Kingdom, Italy, Switzerland, Denmark, China
The PicoGreen assay is a fluorescence-based method for quantifying double-stranded DNA (dsDNA) in solution. The assay utilizes a proprietary PicoGreen dsDNA-binding dye that exhibits a strong fluorescent signal upon binding to dsDNA, allowing for sensitive and accurate measurement of DNA concentrations.
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The NovaSeq 6000 is a high-throughput sequencing system designed for large-scale genomic projects. It utilizes Illumina's sequencing by synthesis (SBS) technology to generate high-quality sequencing data. The NovaSeq 6000 can process multiple samples simultaneously and is capable of producing up to 6 Tb of data per run, making it suitable for a wide range of applications, including whole-genome sequencing, exome sequencing, and RNA sequencing.
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The EZ DNA Methylation-Gold Kit is a product offered by Zymo Research for bisulfite conversion of DNA samples. It is designed to convert unmethylated cytosine residues to uracil, while leaving methylated cytosines unchanged, enabling the detection and analysis of DNA methylation patterns.
Sourced in United States
The RecoverEase DNA Isolation Kit is a laboratory tool designed for the extraction and purification of DNA from various sample types. It provides a simple and efficient method to isolate high-quality DNA suitable for downstream molecular biology applications.
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The Transpack Packaging Extract is a laboratory equipment product from Agilent Technologies. It is designed for the extraction and purification of analytes from a variety of sample matrices. The core function of this product is to facilitate the sample preparation process.
Sourced in Japan
Lambda phage DNA is a linear double-stranded DNA molecule that serves as the genetic material of the lambda bacteriophage. It has a size of approximately 48.5 kilobase pairs and contains the necessary genetic information for the phage's replication and infection of host bacteria.
More about "Bacteriophage lambda"
Bacteriophage lambda, also known as phage lambda or lambda phage, is a well-studied and widely used model system in molecular biology and genetics.
This temperate bacteriophage, which infects the common gut bacterium Escherichia coli (E. coli), can either enter a lytic cycle, leading to host cell lysis and the release of progeny virions, or a lysogenic cycle, where the phage genome integrates into the host chromosome.
Researchers often leverage bacteriophage lambda as a model organism to gain insights into viral genetics, regulation of gene expression, and host-pathogen interactions.
The HiSeq 2500 and NovaSeq 6000 sequencing platforms, along with tools like the Quant-iT PicoGreen dsDNA Assay Kit and the DNeasy PowerSoil Kit, are commonly used to analyze and quantify lambda phage DNA.
The PicoGreen assay, in particular, is a sensitive method for measuring double-stranded DNA, including unmethylated lambda phage DNA.
For studies involving DNA methylation, the EZ DNA Methylation-Gold Kit can be used to bisulfite-convert DNA samples, while the RecoverEase DNA Isolation Kit allows for the extraction of high-quality DNA from lambda phage.
The Transpack Packaging Extract, on the other hand, is a useful tool for in vitro packaging of lambda phage DNA into phage particles.
By leveraging PubCompare.ai's innovative AI-powered platform, researchers can locate optimal research protocols from the literature, preprints, and patents, and identify the best approaches for their experiments on this important model organism.
The platform's AI-driven comparisons can help enhance the reproducibility and streamline the research process, enabling scientists to make the most of their work on bacteriophage lambda.
This temperate bacteriophage, which infects the common gut bacterium Escherichia coli (E. coli), can either enter a lytic cycle, leading to host cell lysis and the release of progeny virions, or a lysogenic cycle, where the phage genome integrates into the host chromosome.
Researchers often leverage bacteriophage lambda as a model organism to gain insights into viral genetics, regulation of gene expression, and host-pathogen interactions.
The HiSeq 2500 and NovaSeq 6000 sequencing platforms, along with tools like the Quant-iT PicoGreen dsDNA Assay Kit and the DNeasy PowerSoil Kit, are commonly used to analyze and quantify lambda phage DNA.
The PicoGreen assay, in particular, is a sensitive method for measuring double-stranded DNA, including unmethylated lambda phage DNA.
For studies involving DNA methylation, the EZ DNA Methylation-Gold Kit can be used to bisulfite-convert DNA samples, while the RecoverEase DNA Isolation Kit allows for the extraction of high-quality DNA from lambda phage.
The Transpack Packaging Extract, on the other hand, is a useful tool for in vitro packaging of lambda phage DNA into phage particles.
By leveraging PubCompare.ai's innovative AI-powered platform, researchers can locate optimal research protocols from the literature, preprints, and patents, and identify the best approaches for their experiments on this important model organism.
The platform's AI-driven comparisons can help enhance the reproducibility and streamline the research process, enabling scientists to make the most of their work on bacteriophage lambda.