Blue pippin. DNA size-selection was performed using Blue Pippin ...

Once libraries were completed, they were size selected from 20–50 kb

Native human genomic DNA was extracted from fresh blood, and size selection was performed using Blue Pippin (Cassette kit: BUF7510; size range: 30–40 kb). DNA quality was assessed by running 1 ...The published protocol 19 was used with minor modifications: size selection was performed using a Blue Pippin (Sage Science). In some instances we used rnh201-RED instead of rnh201::kan (see results).The resulting SMRTcell templates were size-selected to 15–50 kb by Blue Pippin electrophoresis (Sage Sciences) and sequenced on a PacBio RS II instrument using P6-C4 sequencing chemistry. Data ...PippinHT Quick Guide HTC2010 Marker 20B. 1MB. PippinHT Quick Guide HTC1510 Marker 15C. 1MB. PippinHT Quick Guide HPE7510 Marker 75E 6-10Kb and 15-20kb High Pass. 948KB. PippinHT Quick Guide HPF7510 Marker 75F >30-40kb High Pass. 1MB. PippinHT Quick Guide HRT7510 9-30kb Range +T Marker 75E.ANNOUNCEMENT. To obtain bacteria for use as prey in our studies of predatory Bdellovibrio (), we swabbed water from an urban stream in Providence, RI (41.835°N, 71.443°W), onto Trypticase soy agar and incubated at 28°C.After three rounds of picking and streaking, we grew pure culture overnight in Trypticase soy broth (TSB) at 28°C and then combined the culture 1:1 with 50% glycerol to ...Contact for: PacBio, Blue Pippin, Bioruptor [email protected]. Siranoosh Ashtari. Contact for: NovaSeq, NextSeq & MiSeq sequencing, microRNA library preps, and Covaris [email protected]. Emily Kumimoto. Contact for: Illumina sequencing library preparations [email protected]. Ruta Sahasrabudhe, PhDSelection Chart Pippin Prep BluePippin PippinHT Max. DNA input 5 μg 5 μg 1.5 μg Max. Sample Capacity 5 5 24 Pulsed-Field No Yes Yes Run Times (100 bp - 1.5 kb) 50-90 min 50-90 min* 25-45 min* Size Selection Range 100 bp - 1.5 kb 100 bp - 50 kb 100 bp - 1.5 kb High-Pass Size Filtering No Yes Yes Low-Pass Size Filtering Yes Accuracy > 93% ...BN124141 Pippin Product Line Brochure (4 pages): Flyers: BN0205147. Paired-end sequencing flyer. for Illumina platforms. BN0205148. Pippin Pulse flyer. Pulsed-Field for gel boxes. BN0205149.Blue Pippin Usage. The Blue Pippin is available for user operation for $12/sample after initial training. Alternatively, samples can be dropped off and ran by GSC staff. Please email us at [email protected] for training or to set up a time to drop off samples to be run on the Blue Pippin.Size selection on the Pippin is easier, safer, and more reproducible than traditional agarose gel extraction protocols involving a UV illuminator and a razor blade. ... Fragment Analyzer traces of 5 different Blue Pippin size selected Illumina libraries. Fragments between 275 and 525 bp were targeted in each library.Background Bacillus cereus is ubiquitous in nature, found in environments such as soil, plants, air, and part of the insect and human gut microbiome. The ability to produce endospores and biofilms contribute to their pathogenicity, classified in two types of food poisoning: diarrheal and emetic syndromes. Here we report gap-free, whole-genome sequences of two B. cereus strains isolated from ...Newtown pippin apples 2. Newtown Pippin apple. Newtown Pippin is a popular, all-American green apple from New York City. This apple has a smooth peel, often with a bit of gold russeting on it. The peel is a true green when freshly picked, but matures to a yellow as the apple becomes sweeter in storage.Conductivity / pH Meter. GE Biacore 3000 Surface Plasmon Resonance (SPR) Malvern NanoSight NS300. Malvern Zetasizer Nano ZS. Milli-Q Advantage A10 Water System. MiSonix Ultra Sonicator. New Brunswick Innova 44R Shakers. Other Analytical Core Instruments. Shimadzu UV-1800 UV-Vis Spectrophotometer.Cassette Kit Product Number Cassette Type Software DNA Control Kit Product Number BLG7510 0.75% and Capture 2 – 5 kb Marker D1 CBC7501 BLG7510 0.75% Band Capture 5 – 10 kb Marker D1 CBC7601Pippin Prep DNA Size Selection System Selects 100 bp - 1.5 kb. SageELF Whole Sample Fractionation System DNA (up to 40 kb) or Proteins (up to 500 kDa). Pippin Pulse Electrophoresis Power Supply Resolves DNA up to 400kb on a midi gel box. Applications. Transposase Enzyme Linked Long-Read Sequencing ...We purified the input of 3.2 µg purified SMRTbell library to load into the Blue Pippin 0.75% Agarose Cassette using cassette definition 0.75% DF Marer S1 3 to 10 kb Improved Recovery for the run protocol. We collected fragments greater than 7 kb from the cassette elution well and purified and concentrated the size-selected SMRTbell library ...selected using the Blue Pippin (Sage Science, United Kingdom). Illumina libraries were constructed with a PCR-free method. using NEBNext End Repair, NEBNext dA-t ailing and Blunt T/A.A subset of the samples were sent to IBIS (n = 96, including 16 samples from each population) for PstI/MspI library preparation following the procedure of Poland et al. with the following modifications: addition of a size selection step using a Blue Pippin 2% agarose cassette with time settings to elute between 45 and 60 min and a plate barcode ...This video covers the steps and processes for setting up a Pippin DNA size selection system.The entire elution was size selected on a 3% agarose cassette using the Blue Pippin system, targeting either 190 or 200 bp using "tight" settings. The 40 μL elution was collected from blue pippin and analyzed using High Sensitivity DNA bioanalyzer. Dilution is usually not necessary for this pool, but think about your expected concentration ...Blue pumpkins are not widespread commercially, but the pumpkins offer a thick, smooth, and mildly flavored flesh for sweet and savory culinary preparations. Nutritional Value Blue pumpkins are a source of fiber to regulate the digestive tract, and beta-carotene, a natural compound within the flesh converted into vitamin A in the body.The Blue Wizards as seen by Ralph Damiani. The time that the Blue Wizards arrived in Middle-earth is uncertain. In Unfinished Tales, Tolkien wrote that the five Istari came to Middle-earth together in TA 1000. However, in The Peoples of Middle-earth, they are said to have arrived in the Second Age, around the year SA 1600, the time of the ...For each isoform, blocks in blue represent exons, and lines between blocks represent introns. Red triangles indicate the position of primers used for RT-PCR. b RT-PCR validation of the differential intron retention level of PB.13680. cDNA from 5 h, 15 h and 30 h germinating seeds and leaf samples were used for RT-PCR. The gel bands show DNA ...Higher molecular weight fragments require a dedicated lane to run a calibration marker. Run times are as little as 30 minutes. To resolve very large DNA fragments, pulsed-field runs may last several hours. View the Blue Pippin cassette reference chart to explore the DNA size selection options and run times.Shearing to 10 kb with Covaris G-tubes (5000 x g for 1 min each way) achieves similar results. Alternatively, for longer reads it is recommended not to shear and perform the ligation protocol as recommended, or include a size selection step with the Blue Pippin (Sage Sciences). Sequencing outcomes for all options are given in table below.Figure Legend Snippet: Fragment analysis of cDNA (after library preparation) Blue line: Amplified cDNA cleaned using 0.4× AMPure beads, Black line: Amplified cDNA size selected using agarose gel on a BluePippin Instrument. Samples were analyzed on a Fragment Analyzer system using the HS NGS Fragment assay reagents (1-6000 bp). RFU: Raw fluorescence value, LM/UM: Lower/Upper Marker needed ...Upgrading the Pippin Instrument Software. 71. 21 Preventative Maintenance - Rinsing Electrodes. 73. Electrode Rinse Procedure. 73. 22 Warranty and Service. 74. ... 3 Blue-Pippin Installation Procedure. 5. Packaging and Components. 5. Instrument and Monitor Dimensions. 5. Installation. 6. Rear Panel of the Bluepippin. 7.Sequencing of samples was performed using MiSeq Reagent Kit v3 (600 cycle; 2–300 bp) (Illumina, San Diego, CA, USA). For Long-read WGS, the library preparation and size selection were performed using PacBio Template Preparation 1.0 kit (Pacific Biosciences, Menlo Park, CA, USA) and Blue Pippin (Sage Sciences, Beverly, …The BluePippin is an updated version of Sage’s Pippin Prep system, to which a pulsed-field power supply has been added. Pulsed field gel electrophoresis allows larger fragments of DNA separated with high resolution and accuracy. Using pre-cast gels, the BluePippin can automatically collect DNA targets up to 50 kilobase pairs, with minimal ... Barcoded samples were then pooled and an additional clean-up with 1.5× Serapure solution was performed. The pooled library was size-selected using a Blue Pippin (Sage Science), retaining only those fragments 300 bp ± 50 bp in length. This size-selection range was chosen by performing an in silico digestion of the published prairie rattlesnake, C.They are all embellished with the same fanciful Early Bird pattern, consisting of a light blue background, adorned with a bird and exotic flowers. The porcelain ...The Blue Pippin also does your size selection, so you don't burn out pores sequencing lots of little stuff. This should help yield too. Then it's all down to the library prep, and @gringer's answer has some good tips on that. Technical note ALTERNATIVE SIZE SELECTION METHODS FOR SMRTBELL ® PREP KIT 3.0 Introduction In Procedure & checklist — Preparing whole genome and metagenome sequencing libraries using SMRTbell prep kit 3.0, size-selection beads are used to remove short DNA fragments and enrich for the long fragments that are most valuable for …a, Percentage of the nongap GRCh37 human genome covered by at least ten reads from 28-fold coverage NGS (2 × 250 bp, HiSeq 2500) and CCS (13.5 kb) datasets at different mapping quality thresholds.Shop now on Smallable: Sea NY - Pippin Patchwork Dress - Navy blue. Plus discover our selection of long dresses.The Blue Pippin is a powerful automated tool to collect DNA fragments up to 50 kb or size select proteins. It facilitates library construction for the most popular Next Generation Sequencing platforms. Features : Saves time and effort compared to manual gel purification Sample-to-sample reproducibility streamlines researchPippin Prep DNA Size Selection System Selects 100 bp – 1.5 kb. SageELF Whole Sample Fractionation System DNA (up to 40 kb) or Proteins (up to 500 kDa). Pippin Pulse ...Empress plum. Empress, also widely-known as Blue Imperatrice, is an unusually late-season dark blue / purple European plum. The plums have a sweet sugary flavor, but the golden yellow flesh is quite dry. The plums are "persistent", and if not picked will hang on the tree well into late fall. They can also be kept in a fridge for several weeks.Cassette Kit Product Number Cassette Type Software DNA Control Kit Product Number BLG7510 0.75% and Capture 2 - 5 kb Marker D1 CBC7501 BLG7510 0.75% Band Capture 5 - 10 kb Marker D1 CBC7601Pippin Prep DNA Size Selection System Selects 100 bp - 1.5 kb. SageELF Whole Sample Fractionation System DNA (up to 40 kb) or Proteins (up to 500 kDa). Pippin Pulse Electrophoresis Power Supply Resolves DNA up to 400kb on a midi gel box. Applications. Transposase Enzyme Linked Long-Read Sequencing ...Approximately 30 μg of genomic DNA was used to construct PacBio libraries by shearing into ~ 20 kb targeted size fragments with Blue Pippin (Sage Science, Beverly, MA, USA).Author summary Plant sexuality has fascinated scientists for decades. Most plants can self-reproduce but not all. For example, a small subset of species have evolved a system called dioecy, with separate male and female individuals. Dioecy has evolved multiple times independently and, while we do not understand the molecular …Author summary The Neisseria genus contains many genetically related commensals of animals and humans, and two human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. The mechanisms allowing commensal Neisseria to maintain a niche in their host is little understood. To identify genes required for persistence, we screened a library of transposon mutants of Neisseria musculi, a ...The Pippin Prep facilitates library construction for the most popular NGS platforms, and is recommended by Illumina and Ion Torrent for certain workflows. The platform features the ability to collect narrow and even fragment distributions, as well as the flexibility to collect wide ranges of fragments with minimal effort. ...High-molecular-weight (HMW) genomic DNA (>40 kb) was isolated from the agarose plugs using pulsed-field electrophoresis on a Blue Pippin instrument (Sage Science) following the high-pass protocol ...Subsequent to library preparation a blue pippin size selection (Sage Science Inc.) was used to isolate target fragment lengths of long range PCR amplicons. Sequencing was performed on a PacBio-Sequel system for 10 and 20 h for cell-culture derived and BAL samples, respectively.Size selection was performed at the University of Maryland Genomics Resource Center using a Blue Pippin pulse-field gel electrophoresis instrument. A library was constructed and 24 SMRT cells were sequenced on their PacBio RS II using the P5-C3 chemistry. ... The bottom (blue) track shows the testis transcriptome assembly aligned to M_zebra ...Half the sample cost of Pippin Prep and BluePippin . Unparalleled Performance. The PippinHT meets the same performance specifications as the rest of the Pippin line: ... The HT features blue LED detection (fluorescein) like the BluePippin. The maximum amount of DNA that can be loaded is less (1.5 ug vs. 5 ug), as are the loading and elution ...Shop Sage Science Inc 2% Agarose, dye-free, w/ internal standards, BluePippin.100-600 bp.10/pkg. at Fishersci.comHe added a second Pippin Prep as well as the longer-fragment Blue Pippin to his arsenal earlier this year. In Sharpe's lab, which also serves as a core facility for NRC and other Canadian government agencies, assembly projects tend to focus on large plant and fungal genomes. His team relies on Illumina and 454 sequencing, often adopting a ...The BluePippin is an updated version of Sage’s Pippin Prep system, to which a pulsed-field power supply has been added. Pulsed field gel electrophoresis allows larger fragments of DNA separated with high resolution and accuracy. Using pre-cast gels, the BluePippin can automatically collect DNA targets up to 50 kilobase pairs, with minimal ...Jan 5, 2012 · 98 subscribers Subscribe 16K views 11 years ago This video demonstrates how Pippin Prep and BluePippin from Sage Science (www.sagescience.com) perform automated DNA size selection for the... Library DNA was size-selected using a 2% agarose gel cassette of Blue Pippin (Sage Science, Beverley, MA, USA) for a target size range 150-300 bp and quantified with droplet digital PCR (QX-200; BioRad, Hercules, CA, USA). Sequencing was performed on an Illumina HiSeq 4000 to generate 150-nucleotide, single-end reads at a read depth of at least ...For each isoform, blocks in blue represent exons, and lines between blocks represent introns. Red triangles indicate the position of primers used for RT-PCR. b RT-PCR validation of the differential intron retention level of PB.13680. cDNA from 5 h, 15 h and 30 h germinating seeds and leaf samples were used for RT-PCR. The gel bands show DNA ...Blue Pippin Cassette 1.5%, 250-1,500 bp, Internal Marker. Gel cassettes for DNA selections on the Blue Pippin. For smaller fragment sizes, internal standards are used for higher accuracy and increased sample capacity. Higher molecular weight fragments require a dedicated lane to run a calibration marker.We purified the input of 3.2 µg purified SMRTbell library to load into the Blue Pippin 0.75% Agarose Cassette using cassette definition 0.75% DF Marer S1 3 to 10 kb Improved Recovery for the run protocol. We collected fragments greater than 7 kb from the cassette elution well and purified and concentrated the size-selected SMRTbell library ...Product Overview. Documents. GlycoBlue Coprecipitant consists of a blue dye covalently linked to glycogen, a branched chain carbohydrate, which is useful as a nucleic acid coprecipitant. The attached dye increases visibility of the pellet. This product is an ideal coprecipitant in nuclease protection assays at 1/100 dilution of stock solution.Blue Pippin Usage Form Date: Name: PI Name: Account #: Billing Contact: Billing Address: Cassettes Used (enter number): Any problems encountered during run? ITF Notes: Date Billed: Fill form: Try Risk Free. Form Popularity .Posted on August 3, 2023 by Alex. Range+T Size Selection Sage’s DNA size selection technology has been used to help improve PacBio sequencing, particularly for mammalian and complex genome work since the introduction of the BluePippin (2012). Over the last few years, PacBio®’s Hi-Fi circular consensus sequencing … more ».The coolest, funniest hobbit on lord of the rings. When u think someone is cool and funny you call them pippin.Repaired DNAs were selected by a Blue Pippin system to construct SMRTbell DNA libraries with fragment sizes of >10 kb according to the manufacturer’s specification (PacBio, Menlo Park, CA, United States). Library quality was determined using a Qubit 2.0 Fluorometer (Life Technologies, CA, United States), and the average fragment size ...Empress plum. Empress, also widely-known as Blue Imperatrice, is an unusually late-season dark blue / purple European plum. The plums have a sweet sugary flavor, but the golden yellow flesh is quite dry. The plums are "persistent", and if not picked will hang on the tree well into late fall. They can also be kept in a fridge for several weeks.Pippin Pulse Electrophoresis Power Supply Pulsed-field Power for Gel Boxes. Sage Science is pleased to introduce the new Pippin Pulse electrophoresis power supply for analytical gels. They've taken the pulsed-field power supply out of the BluePippin instrument to provide researchers an affordable tool to resolve DNA out to 100 kb and beyond .... Both approaches produced similar total yields of high-quality reDemonstrated Protocol, Last Modified on July 7, 2017, Per Cassette Kit Product Number Cassette Type Software DNA Control Kit Product Number BLG7510 0.75% and Capture 2 - 5 kb Marker D1 CBC7501 BLG7510 0.75% Band Capture 5 - 10 kb Marker D1 CBC7601BluePippin Operations Manual 460013 Rev D 1-1 1 Introduction Thank you for purchasing the BluePippin from Sage Science. The BluePippin is an The library was size selected (15–80 kb) us PacBio 10-20kb (Blue Pippin kit) 21ug 250ng/ul PacBio 30-40kb (Blue Pippin kit) 27ug 250ng/ul 10x Genomics -Chromium (BluePippin > 40kb size selection) 5ug 120ng/ul 10x Genomics - Chromium (no size selection)**** 400ng 15ng/ul * Recommended amounts for submission represent DNA quantities required for one library prep and additional QC.For >20 kb libraries a pulsed-field gel electrophoresis (PFGE) or Pippin Pulse system (Sage Science) is recommended. We evaluate the quality of the sample as: (1) "pass" if majority of DNA is above 48-kb ladder band, (2) ... (blue) and final library (red) run on Bioanalyzer with High sensitivity kit (Agilent). Note that the peak size ... The SageELF is an electrophoresis system that separ...

Continue Reading