Blue pippin.

Building on the success of the Pippin Prep and Blue Pippin size selection technologies, the PippinHT provides the user with the ability to size select up to 24 samples. Sample Flexibility Like the Blue Pippin, the PippinHT has pulsed field capabilities, thus enabling the size selection of DNA fragments intended for use in both short-read ...BluePippin Operations Manual 460013 Rev D 1-1 1 Introduction Thank you for purchasing the BluePippin from Sage Science. The BluePippin is an2. PCR products were purified using BlueCatBio's (Germany) Bluewasher and pooled into a single library using Hamilton's (USA) Startlet. Amplicons were separated by size using Sage Science's (USA) Blue Pippin. 3. Library was sequenced using Illumina's NovaSeq 6000. 4. Bioinformatic analysis using an in-house developed bioinformatic …Pufferfish are ideal models for vertebrate chromosome evolution studies. The yellowbelly pufferfish, Takifugu flavidus, is an important marine fish species in the aquaculture industry and ecology ...Pippin 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 ...

targeting fragments 280–375 bp in size with Blue Pippin (Sage Science), and PCR amplified with indexed primers. Finally, the single-ended fragments weresequenced on the Illumina NextSeq500 with 150 cycles in high output mode [59]. 2.3. De novo assembly readsPulse-field gel electrophoresis was performed with a Blue Pippin instrument by the University of Maryland Genomics Resource Center to select DNA fragments of the proper size. PacBio sequencing was carried out on the PacBio RS II platform with P6-C4 chemistry using nine SMRT cells and on the PacBio Sequel platform using nine additional SMRT ...

Finally, large fragments (>10 kb) were enriched with Blue Pippin device (Sage Science, Inc., Beverly, MA, USA) for sequencing. A total of 15 single-molecule real-time (SMRT) cells were processed, 7 with Sequel and 8 with RS II instruments (PacBio), to generate a total of 67.32 Gb PacBio data. For Oxford Nanopore sequencing, ∼5 μg of genomic ...Samples were pooled into groups of eight individuals for efficient size selection for fragments ranging from 570 to 690 bp using a Blue Pippin, a range expected to yield ∼200,000 loci based on in silico digestion of the B.constrictor genome (Bradnam et al. 2013). We used a Bioanalyzer (Agilent, Santa Clara, CA) to quantify and pool libraries ...

Sep 19, 2018 · The High Pass Plus cassette has a stocky separation column, so DNA has a shorter distance to travel. The wider column and increased taper provide higher resolution for a cleaner and more accurate size cut-off. The larger sample wells now allow a maximum load of 10ug (100% up from standard Blue Pippin cassettes). Applications. This popular instrument is a fluorescence reader for individual tubes that is used in conjunction with reagents kits to quantify dsDNA, ssDNA, RNA, and protein. This reader is easy to use and much more sensitive that the Nanodrop and is the method of choice for quantifying Illumina libraries or low concentration samples.Size select the DNA with Blue Pippin, using High Pass Plus gel cassette and 0.75% Dye Free for 1–10 kb External Standards S1 according to manufacturer’s protocol. Further, 10 μg of DNA is required for each lane, and typically the amplified sample is enough for two lanes. Adjust the cutoff length depending on the fragment size distribution.Then the optimized cycle number was used to generate double-stranded cDNA, followed by size selection using the Blue Pippin TM Size-Selection System to generate three libraries (1–2 kb, 2–3 kb ...

The BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA. For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user.

Pippin Prep DNA Size Selection System Selects 100 bpd - 1.5 kb. SageELF Whole Specimen Fractionation System DNA (up to 40 kb) or Proteins (up toward 500 kDa). Pippin Pulses Electrophoresis Power Supply Resolves DNA up to 400kb on an midi gel box. Applications. Transposase Enzyme Linked Long-Read Sequencing ...

"PIPPIN: I didn't think it would end this way. GANDALF: End? No, the journey doesn't end here. Death is just another path, one that we all must take. The grey rain-curtain of this world rolls back, and all turns to silver glass, and then you see it. PIPPIN: What? Gandalf? See what?8. Nike Air Flight '89. The Nike Air Flight '89 had a design that was slightly based on the Air Jordan 4 and is one of Pippen's sneakers that has endured the test of time, still available on ...Background. Orius laevigatus, a minute pirate bug, is a highly effective beneficial predator of crop pests including aphids, spider mites and thrips in integrated pest management (IPM) programmes.No genomic information is currently available for O. laevigatus, as is the case for the majority of beneficial predators which feed on crop pests.In contrast, genomic information for crop pests is far ...the Pippin with the cover closed. Humidity from the cassette may cause damage to electrodes. Approximate Run Times for "Tight" range Targets Run 1. Close the lid, go to the Main Tab, and make sure the proper protocol is loaded in the "Protocol Name" field. 2. Press "START". The run will automatically stop when every collection is ...Pippin Gel Cassettes. Gel Cassettes are pre-cast with agarose, and use ethidium bromide to visualize DNA and provide more uniform migration of fragments. Cassettes have a capacity to run 4 samples and are shipped in boxes of 10 each. Loading dye and DNA marker (for calibration) sufficient for all 40 runs are provided with each shipment.Using the Blue-Pippin Size-Selection System (Sage Science Inc., Beverly, MA, USA), we enriched and collected one fraction containing fragments >4 kb. The enriched fraction was mixed with unscreened fractions in an equimolar ratio to construct a mixed SMRT cell, which was subsequently run on the PacBio Sequel platform. ...

Both approaches produced similar total yields of high-quality reads (roughly 3.5 gigabases, as shown by the point at which each line in Fig. 1C crosses the y-axis) but the yield of reads greater than 20KB was clearly higher when using the Blue Pippin, as shown by the red line in Figure 1C being higher than the blue line at a value of 20KB on ...This video provides an overview of the basic types of DNA size selection protocols on the Pippin systems, and how they are programmed in the software interface.Blue peaks indicate that the GC content of this region is lower than the average GC content of the genome; (7) GC skew, wherein dark gray represents areas with more G than C content and red represents areas with greater C than G content, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred ...Blue Cross is a registered charity in England and Wales (224392) and in Scotland (SC040154). A company limited by guarantee. Registered company in England and Wales under company number 00363197. Registered address Shilton Road, Burford, Oxfordshire, OX18 4PF.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...Samples were pooled and concentrated using AMPure XP beads (Beckman Coulter) at 1.3× volumetric concentration, size-selected (190-370 bp) using Blue Pippin (Sage scientific), and sequenced in either NextSeq or Novaseq6000 (Illumina) 2 × 151 bp paired-end run using custom primers as described in the past . In total, we sequenced 4417 healthy ...

Samples were pooled into groups of eight individuals for efficient size selection for fragments ranging from 570 to 690 bp using a Blue Pippin, a range expected to yield ∼200,000 loci based on in silico digestion of the B.constrictor genome (Bradnam et al. 2013). We used a Bioanalyzer (Agilent, Santa Clara, CA) to quantify and pool libraries ...

Upgrading Pippin Instrument Software 1. Insert the USB drive with the upgrade folder into the USB port on the front panel of the BluePippin instrument. 2. From the Main Tab, press the “INFO” button. This will launch the information window. 3. From the Information Window, press “SOFTWARE UPGRADE”, press“OK” at the warning prompt ...Molecular characterization is a key step in the risk assessment of genetically modified organisms (GMOs) for regulatory approval. Herein, we describe a method for analyzing copy number, insertion loci, and flanking sequences through whole-genome sequencing (WGS) and bioinformatics. Comprehensive molecular characterization of G2-6 transgenic rice was performed using this pipeline. The results ...The reason that Pippin does not expect to find any tobacco after leaving the Shire is because the Shire is where tobacco is cultivated for smoking. No other place in Middle Earth does so, though it is found throughout the lands. ... (Capstan Blue) in two-ounce tins. That bill also carries a short note from Tolkien: "Quite correct, & I apologize ...the gel. The analytical gel was run with a Pippin Pulse using the 10-48kb pre-set protocol and run for 15 hours. 0.75% SeqKem Gold agarose from Lonza was used. 4 kb 5 kb 8 kb 6 kb 10 kb None (Control DNA) 6 kb 7 kb 8 kb 10 kb High-Pass threshold setting 29 kb 36 kb Marker S1 At the end of a run, marker peaks will be detected in designated ...A disabled black veteran who taught himself to paint, Pippin overcame his handicap — as well as discrimination — to become an overnight sensation in the American art world in the 1940s. Many consider him to be the foremost self-trained American artist of the 20th century, a painter whose artwork is reminiscent of the work of Grandma Moses ...Buy Sea Women's Blue Pippin Smocked Patchwork-printed Cotton Maxi Apron Dress. Similar products also available. SALE now on!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.

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.

Double digest restriction-site associated sequencing (ddRAD-seq) is a flexible and cost-effective strategy for providing in-depth insights into the genetic architecture of germplasm collections.

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 CBC7601The 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.My bet is that the nanopore folks have (of course!) done a ton of optimisation on two key things: The DNA cleanup; The library preps; I think that for most DNA extractions cleanups can vary a lot, but something like a Blue Pippin will do an exceptional job if you have access to one and can use it (they won't work for SUPER long DNA fragments which can't move through a gel of course).Dec 1, 2020 · Molecular characterization is a key step in the risk assessment of genetically modified organisms (GMOs) for regulatory approval. Herein, we describe a method for analyzing copy number, insertion loci, and flanking sequences through whole-genome sequencing (WGS) and bioinformatics. Comprehensive molecular characterization of G2-6 transgenic rice was performed using this pipeline. The results ... the gel. The analytical gel was run with a Pippin Pulse using the 10-48kb pre-set protocol and run for 15 hours. 0.75% SeqKem Gold agarose from Lonza was used. 4 kb 5 kb 8 kb 6 kb 10 kb None (Control DNA) 6 kb 7 kb 8 kb 10 kb High-Pass threshold setting 29 kb 36 kb Marker S1 At the end of a run, marker peaks will be detected in designated ...In most cases PCR bubble artifacts can not be removed by SPRI bead size selections or Blue Pippin size selections; if necessary, a “Reconditioning PCR” is the best option. However, to avoid unnecessary complexity loss of the library and introduction of polymerase errors, it would be best to optimize the library preparation protocol for 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 ...Page 1 PN 101-987-800 Version 02 (November 2021) Procedure & Checklist - Preparing HiFi SMRTbell® Libraries from Ultra-Low DNA Input 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.A Blue Pippin size selection system removed the fragments smaller than 20 kb. The constructed library was validated with a 2100 Bioanalyzer (Agilent). After annealing the sequencing primer to the SMRTbell template, DNA/Polymerase Binding kit P6 was used to bind the DNA polymerase.

Selection 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 No No Yes Specifications*Blue Pippin Size-Selection System. The first step of the protocol was cDNA synthesis with adapters. and PCR cycle optimization followed by large-scale PCR amplification. PCR products were then size.Define pippin. pippin synonyms, pippin pronunciation, pippin translation, English dictionary definition of pippin. n. 1. Any of several varieties of apple. 2. The seed of a fleshy fruit; a pip. …The Apple Pippin is a defunct open multimedia technology platform, designed by Apple Computer, and marketed as PiPP!N. According to Apple, Pippin was directed at the home market as "an integral part of the consumer audiovisual, stereo, and television environment." ... Sonoran Blue 1996 NA, JP WebViewer with MS Internet Explorer: Non-game, Web ...Instagram:https://instagram. gastronomia de mexicoovo coolmathgameorganizational structure articlesmaster ed The SageELF is an electrophoresis system that separates DNA or protein samples by size, and then fractionates the whole sample, or section of sample, into 12 fractions. The system is equipped with pulsed-field electrophoresis for resolving large DNA. Fractionation ranges are estimated and adjusted in software, and fractions are collected in buffer. los puertorriquenosjeff boschee ku Hi, I am a kind of enthusiast and would like to improve data on my genome with nanopore long reads. Do you possibly know of any lab that performs… functional neurocognitive imaging near me selection with either AMPure PB beads (red) or the BluePippin system (blue). Since the genomic DNA were partially degraded, SMRTbell Libraries were constructed without additional fragmentation. Long continuous read lengths are essential for applications such as de novo assembly and Isoform Sequencing (Iso-Seq).Xochitl Gomez and Ariana Madix topped the leaderboard in Week 4 of "Dancing With the Stars" (ABC) Sharon Knolle. October 17, 2023 @ 7:03 PM. This article contains spoilers for the Oct. 17 episode ...