Sageelf

Manufactured by Sage Science

Sourced in United States

The SageELF is a compact, automated electrophoresis system designed for DNA and RNA separation and analysis. It utilizes a patented technology to provide consistent, high-resolution results. The SageELF is capable of performing a wide range of electrophoresis applications, including genomic DNA, PCR products, and RNA.

Automatically generated - may contain errors

Lab products found in correlation

Femto pulse, by Agilent Technologies (3 mentions) Bluepippin, by Sage Science (3 mentions) Smrtbell express template prep kit 2, by Pacific Biosciences (3 mentions) Sequel 2, by Pacific Biosciences (3 mentions) Template prep kit v1, by Pacific Biosciences (2 mentions) G tube, by Covaris (2 mentions) Truseq nano dna library preparation kit, by Illumina (2 mentions) Sage elf, by Illumina (2 mentions) Megaruptor system, by Diagenode (2 mentions) Smrtbell template prep kit 1, by Pacific Biosciences (2 mentions) Megaruptor 2, by Diagenode (2 mentions) Femto pulse system, by Agilent Technologies (2 mentions) Genomic dna 165 kb kit, by Agilent Technologies (2 mentions) Dneasy plant maxi kit, by Qiagen (2 mentions) Nanodrop 1000, by Thermo Fisher Scientific (2 mentions) Streptavidin beads, by Thermo Fisher Scientific (1 mentions) Hindiii, by Thermo Fisher Scientific (1 mentions) Klenow enzyme, by Thermo Fisher Scientific (1 mentions) Hindiii, by New England Biolabs (1 mentions) Biotin 14 dctp, by Thermo Fisher Scientific (1 mentions)

15 protocols using sageelf

PacBio Sequel II HiFi Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

A 16-μg sample in 200 μl of nuclease-free water was sent to McDonnell Genome Institute (Washington University in Saint Louis) for library preparation and sequencing according to the standard protocol of PacBio (Pacific Bioscience, www.pacb.com/). A HiFi library was generated by (1) genomic DNA shearing, (2) DNA damage repair and end repair, (3) ligation of SMRTbell hairpin adapters, (4) isolation of target fragment sizes using SageELF (Sage Science) fractions 1–18 kb, and (5) DNA polymerase binding. The resulting SMRTbell library was sequenced on one SMRT cell 8M on a Sequel II instrument. Consensus reads (CCS reads) were generated using the CCS algorithm (https://github.com/PacificBiosciences/ccs), generating 18.2 Gb of CCS ≥ Q20 data.

Payne Z.L., Penny G.M., Turner T.N, & Dutcher S.K. (2022). A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis. Plant Communications, 4(2), 100493.

+ Open protocol

+ Expand

HiFi Library Preparation and Sequencing

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Isolated DNA was prepared for HiFi library preparation as described^{3 (link)}. Briefly, DNA was sheared to an average size of about 15 kbp using Covaris gTUBE, and the quantity and size were checked using Qubit (Thermo Fisher) and FEMTO Pulse (Agilent) instruments. Fragments underwent library preparation using the Template Prep Kit v1 (PacBio) and then fractionation on a SageELF (Sage Science) instrument. After evaluating size, fractions averaging 11, 13 or 15 kbp were sequenced on a Sequel II (PacBio) instrument using Sequel II chemistry v1 or v2EA (Early Access beta). After sequencing, raw data were analyzed with SMRT Link 7.1 or 8.0 using the CCS protocol with a cutoff minimum of three passes and estimated accuracy of 0.99. In total, 18 SMRT Cell 8Ms were run for the Puerto Rican trio (HG00731, HG00732 and HG00733) for an average yield per sample of 91 Gbp of HiFi reads (Supplementary Table 7).

Porubsky D., Ebert P., Audano P.A., Vollger M.R., Harvey W.T., Marijon P., Ebler J., Munson K.M., Sorensen M., Sulovari A., Haukness M., Ghareghani M., Lansdorp P.M., Paten B., Devine S.E., Sanders A.D., Lee C., Chaisson M.J., Korbel J.O., Eichler E.E, & Marschall T. (2020). Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nature Biotechnology, 39(3), 302-308.

+ Open protocol

+ Expand

Chromosome Conformation Capture in Broomcorn Millet

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

The leaf tissue from 3-week-old plants was collected and flash-frozen in liquid nitrogen. Genomic DNA was extracted from the leaf tissue using DNeasy Plant Maxi kit (Qiagen). For the Illumina PCR-free library, genomic DNA was fragmented in a Covaris S220 and separated on a SAGE-ELF (Sage Science) following the manufacturer’s instructions. The fraction that is 310~450 bp in size from SAGE-ELF were used for PCR-free library construction using TruSeq Nano DNA Library Preparation Kit (Illumina). The 20-kb PacBio library were prepared and sequenced on PacBio RS II using P6-C4 chemistry at Tianjin Biochip Corporation, following the manufacturer’s standard protocols.
Hi-C was performed following a published protocol^{48 (link)}. Briefly, 2 g of 10-day-old broomcorn millet seedlings were fixed in 1% formaldehyde solution. The nuclei/chromatin was extracted from the fixed tissue and digested with HindIII (New England Biolabs). The overhangs resulting from HindIII digestion were filled in by biotin-14-dCTP (Invitrogen) and the Klenow enzyme (NEB). After dilution and re-ligation with T4 DNA ligase (NEB), genomic DNA was extracted and sheared to a size of 300−500 bp with Bioruptor (Diagenode). The biotin-labeled DNA fragments were enriched using streptavidin beads (Invitrogen) and subject to library preparation.

Zou C., Li L., Miki D., Li D., Tang Q., Xiao L., Rajput S., Deng P., Peng L., Jia W., Huang R., Zhang M., Sun Y., Hu J., Fu X., Schnable P.S., Chang Y., Li F., Zhang H., Feng B., Zhu X., Liu R., Schnable J.C., Zhu J.K, & Zhang H. (2019). The genome of broomcorn millet. Nature Communications, 10, 436.

+ Open protocol

+ Expand

Genomic DNA Extraction and Library Preparation

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genomic DNA was extracted using the Plant DNeasy Maxi Kit (Qiagen). For the two small-size libraries, genomic DNA was fragmented in a Covaris S220 and separated on a SAGE-ELF (Sage Science). Fractions from the SAGE-ELF that have an average size of approximately 380 bp and an average size of around 450 bp were used for PCR-free library construction using the TruSeq Nano DNA Library Preparation Kit (Illumina). The two medium-size libraries (5 kbp and 8 kbp) were prepared using the GS FLX Titanium Kit (Roche) following standard protocols. All the Illumina libraries were then sequenced on a HiSeq2500 at Core Facility for Genomics of Shanghai Center for Plant Stress Biology (PSC). The 20-kb PacBio library was prepared and sequenced at Tianjin Biochip Corporation, following the manufacturer's standard protocols.

Zou C., Chen A., Xiao L., Muller H.M., Ache P., Haberer G., Zhang M., Jia W., Deng P., Huang R., Lang D., Li F., Zhan D., Wu X., Zhang H., Bohm J., Liu R., Shabala S., Hedrich R., Zhu J.K, & Zhang H. (2017). A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value. Cell Research, 27(11), 1327-1340.

+ Open protocol

+ Expand

SMRTbell Library Preparation and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

Three libraries were constructed using the SMRTbell Template Prep Kit 1.0 (Pacific Biosciences). In brief, genomic DNA (gDNA) was mechanically sheared to 60 kb using the Megaruptor system (Diagenode) followed by DNA damage repair and DNA end repair. Universal blunt hairpin adapters were then ligated onto the gDNA molecules after which non-SMRTbell molecules were removed with exonuclease. Pulse-field gels were run to assess the quality of the SMRTbell libraries. Two libraries were size-selected using SageELF (Sage Science) at 30 kb and 20 kb, the third library was size-selected at 20 kb using BluePippin (Sage Science). Prior to sequencing, another DNA-damage repair step was performed and quality was assessed with pulse-field gel electrophoresis. A total of 177 SMRT cells were run on the RS II using P6-C4 chemistry and 6 h videos.

Matthews B.J., Dudchenko O., Kingan S.B., Koren S., Antoshechkin I., Crawford J.E., Glassford W.J., Herre M., Redmond S.N., Rose N.H., Weedall G.D., Wu Y., Batra S.S., Brito-Sierra C.A., Buckingham S.D., Campbell C.L., Chan S., Cox E., Evans B.R., Fansiri T., Filipović I., Fontaine A., Gloria-Soria A., Hall R., Joardar V.S., Jones A.K., Kay R.G., Kodali V.K., Lee J., Lycett G.J., Mitchell S.N., Muehling J., Murphy M.R., Omer A.D., Partridge F.A., Peluso P., Aiden A.P., Ramasamy V., Rašić G., Roy S., Saavedra-Rodriguez K., Sharan S., Sharma A., Smith M.L., Turner J., Weakley A.M., Zhao Z., Akbari O.S., Black WC I.V., Cao H., Darby A.C., Hill C.A., Johnston J.S., Murphy T.D., Raikhel A.S., Sattelle D.B., Sharakhov I.V., White B.J., Zhao L., Aiden E.L., Mann R.S., Lambrechts L., Powell J.R., Sharakhova M.V., Tu Z., Robertson H.M., McBride C.S., Hastie A.R., Korlach J., Neafsey D.E., Phillippy A.M, & Vosshall L.B. (2018). Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature, 563(7732), 501-507.

+ Open protocol

+ Expand

Whole-Genome Sequencing with PacBio and Illumina

Check if the same lab product or an alternative is used in the 5 most similar protocols

For whole-genome sequencing, large-insert SMRTBell libraries (>20 kb), selected using a SageElf (Sage Science, Inc., Beverly, MA, USA), were prepared according to standard manufacture protocols and sequenced at the BYU DNA Sequencing Center (Provo, UT, USA) using P6-C4 chemistry on a Sequel II instrument (Pacific BioSciences, Menlo Park, CA, USA). For whole genome polishing, DNA was sent to for Illumina HiSeq (2 × 150 bp) sequencing from standard 500‐bp insert libraries. Trimmomatic v0.35^{82 (link)} was used to remove adapter sequences and leading and trailing bases with a quality score < 20 or with an average per-base quality of 20 over a four-nucleotide sliding window. After trimming, any reads shorter than 75 nucleotides in length were removed. Raw PacBio and Illumina reads have been deposited in GenBank.

Revolinski S.R., Maughan P.J., Coleman C.E, & Burke I.C. (2023). Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome. Communications Biology, 6, 326.

+ Open protocol

+ Expand

Tn5 Transposon-Based Library Preparation

Check if the same lab product or an alternative is used in the 5 most similar protocols

An amount of 3 μg high-quality genomic DNA was set up for Tn5 tagmentation reaction followed by strand displacement (Transgen, Beijing, China). The DNA fragments were conducted to size selection by SageELF (Sage Science, Beverly, MA, USA), and the favorite sizes were collected for further use. The circularization followed end-repair, and A-tailing of linear DNA was prepared at 0.1 ng/μL in reaction buffer with 0.1 U/μL T4 DNA ligase (ABclonal, Wuhan, China) at 16 °C overnight. The circle DNA was processed with 1U/uL DNase at 37 °C for 30 min to remove linear DNA and then was sheared with sonication (Sonics, Newtown, CT, USA) to obtain 300 bp fragments. The short fragments were prepared Illumina-compatible DNA library with NEBNext Ultra II kit (NEB, Ispawich, MA, USA) according to the manufacturer’s guide. The 300~500 bp All-seq library was submitted to HiSeq3000 platform sequencing after PCR cleanup and size selection by Blue Pippin (Sage Science, Beverly, MA, USA).

Li X., Zhang X., Luo Y., Liu R., Sun Y., Zhao S., Yu M, & Cao J. (2022). Large Fragment InDels Reshape Genome Structure of Porcine Alveolar Macrophage 3D4/21 Cells. Genes, 13(9), 1515.

+ Open protocol

+ Expand

High-quality PacBio Sequencing of Camellia japonica

Check if the same lab product or an alternative is used in the 5 most similar protocols

For long-read PacBio sequencing, high-molecular weight (HMW) DNA of C. japonica was isolated from root cultures using the NucleoBond HMW DNA kit (Macherey Nagel, Germany), quality was assessed with a FEMTOpulse device (Agilent, USA), and quantity was measured by the Quantus fluorometer (Promega, USA). A HiFi library was then prepared according to the “Procedure & Checklist - Preparing HiFi SMRTbell® Libraries using SMRTbell Express Template Prep Kit 2.0” manual with an initial DNA fragmentation by Megaruptor 3 (Diagenode, Belgium) and final library size binning into defined fractions by SageELF (Sage Science, USA). Size distribution was again controlled by FEMTOpulse (Agilent, USA). Polymerase-bound SMRTbell complexes were formed according to standard protocols (Pacific Biosciences of California Inc., USA) and loaded at an on-plate concentration of 85 pM (14, 15, 20, and 26 kb mean length). SMRT sequencing was performed using one 8 M SMRT cell per library (30 h movie time, 2 h pre-extension time) on the Pacific Biosciences Sequel II device, generating a total of 80 Gb (HiFi CCS). The SMRTbell libraries were sequenced at IPK Gatersleben.

Kuo Y.T., Câmara A.S., Schubert V., Neumann P., Macas J., Melzer M., Chen J., Fuchs J., Abel S., Klocke E., Huettel B., Himmelbach A., Demidov D., Dunemann F., Mascher M., Ishii T., Marques A, & Houben A. (2023). Holocentromeres can consist of merely a few megabase-sized satellite arrays. Nature Communications, 14, 3502.

+ Open protocol

+ Expand

Proteome Fractionation and Digestion

Check if the same lab product or an alternative is used in the 5 most similar protocols

For protein fractionation and digestion, L. monocytogenes protein pellets were dissolved in 1× SDS sample buffer (2% SDS, 50 mM Tris-HCl pH 6.8, 10% glycerol; 1% DTT) and quantified using a 2D Quant Kit (GE Healthcare, Chicago, IL, USA). To increase coverage of each proteome, 350 µg of proteins were fractionated into twelve molecular weight (MW) fractions using Sage ELF (Sage Science, Beverly, MA, USA). After fractionation, protein purity was verified using Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Fractions were desalted on HiPPR spin columns (Thermo Fisher Scientific, Waltham, MA, USA). In-solution digestion was conducted as follows: each fraction was reduced with 100 mM DTT (15 min at 65 °C), alkylated with 100 mM iodoacetamide (IAA) 30 min at room temperature in the dark, and digested overnight with Trypsin/Lys-C Mix (Promega, Madison, WI, USA) at 37 °C. Tryptic peptides were acidified with formic acid, concentrated by Speed-Vac, and stored at −80 °C. Immediately before mass spectrometry, they were dissolved in 2% acetonitrile/0.1% formic acid and subjected to LC-MS/MS. Protein fractionation was performed at Institute for Genomics, Biocomputing and Biotechnology (IGBB-MSU).

Gomaa B., Lu J., Abdelhamed H., Banes M., Pechanova O., Pechan T., Arick MA I.I., Karsi A, & Lawrence M.L. (2024). Identification of Protein Biomarkers for Differentiating Listeria monocytogenes Genetic Lineage III. Foods, 13(9), 1302.

+ Open protocol

+ Expand

Long-read SMRTbell Library Preparation

Check if the same lab product or an alternative is used in the 5 most similar protocols

Three libraries were constructed using the SMRTbell Template Prep Kit 1.0 (Pacific Biosciences). Briefly, genomic DNA (gDNA) was mechanically sheared to 60 kb using the Megaruptor system (Diagenode) followed by DNA damage repair and DNA end repair. Universal blunt hairpin adapters were then ligated onto the gDNA molecules after which non-SMRTbell molecules were removed with exonuclease. Pulse field gels were run to assess the quality of the SMRTbell libraries. Two libraries were size selected using SageELF (Sage Science) at 30 kb and 20 kb, the third library was size selected at 20 kb using BluePippin (Sage Science). Prior to sequencing, another DNA damage repair step was performed and quality was assessed with pulse field gel electrophoresis. A total of 177 SMRT cells were run on the RS II using P6-C4 chemistry and 6 hr movies.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!