Sageelf system

Manufactured by Sage Science

Sourced in United States

The SageELF system is a laboratory instrument designed for the automated separation and purification of nucleic acids, such as DNA and RNA. It utilizes a proprietary electrophoresis technology to perform size-based fractionation of samples.

Automatically generated - may contain errors

Lab products found in correlation

Megaruptor, by Diagenode (3 mentions) Sageelf native agarose for dna 0.75 1 18kb cassette, by Sage Science (2 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (2 mentions) Agilent bioanalyzer 2100 system, by Agilent Technologies (2 mentions) Smarter pico pcr cdna synthesis kit, by Takara Bio (2 mentions) Smrtbell template preparation kit 1, by Pacific Biosciences (2 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Femto pulse, by Agilent Technologies (1 mentions) Dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Trypsin gold, by Promega (1 mentions)

Spelling variants of this product

SageELF (15 citations)

6 protocols using sageelf system

Long Fragment Sequencing of Human Genome

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

Library preparation was performed on the human reference genome sample HG002 obtained from NIST. Genomic DNA was sheared using the Megaruptor from Diagenode with a long hydropore cartridge and a 20 kb shearing protocol. Prior to library preparation, the size distribution of the sheared DNA was characterized on the Agilent 2100 BioAnalyzer System using the DNA 12000 kit. In order to tighten the size distribution of the SMRTbell library, the sample was separated into 3 kb fractions on the SageELF System from Sage Science using the SageELF Native Agarose for DNA 0.75% 1–18kb cassette (Sage Science Product No. ELD7510). Fractions having the desired size distributions were identified on the Agilent 2100 BioAnalyzer using the DNA 12000 kit (Supplementary Figure 1c–f). Fractions centered at 10 kb, 15 kb, and 18 kb were used for sequencing with the 15 kb fraction selected for high-coverage sequencing.

Wenger A.M., Peluso P., Rowell W.J., Chang P.C., Hall R.J., Concepcion G.T., Ebler J., Fungtammasan A., Kolesnikov A., Olson N.D., Töpfer A., Alonge M., Mahmoud M., Qian Y., Chin C.S., Phillippy A.M., Schatz M.C., Myers G., DePristo M.A., Ruan J., Marschall T., Sedlazeck F.J., Zook J.M., Li H., Koren S., Carroll A., Rank D.R, & Hunkapiller M.W. (2019). Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature biotechnology, 37(10), 1155-1162.

+ Open protocol

+ Expand

PacBio Sequencing of Venom Gland cDNA

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

We prepared cDNA libraries from the venom gland for PacBio sequencing using the manufacturer’s protocol with a SMARTer Pico PCR cDNA Synthesis Kit (TAKARA Clontech) and SMRTbell Template Preparation Kit 1.0 (PacBio). We enriched longer cDNAs with a SageELF system (Sage Science, Inc). Sequencing was performed on a PacBio RS II, yielding a total of 179,143,509 reads with an average read length of 2,300 bp (Supplementary Table S4b). Most of these reads are long enough to be full-length transcripts and they were directly annotated with BLASTX against UniProt. PacBio reads are available from DRA under accession no. DRA006601.

Shibata H., Chijiwa T., Oda-Ueda N., Nakamura H., Yamaguchi K., Hattori S., Matsubara K., Matsuda Y., Yamashita A., Isomoto A., Mori K., Tashiro K., Kuhara S., Yamasaki S., Fujie M., Goto H., Koyanagi R., Takeuchi T., Fukumaki Y., Ohno M., Shoguchi E., Hisata K., Satoh N, & Ogawa T. (2018). The habu genome reveals accelerated evolution of venom protein genes. Scientific Reports, 8, 11300.

+ Open protocol

+ Expand

PacBio Transcriptome Sequencing and Annotation

Cited 1 time

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

Transcriptome analyses by PacBio reads were conducted as described in the previous our work [7 (link)]. Briefly, cDNA libraries from the venom gland for PacBio sequencing were prepared by using the manufacturer’s protocol with a SMARTer Pico PCR cDNA Synthesis Kit (TAKARA Clontech) and SMRTbell Template Preparation Kit 1.0 (PacBio). Longer cDNAs were enriched with a SageELF system (Sage Science, Inc.). Sequencing was performed on a PacBio RS II, yielding a total of 179,143,509 bps of 2300 bp average read length. N50 of PacBio reads was 5000 and not required for further assembly. Most of these reads are long enough to be full-length transcripts and directly annotated with BLASTX against UniProt. PacBio reads are publicly available from DDBJ under accession no. DRA006601.

Ogawa T., Oda-Ueda N., Hisata K., Nakamura H., Chijiwa T., Hattori S., Isomoto A., Yugeta H., Yamasaki S., Fukumaki Y., Ohno M., Satoh N, & Shibata H. (2019). Alternative mRNA Splicing in Three Venom Families Underlying a Possible Production of Divergent Venom Proteins of the Habu Snake, Protobothrops flavoviridis. Toxins, 11(10), 581.

+ Open protocol

+ Expand

High-Molecular-Weight DNA Isolation and Sequencing

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

High-molecular-weight DNA was isolated from frozen cell pellets using a Qiagen MagAttract HMW DNA kit and sheared using a Diagenode Megaruptor I to 20 kb mode size. At all steps, DNA quantity was checked on a Qubit Fluorometer I with a dsDNA HS Assay kit (Thermo Fisher), and sizes were examined on a FEMTO Pulse (Agilent Technologies) using a Genomic DNA 165 kb kit. SMRTbell libraries were prepared for sequencing according to the protocol ‘Procedure & Checklist—Preparing HiFi SMRTbell Libraries using the SMRTbell Express Template Prep Kit 2.0’. After SMRTbell generation, material was size-selected on a SageELF system (Sage Science) using the ‘0.75% 1-18 kb’ program (target 3,450 bp in well 12), and some combinations of fraction 3 (average size of 15–21 kb), fraction 2 (average size of 16–27 kb) and fraction 1 (average size of 20–31 kb) were selected for sequencing, depending on the empirical size measurements and available mass. The selected library fractions were bound with Sequencing Primer v.2 and Sequel II Polymerase v.2.0 and sequenced on Sequel II instruments (PacBio) on SMRT Cells 8M using Sequencing Plate v.2.0, diffusion loading, 2 h of pre-extension and 30 h of movie times. Samples were sequenced to a minimum HiFi data amount of 108.5 Gbp (35× estimated genome coverage) on four SMRT Cells.

Liao W.W., Asri M., Ebler J., Doerr D., Haukness M., Hickey G., Lu S., Lucas J.K., Monlong J., Abel H.J., Buonaiuto S., Chang X.H., Cheng H., Chu J., Colonna V., Eizenga J.M., Feng X., Fischer C., Fulton R.S., Garg S., Groza C., Guarracino A., Harvey W.T., Heumos S., Howe K., Jain M., Lu T.Y., Markello C., Martin F.J., Mitchell M.W., Munson K.M., Mwaniki M.N., Novak A.M., Olsen H.E., Pesout T., Porubsky D., Prins P., Sibbesen J.A., Sirén J., Tomlinson C., Villani F., Vollger M.R., Antonacci-Fulton L.L., Baid G., Baker C.A., Belyaeva A., Billis K., Carroll A., Chang P.C., Cody S., Cook D.E., Cook-Deegan R.M., Cornejo O.E., Diekhans M., Ebert P., Fairley S., Fedrigo O., Felsenfeld A.L., Formenti G., Frankish A., Gao Y., Garrison N.A., Giron C.G., Green R.E., Haggerty L., Hoekzema K., Hourlier T., Ji H.P., Kenny E.E., Koenig B.A., Kolesnikov A., Korbel J.O., Kordosky J., Koren S., Lee H., Lewis A.P., Magalhães H., Marco-Sola S., Marijon P., McCartney A., McDaniel J., Mountcastle J., Nattestad M., Nurk S., Olson N.D., Popejoy A.B., Puiu D., Rautiainen M., Regier A.A., Rhie A., Sacco S., Sanders A.D., Schneider V.A., Schultz B.I., Shafin K., Smith M.W., Sofia H.J., Abou Tayoun A.N., Thibaud-Nissen F., Tricomi F.F., Wagner J., Walenz B., Wood J.M., Zimin A.V., Bourque G., Chaisson M.J., Flicek P., Phillippy A.M., Zook J.M., Eichler E.E., Haussler D., Wang T., Jarvis E.D., Miga K.H., Garrison E., Marschall T., Hall I.M., Li H, & Paten B. (2023). A draft human pangenome reference. Nature, 617(7960), 312-324.

+ Open protocol

+ Expand

Long Fragment Sequencing of Human Genome

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

+ Open protocol

+ Expand

Protein Separation and Identification from Venetin-1 and DVr

Cited 1 time

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

Separation of proteins from Venetin-1 and raw coelomic fluid (DVr) was carried out with the development of the automatic SageElf system (Sage Science, Beverly, MA, USA) in a 3% SDS-Agarose gel cassette (ELP3010). It allows separation of proteins in the 10–300 kDa range. All the necessary solutions (Loading buffer) and the marker were supplied with the cassettes in the set. The sample was dissolved in a loading solution to obtain a concentration of 200 mg protein in 26 ml. Then, 4 ml of 0.5 M DTT was added to the sample and the whole mixture was heated for 6 min at 85 °C. After cooling, 10 ml of the loading solution with fluorescent Marker-03 was added to the sample, and the sample was mixed. The proteins prepared in this way were introduced into a 3% SDS-Agarose cassette. The separation (size-based mode) consisted in automatic elution of proteins from the gel for 1 h 20 min and then 30 min. The system was controlled by SageElf software version 1.08. It yielded 12 fractions of the preparation, which were then digested using a standard FASP procedure and trypsin (Trypsin Gold, Promega)^{27 (link),65 (link)}. Fractions obtained from two runs were combined for one FASP procedure. Final cleanup was carried out according to the Stage Tips procedure^{66 (link)}.

Rybicka M., Czaplewska P., Rzymowska J., Sofińska-Chmiel W., Wójcik-Mieszawska S., Lewtak K., Węgrzyn K., Jurczak P., Szpiech A., Nowak J., Musiał N, & Fiołka M.J. (2022). Novel Venetin-1 nanoparticle from earthworm coelomic fluid as a promising agent for the treatment of non-small cell lung cancer. Scientific Reports, 12, 18497.

+ 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!