E gel ex gel

Manufactured by Thermo Fisher Scientific

Sourced in United States, Germany

The E-Gel EX gels are pre-cast agarose gels designed for quick and easy DNA separation and analysis. They provide a simple, rapid, and reliable solution for tasks such as DNA fragment analysis, PCR product verification, and restriction fragment analysis.

Automatically generated - may contain errors

Lab products found in correlation

Agilent 2100 bioanalyzer, by Agilent Technologies (2 mentions) Power snap electrophoresis device, by Thermo Fisher Scientific (2 mentions) E gel ibase power system, by Thermo Fisher Scientific (1 mentions) Kapa library quantification kit, by Agilent Technologies (1 mentions) Chemidoc mp imager, by Bio-Rad (1 mentions) Qubit fluorometric quantification, by Thermo Fisher Scientific (1 mentions) Milli q, by Merck Group (1 mentions) Zymoclean gel dna recovery kit, by Zymo Research (1 mentions) Dna clean concentrator kit, by Zymo Research (1 mentions) Qiaquick pcr purification kit, by Qiagen (1 mentions) Q5 site directed mutagenesis kit, by New England Biolabs (1 mentions) Agencount ampure xp beads, by Beckman Coulter (1 mentions) Antarctic phosphatase, by New England Biolabs (1 mentions) Hpaii, by New England Biolabs (1 mentions) Qiaquick gel extraction kit, by Qiagen (1 mentions) T4 dna ligase, by New England Biolabs (1 mentions)

7 protocols using e gel ex gel

DNA Library Preparation and Size Selection

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

We constructed a library containing 300–390 ng DNA for each sample. Libraries with barcodes were size-selected from within the range of 190–240 bp (insert DNA ranging from 100 to 150 bp) using E-Gel CloneWell Agarose Gels (Invitrogen, Carlsbad, CA, USA). A piece of E-Gels contains six effective wells, each well can run a mixed sample which contains five samples of the NIPS DNA sequencing library. So, a piece of E-Gels can run thirty samples. Per the manufacturer’s instructions: 100 ng DNA per well was loaded on E-Gel EX Gels, 2% (Invitrogen, Carlsbad, CA, USA), a pre-cast 2% agarose gel with 0.8% SYBR stain; the gel was run on E-Gel iBase Power System (Invitrogen, Carlsbad, CA, USA) for approximately 15 min; and DNA with target sizes was retrieved from the bottom wells on the gel. A 50 bp DNA ladder was used as the marker (Invitrogen). The selected library was then tested with an Agilent 2100 Bioanalyzer (Fig. 5) and quantified by real-time polymerase chain reaction (PCR) using KAPA Library Quantification Kits (for the Ion Torrent platform).Figure 5

Selection of the library using E-gels and testing by Agilent 2100 Bioanalyzer. (A) Selection of the library between 190 and 240 bp (insert DNA was from 100 to 150 bp). (B) The selected library was tested using an Agilent 2100 Bioanalyzer.

Liang B., Li H., He Q., Li H., Kong L., Xuan L., Xia Y., Shen J., Mao Y., Li Y., Wang T, & Zhao Y.L. (2018). Enrichment of the fetal fraction in non-invasive prenatal screening reduces maternal background interference. Scientific Reports, 8, 17675.

+ Open protocol

+ Expand

DNA Restriction Digestion Protocol

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

For restriction digestion to remove the outer handles, the 50 µl reaction mix consisted of 1 µg DNA, 1x rCutSmart buffer, 50 U PleI enzyme (concentrated at 5U/µl) in PCR-grade water. The buffer and enzyme were obtained from New England Biolabs (Ipswich, MA, USA). All components were mixed on ice with the enzyme added last, then incubated at 37 °C for 70 min. Analytical agarose gel electrophoresis was performed using E-Gel EX gels (2%, Invitrogen, Thermo Fisher Scientific) on a Power Snap Electrophoresis Device (Thermo Fisher Scientific).

Luescher A.M., Gimpel A.L., Stark W.J., Heckel R, & Grass R.N. (2024). Chemical unclonable functions based on operable random DNA pools. Nature Communications, 15, 2955.

+ Open protocol

+ Expand

Genome-wide CRISPR screening of stimulated human T cells

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

Bulk CD3⁺ primary human T cells from two donors were transduced and cultured as described in the “Genome-wide CRISPRa and CRISPRi screens” section, except library transduction was completed at lower MOI of 0.3. Cells in the stimulated condition were stimulated with 6.25 μl/ml of anti–CD3/CD28/CD2 immunocult. Twenty-four hours later, cells from both the stimulated and nonstimulated condition were sorted for mCherry⁺ (marking dCas9-VP64). Sorted cells were processed to single-cell RNA-seq and sgRNA sequencing libraries by the Institute for Human Genetics (IHG) Genomics Core using Chromium Next GEM Single Cell 3’ Reagent Kit version 3.1 with feature barcoding technology for CRISPR screening, following the manufacturer’s protocol. Before loading the Chromium chip, sorted cells from two blood donors were normalized to 1000 cells/μl and mixed at a 1:1 ratio for each condition. Twenty microliters of cell suspension was loaded into four replicate wells per condition, for a total 80,000 cells loaded per condition. Final sgRNA sequencing libraries were further purified for the correct size fragment by 4% agarose E-Gel EX Gels (Thermo Fisher Scientific) and gel extracted. Libraries were sequenced over two NovaSeq S4 lanes (two stimulated wells and two nonstimulated wells per lane) at a 2:1 molar ratio of the gene expression libraries to sgRNA libraries.

Schmidt R., Steinhart Z., Layeghi M., Freimer J.W., Bueno R., Nguyen V.Q., Blaeschke F., Ye C.J, & Marson A. (2022). CRISPR activation and interference screens decode stimulation responses in primary human T cells. Science (New York, N.Y.), 375(6580), eabj4008.

+ Open protocol

+ Expand

Characterization of mRNA Samples

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

mRNA samples were characterized using the E-Gel iBase Power System with E-Gel EX gels (ThermoFisher) under denaturing conditions with 90% formamide. Gels were imaged using a BioRad ChemiDoc MP imager. Size fractionation was performed with an Agilent 2100 BioAnalyzer (Santa Clara, CA) at an mRNA concentration of 0.6 μg/μL. An RNA ladder (200, 500, 1000, 2000, 4000, 6000 nt) was used to generate a standard curve to convert Bioanalyzer results from migration time to number of bases.

Kauffman K.J., Mir F.F., Jhunjhunwala S., Kaczmarek J.C., Hurtado J.E., Yang J.H., Webber M.J., Kowalski P.S., Heartlein M.W., DeRosa F, & Anderson D.G. (2016). Efficacy and Immunogenicity of Unmodified and Pseudouridine-Modified mRNA Delivered Systemically with Lipid Nanoparticles in Vivo. Biomaterials, 109, 78-87.

+ Open protocol

+ Expand

DNA Purification and Analysis Protocol

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

Following preparative PCR reactions, DNA purification and work-up was performed using the DNA Clean & Concentrator kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocol. The purified product was eluted in PCR-grade water (type 1, 18.2 MΩ cm at 24 °C, Milli-Q®; Merck, Darmstadt, Germany). Analytical agarose gel electrophoresis was performed to confirm product size, using E-Gel EX gels (2% or 4%, Invitrogen, Thermo Fisher Scientific) on a Power Snap Electrophoresis Device (Thermo Fisher Scientific). The same system and conditions were used for preparative AGE purification during sequencing preparation, whereby the desired bands were excised and the DNA extracted using a Zymoclean Gel DNA Recovery Kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s protocol. DNA concentrations were measured using Qubit fluorometric quantification (Thermo Fisher Scientific, Waltham, MA, USA).

Luescher A.M., Gimpel A.L., Stark W.J., Heckel R, & Grass R.N. (2024). Chemical unclonable functions based on operable random DNA pools. Nature Communications, 15, 2955.

+ Open protocol

+ Expand

Generating ZIKV Point Mutations via SDM

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

Using the PRVABC59 synthetic infectious clone as a template, point mutations were generated at polyprotein residues 123, 894, 1404, 2074, 2086, and the double mutant 2074/2086 of the genomic ZIKV sequence by SDM. Q5 Site-Directed mutagenesis kit (New England BioLabs, Ipswich, MA, USA) was used to generate point mutations in the WT infectious clone. Primers for each mutant were designed using NEBaseChanger™. Q5′s Quick protocol was modified to improve the transformation efficiency for WT plasmid (14kb). A gradient PCR with ±5 °C adjustment to predicted annealing temperature was performed for each mutant. PCR amplicon was purified with E-Gel EX gel (Invitrogen) and QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). A minimum of 50 ng of purified PCR product was used in the Kinase, Ligase and DpnI treatment reaction. Transformants were size verified by PCR using primers designed to flank the region containing mutation. The entire length of the WT mutant was sequenced by Elim Biopharm (Hayward, CA, USA).
Primers used in mutagenesis are shown in Supplementary Table S1.

Collette N.M., Lao V.H., Weilhammer D.R., Zingg B., Cohen S.D., Hwang M., Coffey L.L., Grady S.L., Zemla A.T, & Borucki M.K. (2020). Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo. Viruses, 12(11), 1295.

+ Open protocol

+ Expand

MSCC Library Construction Protocol

Cited 1 time

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

The MSCC libraries were constructed according to the description of Guo et al. [21 (link)] with few alterations. For each of the five samples (S0h, S4h, S12h, S24h and S96h), two libraries were constructed. Two custom adaptors that contained a 5′ CG overhang and 3′ NN overhang, respectively, were created. For the HpaII library, 2 μg of genomic DNA combined with standard DNA was digested with HpaII (New England Biolabs [NEB]) for 2 h. Adaptor A was ligated to the resulting fragments. The reaction products were then incubated with Bst DNA polymerase (NEB) for 20 min. After digestion with MmeI (NEB), adaptor B was added to the reaction mixture incubated with T4 DNA ligase (NEB) overnight. The products were purified with Agencount AMPure XP Beads (Beckman) and then run on a 2% E-Gel® EX Gel (Invitrogen). The target band at approximately 140 bp was purified with the QIAquick Gel Extraction Kit (Qiagen). An 8-cycle PCR protocol was performed on the purification products. For the inverse library, after HpaII digestion in the first step, the fragmented ends were deactivated by incubation with Antarctic Phosphatase (NEB). The products were digested with MspI and then treated with the same procedure as the HpaII library.

Liu F., Zhou Y., Zhou D., Kan M., Niu X., Zhang Z., Zhang D., Tao L., He L., Zhan L, & Liu Y. (2014). Whole DNA methylome profiling in lung cancer cells before and after epithelial-to-mesenchymal transition. Diagnostic Pathology, 9, 66.

+ 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!