Pro size 2

Manufactured by Agilent Technologies

Sourced in United States

The PRO Size 2.0 software from Agilent Technologies is a data analysis tool designed for gel electrophoresis applications. It provides automated peak detection and molecular weight calculation capabilities.

Automatically generated - may contain errors

Lab products found in correlation

Fragment analyzer, by Agilent Technologies (12 mentions) Nanodrop, by Thermo Fisher Scientific (2 mentions) Aurum total rna mini kit, by Bio-Rad (2 mentions) Hiseq 4000, by Illumina (2 mentions) Novaseq 6000, by Illumina (2 mentions) Ampure xp bead, by Beckman Coulter (2 mentions) Tde1 enzyme and tagmentation td buffer, by Illumina (2 mentions) High sensitivity genomic dna analysis kit, by Agilent Technologies (1 mentions) 5300 fragment analyzer system, by Agilent Technologies (1 mentions) Trizol, by Thermo Fisher Scientific (1 mentions) Fragment analyser, by Agilent Technologies (1 mentions) Hiseq 4000 platform, by Illumina (1 mentions) Dsdna 905 reagent kit, by Agilent Technologies (1 mentions) Dnf 905 kit, by Agilent Technologies (1 mentions)

17 protocols using pro size 2

Genetic Diversity Assessment of Vicia Species

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

A total of 39 developed CpSSR markers were randomly selected to assess the genetic diversity of Vicia species (20 accessions from seven species; Supplementary Table 1). The PCR mixture (total volume 40 μl) contained 20 ng genomic DNA, 10 pmol each primer, 2.5 mM MgCl₂, 0.25 mM dNTPs, and 0.5 U Taq polymerase (Inclone, Deajeon, South Korea). Polymerase chain reaction amplification was performed under the following conditions: 94°C for 1 min; 30 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C for 30 s; and a final extension at 72°C for 5 min. The size of PCR products was analyzed using the Fragment Analyzer (Advanced Analytical Technologies Inc., Ankeny, IA, United States), and allele sizes were scored using the PROSize 2.0 (Advanced Analytical Technologies). The number of alleles, the major allele frequency, the expected heterozygosity and polymorphic information content were calculated using the PowerMarker v3.25.²The expected heterozygosity formula is as follows:
A closely related diversity measure is the polymorphism information content (PIC):
Phylogenetic analysis of Vicia species (20 accessions from seven species) was performed using UPGMA cluster analysis, and unrooted tree construction was based on the CS chord 1967 distance method in PowerMarker v3.25 software.

Jo I.H., Han S., Shim D., Ryu H., Hyun T.K., Lee Y., Kim D., So Y.S, & Chung J.W. (2022). Complete Chloroplast Genome of the Inverted Repeat-Lacking Species Vicia bungei and Development of Polymorphic Simple Sequence Repeat Markers. Frontiers in Plant Science, 13, 891783.

+ Open protocol

+ Expand

Capillary Electrophoresis-based Genetic Diversity Analysis

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

After capillary electrophoresis separation, the data was opened and processed using the software PROSize® 2.0 version 1.3.1.1 (Advanced Analytical Technologies, Inc., Ames, IA, USA). The data were normalized to the lowest (35 bp) and highest markers (500 bp), and calibrated to the 75–400 bp Range DNA ladder. A peak was considered a putative allele when the percentage of the area under the curve was more than 10%, with a maximum of two counted alleles per individual.
A double-entry matrix was developed with all counted alleles. Simple sequence-repeat alleles were scored as present (1) or absent (0). An index of similarity among pairs was developed, as well as a neighbor-joining method to generate a dendrogram. A bootstrap of 1000 was included to evaluate the robustness of the distribution tree. All analyses were performed with DARwin 6.0.012 software [43 ].

Bastías A., Correa F., Rojas P., Almada R., Muñoz C, & Sagredo B. (2016). Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS). PLoS ONE, 11(7), e0159825.

+ Open protocol

+ Expand

Microsatellite Profiling of Elatior Begonia

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

A total of 21 microsatellite primers developed by Goncalves [28 ] were initially screened with E. elatior DNA for reproducible amplification of 57 accessions. Only six primers (Eela2, Eela4, Eela5, Eela17, Eela18, and Eela21) were able to show amplification on 57 accessions for SSR analysis (Table 3). The remaining primers showed no amplification at all. The amplification reactions were performed in a final volume of 25 μl containing MyTaq Red Mix (MgCl, dNTPs, buffer, and Taq), forward and reverse primers, DNA template, and nuclease-free water. The total amplification cycle was performed in a thermocycler programmed to start at 94°C for 5 min, 10 cycles at 94°C for 1 min, 58°C for 1 min (with a decrease of 1°C per cycle), and 72°C for 1 min plus 30 cycles at 94°C for 40 s, 48°C for 40 s, and 72°C for 1 min, as well as final extension at 72°C for 10 min. The amplification products were separated on Fragment Analyzer and evaluated using the software package ProSize 2.0 (Advanced Analytical, USA). The amplified bands were scored according to the size of DNA ladder (1kb Plus). Each band fragment size was recorded in Microsoft Excel for analysis.

Ismail N.A., Rafii M.Y., Mahmud T.M., Hanafi M.M, & Miah G. (2019). Genetic Diversity of Torch Ginger (Etlingera elatior) Germplasm Revealed by ISSR and SSR Markers. BioMed Research International, 2019, 5904804.

+ Open protocol

+ Expand

DNA Extraction Quality Assessment

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

The final yield of extracted DNA was determined spectrophotometrically using theNanoDropND-1000 (Thermo Fisher SCIENTIFIC, USA). The purity of extracted DNA was indicated by an A260/A280 nm ratio. The quality of extracted DNA was assessed using the Fragment Analyzer (Advanced Analytical Technologies, USA) and High Sensitivity Genomic DNA Analysis Kit (Advanced Analytical Technologies, USA). The percentage of short fragments (≤1,500 bp) and Genomic Quality Number (GQN threshold of 10,000 bp) were calculated by PROSize 2.0 (Advanced Analytical Technologies, USA). Extracted DNA from each sample was diluted approximately to 5 ng/µl, aliquoted and stored at −20 °C. Aliquots were subsequently used in all further methods as starting material.

Videnska P., Smerkova K., Zwinsova B., Popovici V., Micenkova L., Sedlar K, & Budinska E. (2019). Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform. Scientific Reports, 9, 13837.

+ Open protocol

+ Expand

Automated RNA Analysis using Fragment Analyzer

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

Sample separation was performed on a Fragment Analyzer (Agilent Technologies), an automated multiplexed CE system equipped with an LED light source and charged-coupled device detector. RNA was quantitatively and qualitatively analyzed using the RNA Analysis Kit (Agilent Technologies DNF-489-0500). The RNA separation gel was mixed with an intercalating dye (AATI) at a v/v ratio of 10,000:1 for use as the separation matrix. RNA was denatured at 70 °C for 2 min and cooled on ice prior to analysis. Denatured RNA samples were electrokinetically injected at 5 kV for 6 s, and electrophoresis was performed for 40 min at 8 kV. An RNA ladder (AATI) was similarly analyzed as a calibrator for nucleotide size. Data were analyzed using PROSize 2.0 software (Agilent Technologies).

Packer M., Gyawali D., Yerabolu R., Schariter J, & White P. (2021). A novel mechanism for the loss of mRNA activity in lipid nanoparticle delivery systems. Nature Communications, 12, 6777.

+ Open protocol

+ Expand

Profiling P. aeruginosa Infection in C. elegans

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

After the worms were exposed to P. aeruginosa for the experimentally designated times (ranging from 0 to 24 h), they were collected in M9 buffer and decanted 3 times in 15-mL tubes to allow digestion of bacteria inside the worms and to separate adults from any larval progeny (no 5-Fluoro-2′-deoxyuridine was utilized in the P. aeruginosa assays). Following washing, the worm pellets were treated with guanidinium thiocyanate and RNA isolated using phenol/chloroform and ethanol precipitation. The obtained RNA was quantified and subjected to capillary electrophoresis using a 5300 Fragment Analyzer system (Agilent, California, United States of America) using a “standard sensitivity” RNA assay. The obtained electropherograms were analyzed using the ProSize 2.0 software (Agilent) to quantify the relative concentration of distinct rRNA species.
For the analysis of the total RNA content per worm (S1B Fig), sets of 20 adult worms were exposed to the designed treatment for 24 h. Following exposure, the worms were washed with M9 buffer, and individual worms were manually transferred into 0.25-mL guanidinium thiocyanate containing a fixed amount of a 500-nt spike-in RNA (in vitro translated). RNA was isolated by phenol–chloroform extraction followed by ethanol precipitation. RNA was profiled with capillary electrophoresis as described above.

Vasquez-Rifo A., Ricci E.P, & Ambros V. (2020). Pseudomonas aeruginosa cleaves the decoding center of Caenorhabditis elegans ribosomes. PLoS Biology, 18(12), e3000969.

+ Open protocol

+ Expand

Splicing and Intron Retention Analysis

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

RNA was isolated using an Aurum^TM Total RNA mini kit (Bio-Rad) according to package insert with on-column DNase1 treatment. RNA concentrations were determined using a NanoDrop (Thermo) and reverse transcribed with SuperScript VI with random hexamer primers (IDT). The cDNA was then subjected to polymerase chain reaction for 32 cycles using the primer sets listed in Table 2. Resulting PCR products were run via capillary electrophoresis on Fragment Analyzer using the 1-500 bp DNF-905 kit (Agilent) for splicing or on a 1% agarose gel dyed with Gel Green for intron retention assay. Quantification for splicing was done using the integration values of the electropherogram peaks corresponding to inclusion and exclusion products from the Prosize 2.0 software (Agilent), while image J was used to determine band intensities for intron retention assay. To determine the % rescue of a given ES event, Equation 1 was used, where DM_PSI = PSI of untreated DM fibroblasts, WT_PSI = PSI of control fibroblasts, and drug_PSI = PSI of DM fibroblasts treated with indicated drug.

% rescue = [(DM_PSI - drug_PSI) / (DM_PSI - WT_PSI)] * 100

Jenquin J.R., O’Brien A.P., Poukalov K., Lu Y., Frias J.A., Shorrock H.K., Richardson J.I., Mazdiyasni H., Yang H., Huigens RW I.I.I., Boykin D., Ranum L.P., Cleary J.D., Wang E.T, & Berglund J.A. (2022). Molecular characterization of myotonic dystrophy fibroblast cell lines for use in small molecule screening. iScience, 25(5), 104198.

+ Open protocol

+ Expand

Automated RNA Analysis Using Fragment Analyzer

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

Sample separation was performed on a Fragment Analyzer (Agilent Technologies), an automated multiplexed CE system equipped with an LED light source and charged-coupled device detector.
RNA was quantitatively and qualitatively analyzed using the RNA Analysis Kit (Agilent Technologies DNF-489-0500). The RNA separation gel was mixed with an intercalating dye (AATI) at a v/v ratio of 10,000:1 for use as the separation matrix. RNA was denatured at 70 °C for 2 minutes and cooled on ice prior to analysis. Denatured RNA samples were electrokinetically injected at 5 kV for 6 seconds, and electrophoresis was performed for 40 minutes at 8 kV. An RNA ladder (AATI) was similarly analyzed as a calibrator for nucleotide size. Data were analyzed using PROSize 2.0 software (Agilent Technologies).

Packer M., Gyawali D., Yerabolu R., Schariter J., & White P. (2021). A novel mechanism for the loss of mRNA activity in lipid nanoparticle delivery systems.

+ Open protocol

+ Expand

ATAC-seq Sample Preparation for Sea Urchin Embryos

Cited 1 time

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

ATAC sample preparation was carried out according to the Omni-ATAC-seq protocol (Corces et al. 2017 (link)). For each replicate, embryos were washed once in 1 µm filtered seawater, lysed, and ∼50,000 nuclei were isolated for the transposition reaction using the Illumina TDE1 enzyme and tagmentation (TD) buffer (Cat. No. 20034197 and 20034198) (San Diego, CA, USA). Sequencing libraries for each replicate were amplified via PCR after separately determining the optimal number of amplification cycles for each sample using qPCR as described in (Buenrostro et al. 2015 ), and libraries were purified and size selected using Ampure XP Beads at a 1.8:1 bead volume:library volume (Beckman Coulter, Brea, CA, USA). Library quality and transposition efficiency was accessed using a Fragment Analyzer and PROSize 2.0 (Agilent, Santa Clara, CA) at the Duke University Center for Genomic and Computational Biology. H. erythrogramma and L. variegatus libraries were sequenced on an Illumina HiSeq 4000 instrument using 50 bp SE sequencing. H. tuberculata libraries were sequenced on an Illumina NovaSeq 6000 instrument using 50 bp PE sequencing (only SE were used for data analysis).

Davidson P.L., Byrne M, & Wray G.A. (2022). Evolutionary Changes in the Chromatin Landscape Contribute to Reorganization of a Developmental Gene Network During Rapid Life History Evolution in Sea Urchins. Molecular Biology and Evolution, 39(9), msac172.

+ Open protocol

+ Expand

Comprehensive RNA Sequencing of Larval Samples

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

Approximately 50 individuals were collected for each RNA sample and placed in TRIzol (Invitrogen) for RNA extraction according to the manufacturer’s instructions. Samples were diluted in 40 ml RNase-free water and stored at −80°C. RNA concentration was measured by Qubit (Thermo Fisher Scientific) and RNA quality was determined with a Fragment Analyser and PROSize 2.0 (Agilent). In total, 17 samples were sequenced. One sample (8_1M1L: pH_T 8.0, Male 1, Larva) was not processed due to poor RNA quality. Library synthesis and sequencing of the RNA samples were carried out at the Sequencing and Genomic Technology shared resource at the Duke University Center for Genomic and Computational Biology. Sequencing libraries were synthesized with KAPA Stranded mRNA-Seq kits (Roche). Paired-end sequencing greatly aids in the construction of a de-novo transcriptome, but is cost-prohibitive to conduct on all samples; therefore, samples were randomly subjected to either 150 bp paired-end or 50 bp single-end sequencing (see Table S2 for sequencing scheme) on an Illumina HiSeq 4000 platform to maximize transcriptome quality while optimizing cost.

Devens H.R., Davidson P.L., Deaker D.J., Smith K.E., Wray G.A, & Byrne M. (2020). Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma. Molecular ecology, 29(23), 4618-4636.

+ 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!