Abi 3130xl genetic analyzer

Manufactured by Thermo Fisher Scientific

Sourced in United States, United Kingdom, Japan, Germany, Canada

The ABI 3130xl Genetic Analyzer is a capillary electrophoresis instrument designed for DNA sequencing and fragment analysis. It employs laser-induced fluorescence detection to analyze DNA samples. The instrument can process multiple samples simultaneously and provides high-resolution data for various genetic applications.

Automatically generated - may contain errors

Lab products found in correlation

Spelling variants of this product

3130xl Genetic Analyzer (645 citations) ABI PRISM 3130xl Genetic Analyzer (327 citations) ABI 3130XL (189 citations) ABI-3130xl DNA genetic analyzer (10 citations) ABI PRISM 3130xl Genetic Analyzer system (8 citations) ABI Prism 3130xl Genetic Analyzer capillary sequencer (7 citations) ABI 3130XL Genetic Analyzer instrument (4 citations) ABI 3130XL Genetic Analyzer system (3 citations) ABI 3130xl Genetic Analyzer sequencer (2 citations) ABI 3130XL Genetic Analyzer BigDye Terminator (2 citations)

524 protocols using abi 3130xl genetic analyzer

Genetic Variant Confirmation Pipeline

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

SNVs and small indels were confirmed by standard Sanger sequencing. Sanger sequencing was performed on an ABI 3130xl genetic analyzer using a BigDye Direct Cycle Sequencing Kit with M13 tailed primers and a BigDye XTerminator Purification Kit (Thermo Fisher Scientific), according to the manufacturer's instructions.
CNVs were confirmed by Multiplex Ligation‐dependent Probe Amplification (MLPA) using a SALSA MLPA Kit P155‐D2 for the COL3A1 gene, according to the manufacturer's instructions (MRC‐Holland). Electrophoresis was conducted using an ABI 3130xl genetic analyzer (Thermo Fisher Scientific) and the data were analyzed with Coffalyzer.Net (MRC‐Holland).

Yamaguchi T., Hayashi S., Hayashi D., Matsuyama T., Koitabashi N., Ogiwara K., Noda M., Nakada C., Fujiki S., Furutachi A., Tanabe Y., Yamanaka M., Ishikawa A., Mizukami M., Mizuguchi A., Sugiura K., Sumi M., Yamazawa H., Izawa A., Wada Y., Fujikawa T., Takiguchi Y., Wakui K., Takano K., Nishio S, & Kosho T. (2022). Comprehensive genetic screening for vascular Ehlers–Danlos syndrome through an amplification‐based next‐generation sequencing system. American Journal of Medical Genetics. Part a, 191(1), 37-51.

+ Open protocol

+ Expand

Roe Deer Genetic Profiling Protocol

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

Total DNA from all samples was extracted with the Qiagen DNeasy Blood and Tissue Kit following the manufacturer’s protocols. We genotyped each individual with 16 microsatellite markers that were reported as polymorphic for roe deer (Table S1). Products were separated in an ABI 3130 xl Genetic Analyzer with the GeneScan 400HD ROX Size Standard (Applied Biosystems). Genotypes were read with the software GeneMarker (Softgenetics). A fragment of mtDNA control region was amplified by PCR with the primers L-Pro and H-Phe [25] (link). Cycling conditions were 95°C for 15 min; 35 cycles of 94°C for 15 s, 56°C for 15 s, and 72°C for 1 min; and 72°C for 10 min. PCR products were purified using Clean Up (A&A Biotechnology, Gdańsk, Poland). Sequencing reactions were carried out in a 10 µl volume using the Big Dye sequencing kit v.3.1 (Applied Biosystems) with the forward primer. Products were purified with the Exterminator kit (A&A Biotechnology) and separated on an ABI 3130 xl Genetic Analyzer (Applied Biosystems). Sequencing results were analyzed with the ABI DNA Sequencing Analysis software and aligned in BioEdit v.7.0.9 [26] .

Olano-Marin J., Plis K., Sönnichsen L., Borowik T., Niedziałkowska M, & Jędrzejewska B. (2014). Weak Population Structure in European Roe Deer (Capreolus capreolus) and Evidence of Introgressive Hybridization with Siberian Roe Deer (C. pygargus) in Northeastern Poland. PLoS ONE, 9(10), e109147.

+ Open protocol

+ Expand

TARDBP Variant Identification and Haplotyping

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

Peripheral blood samples were collected from patients after written informed consent and genomic DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega). Coding exons and flanking intronic regions of TARDBP (NM_007375.4) were sequenced on an ABI3130XL Genetic Analyzer (Applied Biosystems), using standard protocols for Sanger sequencing, and analysed using DNA Sequencing Analysis Software v.5.1. Variants were classified, according to the ACMG criteria, using Varsome browser [11] (link).
Parental DNA was collected when available to test the inheritance of the identified variants. Eight microsatellite markers in 1p36.22 (D1S450, D1S244, D1S2736, D1S1151, D1S2667, D1S434, D1S489, D1S2697), surrounding the TARDBP gene, were used for haplotype analysis. Electrophoresis was performed on an ABI3130XL Genetic Analyzer (Applied Biosystems) and fragments were analysed using GeneMapper v5.0. Genotype phasing was performed using the software Beagle 5.4 (http://facul ty.washi ngton.edu/brown ing/beagl e/ beagle.html).

Lattante S., Sabatelli M., Bisogni G., Marangi G., Doronzio P.N., Martello F., Renzi A.G., Del Giudice E., Leon A., Cimbolli P., Marchione D., Costantino U., Lucioli G., Bernardo D., Meleo E., Patanella A.K., Romano A., Zollino M, & Conte A. (2023). Evaluating the contribution of the gene TARDBP in Italian patients with amyotrophic lateral sclerosis. European journal of neurology, 30(5).

+ Open protocol

+ Expand

Methylation-Sensitive Amplification Polymorphism

Cited 1 time

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

The MSAP methodology^{26 (link)} is based on the use of isoschizomers HpaII and MspI, a pair of restriction enzymes which recognize the same target site (5′-CCGG-3′) but show different sensitivity to the first or second methylated cytosine. HpaII is able to cut when the external cytosine is hemi-methylated (single strand), whereas MspI cuts when the internal cytosine is hemi- or fully methylated (double strand)^{27 (link),52 (link),53 (link)}. Total genomic DNA was extracted from P. notatum inflorescences at anthesis using the method described by Martínez et al.^{54 (link)}. The developmental stages were classified according to the Laspina et al.^{37 (link)} reproductive calendar. Inflorescences were collected at 9:00 a.m. DNA was used for MSAP analyses as described by Marconi et al.^{55 (link)}. The list of primer combinations used and their relative sequences is provided in Supplementary Table S3. After amplifications, amplified fragments were separated by capillary electrophoresis in an ABI 3130xl Genetic Analyzer (Life Technologies). Comparisons of the patterns produced from samples digested in parallel with EcoRI/HpaII and EcoRI/MspI allowed identification of genomic alterations in the methylation patterns.

Bocchini M., Galla G., Pupilli F., Bellucci M., Barcaccia G., Ortiz J.P., Pessino S.C, & Albertini E. (2018). The vesicle trafficking regulator PN_SCD1 is demethylated and overexpressed in florets of apomictic Paspalum notatum genotypes. Scientific Reports, 8, 3030.

+ Open protocol

+ Expand

Detecting CLDN16 Gene Deletions/Duplications

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

In order to detect the potential gross deletions or duplications in the CLDN16 region, we used a QMPSF assay. Primer pairs for amplification of short exonic fragments corresponding to exons 1–5 of the CLDN16 gene and a sequence control of the HNF1B gene were designed (Table 1). Simultaneous PCR‐amplification was performed in a 20µL reaction mixture containing dNTPs (10 mM), MgCl2, 10% DMSO, KAPA Taq DNA Polymerase (Kapabiosystems, Boston, Massachusetts), dye‐labeled primers (0.3 µM of each primer), and 40 ng of genomic DNA. The amplification conditions consisted of an initial step of denaturation at 94°C for 5 min, followed by 24 cycles of denaturation at 94°C for 20 s, annealing at 60°C for 20 s, and extension at 72°C for 20 s. A final extension was performed at 72°C for 10 min. Then, the samples were denatured and loaded onto an ABI3130xl Genetic Analyzer (Life Technologies). We used the GeneMapper^® Software v. 4.0 (Applied Biosystems, California) for data analysis. Normalization was performed by dividing the peak height of each amplification product by the peak height of the control‐amplified product. Finally, the results obtained from the test samples were compared with the results from a healthy individual and positive control samples.

García‐Castaño A., Perdomo‐Ramirez A., Vall‐Palomar M., Ramos‐Trujillo E., Madariaga L., Ariceta G, & Claverie‐Martin F. (2020). Novel compound heterozygous mutations of CLDN16 in a patient with familial hypomagnesemia with hypercalciuria and nephrocalcinosis. Molecular Genetics & Genomic Medicine, 8(11), e1475.

+ Open protocol

+ Expand

Molecular Phylogenetics of Fungal Species

Cited 2 times

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

Primers for the AFTOL (Assembling the Fungal Tree of Life) genes (ITS, LSU, RPB1, RPB2, TEF1) were designed using the software Primer3 (Untergasser et al. 2012 (link)) based on the reference genome of the SN15 isolate (Hane et al. 2007 (link)). The genes were amplified in P. stipae isolates with conditions for PCR amplification as follows: 96 °C for 2 min, 35 cycles at 96 °C for 30 s, 56 °C for 30 s, 72 °C for 1 min, and a final step at 72 °C for 5 min. Amplified products were purified using manufacturer protocols for illustra Sephadex G-50 fine DNA Grade Column (GE Healthcare, Pittsburgh, USA) and sequenced in an ABI 3130xl Genetic Analyzer (Life Technologies, Applied Biosystems). Raw Sanger sequence reads of each primer were checked for quality and assembled into final gene sequences using Geneious v. 9.1.8 (Biomatters, Auckland, New Zealand). Gene sequences for ITS, LSU, RPB2 and TEF1 were available for P. phragmitis and P. novozelandica (Marin-Felix et al. 2019 (link)). Nucleotide sequences for the remaining species were extracted from the genome sequences available. Final datasets were obtained after a concatenation step using the MAFFT online tool v. 7.0 (Katoh et al. 2019 (link)). The concatenated dataset files were used to reconstruct maximum likelihood trees also in RaxML v. 8.0 (Stamatakis 2014 (link)).

Croll D., Crous P.W., Pereira D., Mordecai E.A., McDonald B.A, & Brunner P.C. (2021). Genome-scale phylogenies reveal relationships among Parastagonospora species infecting domesticated and wild grasses. Persoonia : Molecular Phylogeny and Evolution of Fungi, 46, 116-128.

+ Open protocol

+ Expand

Genetic Analysis of SMN1 and SMN2

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

To determine if each sample contained SMN1 and/or SMN2, exon 7 of SMN was amplified by PCR, using SMN-SEQ7F and SMN-SEQ7R as primers (Vezain et al., 2010 (link)). The PCR conditions were as follows: 5 min 96°C followed by 40 cycles of 30 sec 96°C, 30 sec 56°C and 1 min 72°C followed by a final extension step for 7 min at 72°C. The PCR product was purified using the Wizard SV Gel and PCR Cleanup System (Promega, Madison, WI) according to manufacturer’s directions. The purified PCR product was sequenced with the ABI 3130xl Genetic Analyzer (Life Technologies) automated sequencer, using the BigDye Terminator v3.1 Cycle Sequencing kit (Life Technologies).

Stabley D.L., Harris A.W., Holbrook J., Chubbs N.J., Lozo K.W., Crawford T.O., Swoboda K.J., Funanage V.L., Wang W., Mackenzie W., Scavina M., Sol-Church K, & Butchbach M.E. (2015). SMN1 and SMN2 copy numbers in cell lines derived from patients with spinal muscular atrophy as measured by array digital PCR. Molecular Genetics & Genomic Medicine, 3(4), 248-257.

+ Open protocol

+ Expand

CLL Genomic DNA Isolation and Analysis

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

Genomic DNA was isolated from cell lines and PBMC from CLL samples by standard treatment with Hirt's solution in the presence of 200 μg/ml of proteinase K, followed by phenol/chloroform/isoamyl extraction and ethanol precipitation. The DNA regions of interest were amplified with primers detailed in Supplementary Table S4 and sequenced using the BigDye Terminator v3.1 Cycle Sequencing Kit (Life Technologies, Waltham, MA, USA) according to the manufacturer's specification, with an ABI3130xl Genetic Analyzer (Life Technologies). Copy number variation was performed by real-time PCR using the TaqMan technology. Briefly, 10 ng of DNA was amplified using specific primers and fluorescent probes and a standard internal reference (TaqMan RNase P assay, Life Technologies) Each sample was analyzed in triplicate on 7900HT Real-Time PCR system. Each well was normalized to RNase P to obtain a ΔCt (2^{−(FAM dye Ct−VIC dye Ct)}), and then the average ΔCt for each triplicate was calculated. All samples were then normalized to a calibrator (eight DNA samples from healthy patients) to determine ΔΔCt. As the percentage of B-CLL cells could vary among patients, samples where considered carrying 13q deletion if loss of genetic material at the 13q chromosome region was ⩾25% compared with normal control.

Veronese A., Pepe F., Chiacchia J., Pagotto S., Lanuti P., Veschi S., Di Marco M., D'Argenio A., Innocenti I., Vannata B., Autore F., Marchisio M., Wernicke D., Verginelli F., Leone G., Rassenti L.Z., Kipps T.J., Mariani-Costantini R., Laurenti L., Croce C.M, & Visone R. (2014). Allele-specific loss and transcription of the miR-15a/16-1 cluster in chronic lymphocytic leukemia. Leukemia, 29(1), 86-95.

+ Open protocol

+ Expand

Validation of Microarray Gene Expression

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

To confirm the significant modulation of the differentially expressed genes resulting from microarray data analysis, we performed real-time quantitative PCR using gene-specific primer (Table S3) and ran each experiment in triplicate for analysis robustness. Briefly, cDNA was synthesized from 400 ng of the total RNA using the Advantage RT cDNA Kit (Clontech, Mountain View, CA, USA) following the manufacturer’s instructions. Specifically, samples were incubated at 42 °C for 90 min, followed by 2 min at 90 °C. Quantitative real-time PCR was performed using LightCycler 480 SYBR Green I Master (Roche Diagnostics, Mannheim, Germany) in a 15 µL reaction mixture. β-actin was used as an endogenous reference to normalize gene expression values with the 2^−ΔΔCt method [35 (link)]. PCR products were also confirmed via sequence analysis using the ABI BigDye Terminator Ready Reaction Mix (Life Technologies, Carlsbad, CA, USA) and analyzed on an ABI 3130XL genetic analyzer (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s protocol.

Conteduca G., Cangelosi D., Coco S., Malacarne M., Baldo C., Arado A., Pinto R., Testa B, & Coviello D.A. (2022). NSD1 Mutations in Sotos Syndrome Induce Differential Expression of Long Noncoding RNAs, miR646 and Genes Controlling the G2/M Checkpoint. Life, 12(7), 988.

+ Open protocol

+ Expand

Detailed APOA5 Gene Sequencing Protocol

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

Total genomic DNA was extracted from whole blood using salting-out procedure described by Miller et al. (1988 (link)). A region of 3.7 Kb of APOA5 gene was amplified from each individual in eight overlapping segments using newly designed primer sets (n = 8 pairs) using Primer3 Input software version 0.4.0 (//Frodo.wi.mit.edu/) (Supplementary Table 1). Amplification reactions were performed by PCR in an Applied Biosystems Fast thermal cycler (Version 1.01, Life Technologies, USA). PCR products were purified using Nucleospin® extract II column Kit (Clontech Laboratories, Inc., Version No. PR48598) following the suggested protocol (Macherey-Nagel, Germany). Cycle sequencing was then performed according to the manufacturer's instructions using the BigDye Terminator v.3.1 in a Fast Thermal Cycler (Life Technologies, Applied Biosystems, USA). The extension products were purified using BigDye® XTerminator™ Kit (Life Technologies, Applied Biosystems, USA). Capillary electrophoresis was then performed in ABI-3130xl Genetic Analyzer (Life Technologies, Applied Biosystems, USA).

Jasim A.A., Al-Bustan S.A., Al-Kandari W., Al-Serri A, & AlAskar H. (2018). Sequence Analysis of APOA5 Among the Kuwaiti Population Identifies Association of rs2072560, rs2266788, and rs662799 With TG and VLDL Levels. Frontiers in Genetics, 9, 112.

+ 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!