The largest database of trusted experimental protocols

Abi prism 310 genetic analyser

Manufactured by Thermo Fisher Scientific
Sourced in United States

The ABI Prism 310 Genetic Analyzer is a capillary electrophoresis-based system designed for DNA sequencing and fragment analysis. It utilizes laser-induced fluorescence detection and provides accurate and reliable data for various genetic applications.

Automatically generated - may contain errors

24 protocols using abi prism 310 genetic analyser

1

Microsatellite Instability Analysis Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
As reported (Tanaka et al, 2006 ; Zaky et al, 2008 (link); Watari et al, 2012 (link)), we examined five microsatellite loci on chromosomes for MSI based on the revised Bethesda panel (Umar et al, 2004 (link)) as follows: 2p (BAT26), 4q (BAT25), 2p (D2S123), 5q (D5S346) and 17p (D17S250). The polymerase chain reaction (PCR) products were evaluated for MSI by capillary electrophoresis using an ABI PRISM 310 Genetic analyser (Applied Biosystems, Foster City, CA, USA) and automatic sizing of the alleles using a GeneMapper (Applied Biosystems). The MSI status was judged according to previous reports (Supplementary Figure S2) (Tanaka et al, 2006 ; Zaky et al, 2008 (link); Watari et al, 2012 (link)).
+ Open protocol
+ Expand
2

Molecular Profiling of Oligodendroglioma

Check if the same lab product or an alternative is used in the 5 most similar protocols
We used the P088-C1 Oligodendroglioma SALSA MLPA probe mix (MRC-Holland, the Netherlands) to detect loss of chromosome arms 1p and 19q, copy number variations in CDKN2A and CDKN2B genes, and to determine the status of the most common mutations of IDH1 (R132H and R132C) and IDH2 (R172K and R172M) genes in different glioma subtypes. The results of MLPA analysis have been further considered as the criteria for sample sub-classification for additional comparison, and determining possible differences in gene expression and promoter methylation. The MLPA experiment was prepared according to manufacturer’s protocol and recommendations with 100 ng of input DNA amount. Capillary gel electrophoresis was performed using ABI Prism 310 Genetic Analyser (Applied Biosystems, USA), and we used Coffalyser software (MRC-Holland, the Netherlands) for fragment analysis.
+ Open protocol
+ Expand
3

Insect Species Identification via PCR

Check if the same lab product or an alternative is used in the 5 most similar protocols
PCR products were examined for correct size by agarose gel (2.5%) (Sigma-Aldrich) electrophoresis in 1X TAE buffer. Successively, amplicons were purified using a commercial purification kit (ChargeSwitch PCR Clean-Up Kit, Invitrogen, Grand Island, NY) and sequenced (ABI Prism 310 Genetic Analyser, Applied Biosystems, Foster City, CA) to confirm the identity of the insect species and of the PCR amplified products. The chromatograms of the nucleotide sequences obtained were submitted for BLAST analysis.
+ Open protocol
+ Expand
4

Genetic Analysis of Nephrotic Syndrome Genes

Check if the same lab product or an alternative is used in the 5 most similar protocols
Sanger sequencing was performed in six children before 2014. All exons of NPHS1, NPHS2, PLCE1, LAMB2, LMXIB, COQ6, and COQ2, as well as exons 8 and 9 of WT1, were amplified by the polymerase chain reaction (PCR) method. The primers for NPHS1, NPHS2, PLCE1, WT1, LAMB2, LMXIB, COQ6, and COQ2 were designed on the basis of previously published information regarding the intron-exon boundaries [3 (link), 5 (link)–8 (link), 19 (link), 20 (link)]. The PCR products were purified with a QIA Quick PCR Purification Kit (Qiagen, Hilden, Germany). The purified products were cycle-sequenced with Big Dye terminators (Applied Biosystems, Foster City, CA, USA), and the cycle sequence products were analysed with an automated sequencer (ABI Prism 310 Genetic Analyser). The novel mutations were investigated in a number of mutation databases on human populations, such as the ExAC Browser (http://exac.broadinstitute.org/), the 1000 Genomes Project (http://www.internationalgenome.org/), HGMD (http://www.hgmd.cf.ac.uk/ac/index.php), and, in the 100 healthy control subjects, by direct sequencing.
+ Open protocol
+ Expand
5

DNA Methylation Analysis by MSAM

Check if the same lab product or an alternative is used in the 5 most similar protocols
As a pair of isoschizomers was used HpaII and MspI which recognise tetranuclotide CCGG, but have differential sensitivity to methylation at the inner or outer cytosine. The first sample containing 250 ng of DNA was digested by EcoRI and MspI restriction enzymes and the second equivalent sample by EcoRI and HpaII restriction enzymes. Subsequent adaptor ligation and pre-amplification reactions, using adaptors and primers designed for EcoRI and HpaII/MspI combinations, were performed as in [37 ]. In the case of selective amplification, three differently labelled EcoRI-derived primers, EcoRI-ACA (FAM), EcoRI-AGC (NED) and EcoRI-ACG (JOE), were combined with five HpaII/MspI-derived primers, HpaII/MspI-TCAA, HpaII/MspI-TCAC, HpaII/MspI-TCGC, HpaII/MspI-GCAT, and HpaII/MspI-TACC. This means altogether 15 primer combinations were used. Amplification products were separated electrophoretically using capillary system of ABI PRISM 310 genetic analyser (Applied Biosystems). GeneScan 500 ROX (Applied Biosystems) was used as a size standard and POP 4 polymer (Applied Biosystems) as a medium for fragment separation.
+ Open protocol
+ Expand
6

Sequencing and Phylogenetic Analysis of Viral Genomes

Check if the same lab product or an alternative is used in the 5 most similar protocols
A 4 μL aliquot of the purified amplicon DNA and the BigDye Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems) was used for cycle sequencing according to the manufacturer’s instructions. Besides primers SIN-Reg-B and cSIN-Reg-B (see above), primers Sin-Reg-B-nf: 5’- ATGACATCAAGATTAGCACC-3’ (position 8872–8891) and Sin-Reg-B-nr: 5’- TGATGCGACGGCTAAG –3’ (position 9734–9749) were used in sequencing reactions to reach full redundancy. The reaction was purified using Centri-Sep columns as recommended (Princeton Separations Inc, Adelphia, USA) and analysed by an ABI PRISM 310 Genetic Analyser (Applied Biosystems).
Sequences were aligned using GramAlign v3.0 [33 (link)]. A Maximum clade credibility (MCC) tree with dated tips and internal nodes was inferred using a MCMC Bayesian approach under the GTR model with gamma-distributed rate variation (Γ) and a proportion of invariable sites (I) using a relaxed (uncorrelated lognormal) molecular clock [34 (link)] in BEAST version 1.8.4 [35 (link)]. Four independent MCMC runs of four chains each were run for 10,000,000 states. The First 1,000,000 were used as burning and the MCC was establish from the remaining states. A median joining network [36 (link)] of the sequences was constructed and edited using a 2,190-character set in SPLITSTREE v4.12.3 [37 (link)]
+ Open protocol
+ Expand
7

Molecular Profiling of Myeloproliferative Neoplasms

Check if the same lab product or an alternative is used in the 5 most similar protocols
The JAK2V617F mutation was detected by allele‐specific polymerase chain reaction (PCR) according to the protocol of Baxter et al.27 and confirmed by direct Sanger sequencing. Quantitative analysis of the allele burden of the JAK2V617F mutation was performed by real‐time quantitative PCR using JAK2 MutaQuant (Ipsogen Inc). The cut‐off used for defining a case as negative for JAK2V617F mutation was 0.5%.
Myeloproliferative leukaemia (MPL) proto‐oncogene, thrombopoietin receptor (MPL) mutations, in particular W515L, W515K, W515A, S505N, and G509C, were tested by direct sequencing of exon 10. The primers used were as follows: MPL10F 5' TAGCCTGGATCTCCTTGGTG 3′; MPL10R 5' CCTGTTTACAGGCCTTCGGC 3′.
Mutations in exon 9 of the calreticulin (CALR) gene were also assessed using a bidirectional sequencing approach as previously described.28 All sequencing analyses were performed on an ABI PRISM 310 Genetic Analyser (Applied Biosystems) using the Big Dye Terminator v1.1 Cycle Sequencing Kit (Applied Biosystems).
+ Open protocol
+ Expand
8

FBN1 Gene Mutation Screening

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

Step 1: In the first phase, we screened for mutations of the FBN1 gene with the use of next-generation sequencing (NGS) technique as previously described [31 (link)]. We applied a Roche GS Junior platform.

Step 2: Homopolymer regions were investigated with Sanger sequencing with the use of ABI Prism 310 Genetic Analyser (Applied Biosystems) and all the detected (likely) pathogenic mutations were confirmed by this technique.

+ Open protocol
+ Expand
9

Genotyping HOXB13 Germline Mutation

Check if the same lab product or an alternative is used in the 5 most similar protocols
Germline DNA samples of both patients (HPC311 and P308T) sharing the same HOXB13 germline mutation were genotyped for the 11 microsatellite markers (6 localized in chromosome 17 and one for chromosome 2, 3, 5, 9 and 13) indicated in S2 Table. All 11 markers were assayed by PCR using fluorescently end-labeled primers (S2 Table) and capillary electrophoresis was performed on an ABI PRISM 310 Genetic Analyser (Applied Biosystems, Foster City, CA).
+ Open protocol
+ Expand
10

Mitochondrial 16S rDNA Amplification and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols
A fragment from the Mitochondrial 16S rDNA (407 bp) was amplified by PCR using primers 16S-F and 16S-R as reported previously [10 (link)] in a 2720 thermal cycler (Applied Biosystems, Foster City, California). The amplicons were examined on 1.5 % agarose gel stained with ethidium bromide for DNA visualization under UV light. The purified PCR products were directly cycle-sequenced from both directions on ABIPRISM 310 Genetic Analyser (Applied Biosystems, Foster City, California) using the BigDye Terminator Cycle Sequencing Kit 1.1 (Applied Biosystems, Foster City, California). Individual mite consensus sequences were manually trimmed of primer sequences, aligned, compared and edited using BioEdit v7.0.9.0 [16 ].
+ 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?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!