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Abi prism 3730 l dna sequencer

Manufactured by Thermo Fisher Scientific
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The ABI Prism 3730xl DNA Sequencer is a high-throughput capillary electrophoresis system designed for DNA sequencing applications. The core function of this instrument is to perform automated DNA sequencing through the use of fluorescently-labeled DNA fragments and laser-induced fluorescence detection.

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Lab products found in correlation

Hotstar taq polymerase, by Qiagen (1 mentions) Random hexamer primer, by Promega (1 mentions) Escherichia coli rnase h, by New England Biolabs (1 mentions) Superscript 3 reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Qiaquick pcr purification kit, by Qiagen (1 mentions) Pgem t easy vector, by Promega (1 mentions)

Close spelling variants of this product

ABI PRISM 3730 DNA Sequencer ABI 3730 × l DNA Sequencer ABI PRISM 3730 sequencer ABI 3730×L sequencer ABI 3730 DNA sequencer ABI Prism DNA sequencer ABI 3730 sequencer ABI PRISM 3730 3730 L sequencers 3730 DNA sequencer

3 protocols using abi prism 3730 l dna sequencer

1

Validation of Fusion Gene Expression

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Known and novel fusion genes were verified using reverse transcription polymerase chain reaction (RT-PCR) followed by Sanger sequencing. RT-PCR of fusion genes used forward and reverse primer pairs in Supplementary Table S3. For reactions, 10 ng cDNA, 400 nM primer, and 0.5 units of HotstarTaq polymerase (Qiagen) were used in 20-μl reactions. RT-PCR was: 15 min at 94°C, 38 cycles at 94°C for 30 sec, 58°C for 30 sec, and 72°C for 1 min, with 5 min at 72°C. PCR products were confirmed via direct sequencing using an ABI Prism 3730×l DNA Sequencer (Applied Biosystems) and Big-Dye Terminator ver3.1 Cyclic Sequencing kit (Applied Biosystems, CA, USA).
Shin D.H., Lee D., Wan Hong D., Hyun Hong S., Hwang J.A., Il Lee B., You H.J., Kook Lee G., Kim I.H., Lee Y.S, & Han J.Y. (2016). Oncogenic function and clinical implications of SLC3A2-NRG1 fusion in invasive mucinous adenocarcinoma of the lung. Oncotarget, 7(43), 69450-69465.
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2

Multi-Locus Sequence Typing of Acinetobacter baumannii

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MLST was performed by using primers from Bartual et al. described previously except for cpn60-R, gdhB-R, rpoD-F and rpoD-R primers, which were designed in house (Table 1), and gpi, which was described by Karah et al.24 (link),25 (link) Briefly, 3–5 colonies are placed into a 96 well plate containing 100 μl of deionized water. The bacteria were then boiled at 100°C for 15 minutes to release the genomic DNA. Standard DNA amplification and sequencing using an ABI Prism 3730×l DNA sequencer (Applied Biosystems, Foster City, CA) with BigDye fluorescent terminators of the seven housekeeping genes: gltA, gyrB, gdhB, recA, cpn60, gpi and rpoD, was performed on all 68 isolates. The nucleotide sequences were compared to existing sequences in the MLST database (http://pubmlst.org/abaumannii/) and assigned a sequence type (ST) number according to their allelic profiles. For cluster analysis and assignment into clonal complexes, which differed by one allele, eBurst was used: http://eburst.mlst.net/v3/mlst_datasets/.
Johnson J.K., Robinson G.L., Zhao L., Harris A.D., Stine O.C, & Thom K.A. (2016). Comparison of molecular typing methods for the analyses of Acinetobacter baumannii from ICU patients. Diagnostic microbiology and infectious disease, 86(4), 345-350.
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3

Fusion Gene Validation Protocol

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First-strand cDNA was synthesized from 500–1000 ng of total RNA with random hexamer primers (Promega) using SuperScript III reverse transcriptase (Invitrogen). Reverse transcription was performed for 60 min at 55°C followed by 15 min at 70°C to inactivate the reaction. Escherichia coli RNase H (New England Biolabs) was added to remove RNA complementary to cDNA. Primers (Supplemental Table 3) were designed as flanking fusion points. PCR products were purified using a QIAquick PCR purification kit (Qiagen) and cloned into pGEM-T easy vector (Promega) and then sequenced by a ABI Prism 3730×l DNA sequencer (Applied Biosystems). Sixty-four out of 67 (95.5%) fusion genes were confirmed by sequencing.
Bao Z.S., Chen H.M., Yang M.Y., Zhang C.B., Yu K., Ye W.L., Hu B.Q., Yan W., Zhang W., Akers J., Ramakrishnan V., Li J., Carter B., Liu Y.W., Hu H.M., Wang Z., Li M.Y., Yao K., Qiu X.G., Kang C.S., You Y.P., Fan X.L., Song W.S., Li R.Q., Su X.D., Chen C.C, & Jiang T. (2014). RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas. Genome Research, 24(11), 1765-1773.
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