The largest database of trusted experimental protocols

Seqplex dna amplification kit

Manufactured by Merck Group

The SeqPlex DNA Amplification Kit is a laboratory tool designed for the amplification of DNA samples. It provides a method for generating amplified DNA libraries from small amounts of input DNA, suitable for various genomic applications.

Automatically generated - may contain errors

3 protocols using seqplex dna amplification kit

1

Quasi-Random Priming and DOP-PCR for Single-Cell Libraries

Check if the same lab product or an alternative is used in the 5 most similar protocols
Single cell libraries constructed using quasi-random priming (QRP) and degenerate oligonucleotide primed PCR (DOP) were prepared from isolated nuclei without nucleosome depletion and brought up to 1 mL of NIB, stained with 5 µL of 5 mg/ml DAPI (Thermo Fisher, Cat. D1306) then FANS sorted on a Sony SH800 in single cell mode. One nucleus was deposited into each single well containing the respective sample buffers. QRP libraries were prepared using the PicoPlex DNA-seq Kit (Rubicon Genomics, Cat. R300381) according to the manufacturer’s protocol and using the indexed PCR primers provided in the kit. DOP libraries were prepared using the SeqPlex DNA Amplification Kit (Sigma, Cat. SEQXE-50RXN) according to the manufacturer’s protocol, but with the use of our own custom PCR indexing primers that contain 10 bp index sequences. To avoid over-amplification, all QRP and DOP libraries were amplified with the addition of 0.5 µL of 100× SYBR Green (FMC BioProducts, Cat. 50513) on a BioRad CFX thermocycler in order to monitor the amplification and pull reactions that have reached mid-exponential amplification.
+ Open protocol
+ Expand
2

Hydroxymethylation Profiling by hmC-seq

Check if the same lab product or an alternative is used in the 5 most similar protocols
>500 ng of genomic DNA is sheared to ~300 bp long fragments prior to immunoprecipitation (IP) with antibodies against 5hmC (Active motif rabbit polyclonal against hydroxymethylation cat#39769). For full protocols see17 (link). 10% of the input is also taken prior to immunoprecipitation. In all stages DNA was purified using DNA Clean & Concentrator™ (Zymo Research).The IP and input samples undergo 10 cycles of whole genome amplification following associated protocols (Sigma-Aldrich SeqPlex DNA Amplification Kit). Sequencing libraries are made from 100 ng of DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. Samples were then pooled in a 1:1 ratio and sequenced on a single Ion Proton P1 microwell chip (Life Technologies™). Sequence reads were mapped to the reference genome using the supplied TMAP mapping software and the resulting BAM file processed for downstream data analysis.
+ Open protocol
+ Expand
3

Laser-Capture Microdissection of Pancreatic Lesions

Check if the same lab product or an alternative is used in the 5 most similar protocols
Harvested pancreas tissues were embedded in OCT. Serial sections were prepared on PEN slides for laser-capture microdissection (LCM). PanIN-2/3 lesions (identified from flanking H&E slides) were laser-captured from serial sections onto Capsure LCM Caps using an ArcturusXT LCM instrument. Caps were extracted using the PicoPure DNA extraction kit from Thermo Fisher Scientific (Waltham, MA). Extracted DNA was amplified using the SeqPlex DNA Amplification Kit (Sigma-Aldrich, St. Louis, MO) and tested for quality using a Bioanalyzer 2100 and run on a 1% gel prior to library preparation. Sample libraries were prepared using the Swift Biosciences Kit (Accel NGS 2 plus) and Agilent Sure Select XT Mouse Exome post-capture kit following manufacturer's instructions. Sample libraries were pooled and run paired-end (2x75 bp) on an Illumina NextSeq 500 for an average of 90M reads per sample.
+ 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!