Journal: Data in Brief

Article Title: Polymerase chain reaction-based gene removal from plasmids

doi: 10.1016/j.dib.2015.04.024

Figure Lengend Snippet: Complete DpnI digestion can be achieved in Phusion master mix. (A)?The graphic representation of pCRII-U85 plasmid marked with four segments and 28 DpnI restriction sites. Purple: u85 , cyan: f1 , green: kanR , and yellow: ampR . The expected DpnI digestion pattern is shown on the right. Both the graphic representation and the digestion pattern were generated by a software named (A Plasmid Editor (APE) developed by M. Wayne Davis), (B)?DpnI digestion of the pCRII-U85 plasmid. A total amount of 400 ng plasmid was used in each reactions. All reactions were performed at 37 °C. Lane 1: DNA ladder, Lane 2: undigested DNA, Lane 3: 30 min digestion in the fast-digestion buffer from the vendor, Lane 4: 30 min digestion in 1× Pfusion Master Mix, Lane 5: 30 min digestion in water, Lane 6: 30 min digestion in 2× Pfusion Master Mix, Lane 6: 60 min digestion in 2× Pfusion Master Mix. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: Phusion DNA polymerase master mix was purchased from NEB (Cat. #: M0531S).

Techniques: Plasmid Preparation, Generated, Software

Journal: Cell Reports Methods

Article Title: Retrospective cell lineage reconstruction in humans by using short tandem repeats

doi: 10.1016/j.crmeth.2021.100054

Figure Lengend Snippet: Duplex MIPs-based cell lineage workflow (A) Design of duplex MIPs precursor: desired targets are selected from our cell lineage database and precursors are designed. (B) Duplex MIPs preparation: duplex MIPs precursors are synthesized on a microarray, pooled and amplified by PCR. The product is digested by MlyI to remove the universal adaptors (orange and green), purified and diluted to obtain active duplex MIPs. (C) Duplex MIPs and template DNA are mixed together to allow annealing of the targeting arms (blue and yellow) to the regions flanking the targeted sequence in the template DNA, the products are then circularized by gap filling, facilitated by DNA polymerase and ligase. Linear DNA, including excess MIPs and template DNA, is eliminated by exonucleases digestion. The Illumina sequencing library is generated individually for each sample in a PCR step, facilitating addition of adaptors and barcodes. Libraries are pooled and sequenced by using Illumina next-generation sequencing platform, followed by analysis of the raw reads to detect mutations. The latter are then used to infer the cell lineage tree.

Article Snippet: Sample specific barcoding PCR was performed using dual-index barcoding primers and NEBNext Ultra II Q5 DNA Polymerase.

Techniques: Synthesized, Microarray, Amplification, Purification, Sequencing, Generated, Next-Generation Sequencing

Journal: Cell Reports Methods

Article Title: Retrospective cell lineage reconstruction in humans by using short tandem repeats

doi: 10.1016/j.crmeth.2021.100054

Figure Lengend Snippet:

Article Snippet: Sample specific barcoding PCR was performed using dual-index barcoding primers and NEBNext Ultra II Q5 DNA Polymerase.

Techniques: Recombinant, Purification, Sequencing, Software