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1.5 mm biopsy punch

Manufactured by Integra LifeSciences

The 1.5 mm biopsy punch is a precision surgical instrument designed for obtaining small tissue samples. It features a sharp, circular cutting edge that can cleanly excise a cylindrical tissue specimen of 1.5 mm in diameter.

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2 protocols using 1.5 mm biopsy punch

1

Single-cell RNA-seq of tissue-adjacent cells

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Cells on and in the region adjacent to the 350 μm diameter electrodes were manually dissected using a 1.5 mm biopsy punch (Integra LifeSciences). RNA was harvested using NucleoSpin RNA XS Kit (Macherey-Nagel) and converted into cDNA using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories). DNA libraries were prepared with Ion Xpress™ Plus gDNA Fragment Library Preparation kit and sequenced by an Ion Proton next-generation sequencer (Thermo Fisher Scientific Inc.). The resulting sequences were aligned to the human transcriptome and genome (hg38) using a two-stage alignment pipeline employing STAR and TMAP read aligners [36 (link)]. The number of reads per protein-coding mRNA was determined using Partek Genomics Suite (Partek Inc.), and the dataset was normalized using the trimmed mean of the M-values method [37 (link)]. Genes with reads per million (RPM) ≥1 in three or more samples were selected (S1 Table), and differential expression and statistical analysis were carried out using the classic implementation of edgeR (S2 Table) [38 (link)]. The RNA-Seq data and methods can be accessed through the Gene Expression Omnibus (GEO: GSE146884).
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2

PDMS Microfluidic Device Fabrication

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Microfluidic channels of dimensions 200 × 75 μm2 (width by height) were designed using CleWin software, and PDMS microfluidic devices were fabricated from molds created using standard photolithography. In brief, the chrome mask design was patterned onto a 4 in. Si wafer coated with SU-8 2075 photoresist. When the Si-wafer molds were ready, PDMS mixture from combining Sylgard 184 base to curing agent at a 10:1 ratio was poured onto the Si wafer and baked at 70 °C for ~20 min. The PDMS replicas were then bonded to glass slides via oxygen plasma treatment in a plasma cleaner (PDC-32G, Harrick Plasma). Cube-shaped PDMS blocks (0.5 × 0.5 × 0.5 cm3) were used as microfluidic connectors for attachment of PTFE tubing to the microfluidic devices. The connectors were perforated with a 1.5 mm biopsy punch (Integra Life Sciences, Mansfield, MA) and attached to the PDMS-glass devices using freshly degassed PDMS. The microfluidic devices were then left to bake in an oven at ~80 °C for 30 min, and the microchannels were later treated with Aquapel, flushed with nitrogen, and baked at ~80 °C for 30 min.
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