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Pen membrane glass slides

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PEN membrane glass slides are a type of laboratory equipment designed for microscopy applications. These slides feature a polyethylene naphthalate (PEN) membrane affixed to a glass surface, providing a substrate for sample preparation and analysis. The PEN membrane offers a stable and durable surface for various microscopy techniques.

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20 protocols using pen membrane glass slides

1

Aging Muscle Fiber Analysis

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Thirty‐month‐old male Fischer 344 x Brown Norway F1 hybrid rats (Rattus norvegicus) were purchased from the National Institute on Aging colony maintained by Harlan Sprague Dawley (Indianapolis, IN, USA). β‐guanidinopropionic acid was synthesized as described (Herbst et al., 2013)] from cyanamide and β‐alanine. GPA was purified by recrystallization and the synthesis confirmed by mass spectrometry and IR spectroscopy. β‐GPA was formulated to 1% by weight in 6% fat rodent chow (Harlan‐Teklad, Madison, WI, USA) and fed for 4 months ad libitum. Rats were housed on a 12‐h light/dark cycle. No significant difference was observed in the survival of rats treated with β‐GPA vs controls. Animals were euthanized, the quadriceps muscles dissected from the animals, weighed, bisected at the mid belly, embedded in optimal cutting temperature compound (Sakura Finetek, Torrance, CA, USA), flash frozen in liquid nitrogen, and stored at −80 °C. A minimum of one hundred 10‐μm‐thick consecutive transverse cross sections were cut with a cryostat at −20 °C and placed on Probe‐On‐Plus slides or PEN membrane glass slides (Life Technologies, Carlsbad, CA, USA) for laser microdissection. Slides were stored at −80 °C until needed.
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2

Transverse Cryo-Sectioning of Tick Biopsies

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The TAMU, College of Veterinary Medicine & Biomedical Science histology core performed transverse cryo-sectioning (10 μm) of tick attachment biopsies using Leica CM1850 UV Cryostat (Deer Park, IL). The rationale for transverse sectioning is that the location of tick mouthparts in the section guided the location of the tick attachment cement. Sectioning of biopsies began from the tick side and proceeded along the length of the mouthpart and finishing at the tick-feeding cavity where tick mouthparts were absent. Cryosections were placed onto PEN membrane glass slides (Life Technologies, Austin, TX, USA) which allowed for efficient recovery of dissected sections onto sample caps. Slides were stored in a slide box with a desiccant at – 80 °C until laser capture microdissection.
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3

Histochemical Analysis of Skeletal Muscle

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Mice were euthanized, quadriceps muscles dissected from the animals, bisected at the mid belly and frozen in liquid nitrogen. A portion of each frozen muscle was embedded in optimal cutting temperature compound (Sakura Finetek, Torrance, CA), flash frozen in liquid nitrogen and stored at -80°C. A minimum of one hundred 10μm thick consecutive transverse cross-sections were cut with a cryostat at -20°C and placed on Probe-On-Plus slides or PEN membrane glass slides (Life Technologies) for laser microdissection. Slides were stored at -80°C until needed.
At 100um intervals, sections were stained for cytochrome c oxidase (COX, brown) or succinate dehydrogenase (SDH, blue) as previously described.(Wanagat, Cao et al. 2001 (link)) A third slide was dual stained, first for COX and then for SDH. ETC abnormal fibers appear blue on a brown background following dual staining (Figure 1). Gömöri trichrome and H&E staining were performed according to standard protocols.(Sheehan and Hrapchak 1980 )
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4

Muscle Biopsy Sectioning and Imaging Protocol

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Open quadriceps muscle biopsies were taken under local anesthesia from all patients as well as from controls. All muscle biopsies were frozen in liquid nitrogen-cooled isopentane and stored at −80 °C until processed. Adjacent 10-µm sections were cut using a cryostat microtome and mounted on PEN membrane glass slides (Thermofisher). In this study, we used both transversal and longitudinal sections of the muscle biopsy (Fig. 1A,B). We were successful in obtaining longitudinal sections from only three of the muscle biopsies (patients 1, 3 and 5), due to the known difficulties in cutting sections from frozen tissue through long segments of individual muscle fibers21 (link).

Representative muscle biopsies: COX/SDH staining and ddPCR plots. (A) Longitudinal biopsy section. (B) Transverse biopsy section with COX negative cell labelled as 1. (C) RBF cell labelled as 2. (D) Intermediate cell labelled as 3 and COX positive cell labelled as 4. (E) Example of ddPCR 1D plot where each droplet from a sample is plotted on the graph of fluorescence intensity vs. droplet number. All positive droplets, blue for FAM or green for HEX, are scored as positive and each is assigned a value of 1. All negative droplets (grey), are scored as negative. (F) The histogram which plots amplitude vs. the frequency of the populations of droplets.

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5

Laser Microdissection of BRCA-WT and BRCA-mut PDAC

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Fresh frozen blocks of BRCA-WT and BRCA-mut PDAC tumors were obtained from MSKCC (Supplementary Data 1). 7 mm sections were sliced in a cryostat and placed on PEN Membrane Glass Slides (Thermo Fisher Scientific, LCM0522). Then, sections were stained using the Histogene™ LCM Frozen Section Staining Kit (Thermo Fisher Scientific, KIT0401) and stromal regions were dissected. Immune islands, cancer cells and blood vessels were excluded from microdissection. Slides were left to dry for 5 min at RT followed by microdissection using the Arcturus (XT) laser microdissection instrument (Thermo Fisher Scientific, #010013097). Infrared capture was used to minimize RNA damage. CapSure Macro LCM caps (Thermo Fisher Scientific, #LCM0211) were used to capture microdissected tissue. Microdissected tissue from each sample was incubated for 1 h in 65 °C in the lysis buffer of the RNA extraction kit and frozen at −80 °C. RNA extraction was performed using the PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific, KIT0204) according to the manufacturer’s instructions.
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6

Laser Microdissection of Rotated Root Cortex

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Root segments of length 5 mm were obtained from the bent parts of the third nodal roots of Z. nicaraguensis and fixed in 100% methanol. After fixation, the samples were embedded in paraffin and sectioned to a thickness of 12 µm. Serial transverse sections were placed on polyethylene naphthalate (PEN) membrane glass slides (Thermo Fisher Scientific). The paraffin on the sections was removed by immersing the slides in 100% Histoclear II (National Diagnostics) for 10 min, followed by air-drying at room temperature. The sections were then subjected to laser microdissection (LM) as described by Takahashi et al. (2010) (link). The cortex on the concave and convex sides of the rotated third nodal roots were collected from the tissue sections using a Zeiss PALM MicroBeam Laser Microdissection System (Carl Zeiss).
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7

Laser Capture Microdissection of Cortical Layers

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Tissue sections (20 μm thickness) from frozen brains were collected on PEN membrane glass slides (Thermo Fisher Scientific, MA, USA) using Leica CM1950 cryostat (Wetzlar, Germany) and subsequently stained with Thionin. Briefly, slides were fixed and washed in 75% and 50% ethanol for 5 min and 1 min, and then stained with 0.2% Thionin (Sigma-Aldrich, MI, USA) for 10 min and rinsed in Milli-Q water. The slides were then dehydrated in a graded ethanol series twice (in 50% ethanol, 75% ethanol, 95% ethanol and 100% ethanol for 30 sec each) and lastly with Xylene for 3 min. Layer 2/3 of stained tissue was identified and captured using the ArcturusXT laser capture microdissection (LCM) system (Thermo Fisher Scientific, MA, USA (Supplementary Fig. 1). A total of 30–40 mm2 (~10–20μg of total protein) of layer 2/3 was collected per sample based on previously described estimates (He et al., 2013 (link); Wisniewski, 2013 ), out of which 15–20 mm2 (approximately 250,000– 300,000 cells) yielding ~5–10μg of total protein. ~2.5μg was used for MS analysis.
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8

Cryosectioning and Laser Capture Microdissection

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For each strain of mice, more than three frozen heads were cryosectioned at 10 μm thickness on a Leica CM1850 cryostat. Sections were mounted onto PEN Membrane Glass Slides (Thermo Fisher Scientific) and immediately stained using 1% Methyl Green (Sigma‐Aldrich) in 0.1% diethyl pyrocarbonate (DEPC, Sigma‐Aldrich)‐treated water followed by four times for 30 s in DEPC water and then allowed to dry for 5 min. Laser capture microdissection was performed using CapSure® Macro LCM Caps (Thermo Fisher Scientific) on an ArcturusXT™ LCM instrument within 30 min of sectioning. Samples were stored in Tri‐Reagent (Sigma‐Aldrich) at −80°C until further processing.
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9

Laser Microdissection of Cryosectioned Tumor Samples

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LMD was performed at the Histopathology Core of UT Southwestern Medical Center as previously described117 . Briefly, 10 µm cryo-sections of tumors were mounted onto PEN membrane glass slides (Thermo Fisher Scientific, LCM05220). Sections were then stained using Histogene™ Staining Solution (Thermo Fisher Scientific, KIT0415), washed with high-performance liquid chromatography (HPLC)-grade water and subjected to LMD using a Leica LMD System. LMD sections were recovered in 0.2 mL tubes, immediately snap-frozen and stored at −80 °C until the analysis. Four replicates per sample were prepared.
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10

Leaf Tissue Cryosectioning and LCM

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Leaf samples were harvested close to the midvein region comprising both palisade and vascular cell types. The leaf samples were directly embedded in cryomold filled with OCT® embedding polymer (VWR, Radnor, PA, USA) and the blocks were frozen using liquid nitrogen. These blocks were used for cryosection process using CryoStarTM NX70 cryostat that generated 12 μm cross sections of leaf tissue. The obtained cryosections were placed on PEN membrane glass slides (Thermo Fisher Scientific, Waltham, MA, USA) and washed using ice cold 70% ethanol for 2 min, 85% ethanol for 1 min, and 100% ethanol for 1 min. The slides were dried and used for the LCM procedure described previously (Balasubramanian et al., 2021 (link)). Approximately 500–1000 mesophyll palisade cells and about 1000–2000 vascular cells were collected for transcriptome analysis (Figure S1).
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