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10 protocols using lmd6000 microscope

1

Cryo-sectioning and Laser Microdissection of Anemone Tissues

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One anemone from each of the eight 500-ml tanks was collected at 11:00 a.m. (~6 hours into the light period), immediately snap-frozen in liquid nitrogen, embedded in the Tissue Freezing Medium (Electron Microscopy Sciences), and stored at −80°C until cryosectioning. The cryostat (CM3050 S, Leica) was prechilled to a chamber temperature of −23°C, and samples were equilibrated to the chamber temperature for 20 min and then sectioned at a thickness of 8 μm. Sections were then transferred onto precooled ribonuclease (RNase)–free polyester membrane metal frame slides (Leica) and air-dried for 5 min in a RNase-free fume hood.
Gastrodermal and epidermal cell layers were identified in sections (mostly from tentacles) at both ×10 and ×20 magnifications using a Leica LMD 6000 microscope with Leica filter cubes B/G/R and A. Each region of interest was traced individually using the LMD software and dissected using an ultraviolet laser beam. The dissected pieces were collected in CapSure Macro LCM Caps (Thermo Fisher Scientific) containing 40 μl of RNA extraction buffer from the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific). The harvested cells were lysed by incubation at 42°C for 30 min, vortexed briefly, and then kept at −80°C until further processing.
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2

Laser Capture Microdissection of Mouse Adrenal Glands

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Cryosections (10 μm) of mouse adrenal glands were collected on membrane slides (PEN-Membrane 2.0 μm; Leica), fixed in ethanol at −20° C, stained with crystal violet, and then dehydrated by passage through successively higher concentrations of ethanol followed by xylene (Pihlajoki et al., 2013 (link); Schillebeeckx et al., 2013 (link)). LCM with a Leica LMD6000 microscope was used to isolate samples from neoplastic or normal tissue. Microdissectates were collected in RNA extraction buffer (RNeasy Mini Kit, Qiagen, Valencia, CA) or Arcturus Picopure RNA isolation kit (Applied Biosystems, Foster City, CA).
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3

Maize and Brachypodium Internode Histochemistry

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Maize internode development was assessed and determined using the vegetative and reproductive stage identification system77 . Maize and Brachypodium internode samples were collected in the glasshouse and stored in 70% EtOH at 4 °C until use. The middle portion of internode nine (IN9) from maize and IN1 of the 1st flowering tiller from Brachypodium plants were used as sectioning material. Transverse stem cross-sections were freehand-cut with a clean razor blade and stained with 0.01% (w/v) aqueous Calcofluor White (CFW) (Sigma-Aldrich) for 8 min in darkness. The sections were washed with water to rinse away excessive CFW stain and stained with 5% (w/v) phloroglucinol (1,3,5-trihydroxy benzene) (Sigma-Aldrich) in 75% EtOH for 5 min in darkness. The stained sections were transferred onto glass slides and then flooded with drops of 12 N HCl. All stained transverse stem cross sections were mounted on glass slides with 30% glycerol and observed immediately on a Leica LMD6000 microscope.
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4

Retinal Morphology and Immunohistochemistry

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Eyes extracted from three rats in each age group were processed for embedding and sectioning using standard protocols, as described previously [19 (link),26 (link)]. One eye of each rat was used for morphological evaluation, while the fellow eye was used for immunohistochemistry. Eyeballs were fixed in 4% paraformaldehyde in phosphate-buffer (pH 7.2), followed by embedding and sectioning for paraffin or cryosections. While the sections stained with hematoxylin and eosin were analyzed by light microscopy for retinal morphology, the ultrastructure was analyzed by electron microscopy. Immunohistochemistry on retinas of 12-month-old rats was performed on paraffin sections. The transverse sections (4 μm) were mounted in silane coated slides. Deparaffinized sections were processed in 10 mM sodium citrate buffer (pH 6.0) and heated for antigen retrieval. After blocking, the respective primary antibodies were added to the sections in a volume of 100 μl and allowed to incubate overnight at 4 °C. After incubation, the sections were washed three times for 5 min in PBS, and 100 μl of respective Alexa Fluor-555 and Alexa Fluor-488 secondary antibodies solution was added. After washing, the slides were mounted in anti-fade reagent containing DAPI and observed under a Leica LMD 6000 microscope (Wetzlar, Germany). Images were captured using appropriate filters.
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5

Tissue Sectioning and Islet Isolation

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All equipment, including microtome, blades, water bath, brushes, and polyethylene naphthalate membrane (PEN-membrane) slides (Applied Biosystems, Foster City, Calif), was sprayed with RNase Away (ThermoFisher) before tissue sectioning. Tissue sections were sliced at a 12-μm thickness (separated by 36 μm), deparaffinized, rehydrated, and stained with hematoxylin and eosin. Slides were air dried, followed by brief incubation on a hot plate and immediately taken to the Leica LMD6000 microscope (Buffalo Grove, Ill) for islet isolation as previously described.37 (link)
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6

Cross-section Analysis of Stem Anatomy

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Transverse stem cross sections of the second internode were hand‐cut with a razor blade and stained with 5% (w/v) phloroglucinol in 75% EtOH for 5 min in darkness. The stained sections were flooded with a few drops of 12 N HCl and mounted on glass slides with 30% glycerol. Samples were immediately observed on a Leica LMD6000 microscope and images were captured.
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7

Epidermal Stomatal Quantification Protocol

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Adaxial (upper) and abaxial (lower) epidermis were prepared according to a protocol derived from the "Tape-Arabidopsis Sandwich" reported by Wu et al., (2009) . The upper or lower epidermal surface was stuck on a strip of Time tape (Time Med, IL., USA) while the opposite surface was affixed to a strip of Scotch Crystal tape (3M, Minn., USA). The Scotch Crystal tape was then sharply removed, and put in a Petri dish containing 10 mM Tris-Mes buffer pH 6.0, 30 mM KCl to avoid tissue desiccation. Then with the help of a microscope cover slip, the strip has been scraped off to get rid, the best as possible, of mesophyll tissues. Stomata were counted with the help of a Leica LMD6000 microscope. Stomatal index was calculated using the formula S/(E + S), S being the number of stomata per area unit and E the number of ordinary epidermal cells in the same area.
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8

Colon Epithelium Microdissection

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Cryostat sections (10 mm thickness) of OCT-frozen proximal colon from 3 control animals were mounted on PEN-Membrane slides (Leica). Dissection of the epithelial layer and adherent bacteria was carried out using a Leica LMD6000 microscope and Leica Laser Microdissection V 6.5 software. Tissue segments were stored in RX buffer (Qiagen, Valencia, CA) on dry ice and transferred to -20 C prior to DNA extraction.
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9

FFPE Tissue RNA Extraction and Reverse Transcription

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Tissue sections of paraffin-embedded (FFPE) tissues were mounted on nuclease and human nucleic acid free glass MembraneSlides (Leica Microsystems CMS, Wetzlar, Germany, order no. 11505189), deparaffinized and stained with haemalaun. Laser microdissection was performed as described previously 57 (link)58 (link) using a Leica LMD6000 microscope (Leica Microsystems CMS). Laser-microdissected cells were transferred into a reaction tube containing PKD buffer (Qiagen, Germany). RNA was isolated according to manufacturer’s protocol "Purification of total RNA from microdissected FFPE tissue sections" using the RNeasy FFPE Kit (Qiagen, Hilden, Germany). 28 ng RNA were reverse transcribed using random primers as described 18 (link).
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10

Quantification of Islet Graft Composition

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Paraffin-embedded islet grafts (n = 8) were consecutively sectioned, and every other section was stained for insulin (guinea pig polyclonal; dilution 1:400; Fitzgerald, Acton, MA), detected by MACH 3 Rabbit HRP-Polymer Detection (Biocare Medical, Concord, CA) and visualized by 3,3′-diaminobenzidine.36 (link) The insulin area was determined manually using a Leica LMD6000-microscope (Leica Microsystems, Wetzlar, Germany). The total area of the islet graft was calculated as an area under the curve by plotting the known areas.
Sections were double-stained for insulin (Fitzgerald) and glucagon (mouse monoclonal, dilution 1:800; Abcam, Cambridge, UK) with Alexa Fluor 488 (goat anti-guinea pig) and Alexa Fluor 594 (donkey antimouse; dilution 1:250; Invitrogen, Carlsbad, CA) as secondary antibodies. Images were acquired with Zeiss LSM780 (Zeiss, Jena, Germany) confocal. The area of insulin and glucagon was determined with the image software Imaris (Bitplane AG, Zurich, Switzerland). The estimated total α cell area was calculated by multiplying the α cell percentage with the total insulin area for the respective islet graft.
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