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44 protocols using sf100 4

1

Cytospins and Histopathology Protocols

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For cytospins, 1×106 cells were collected in 100ȝL PBS/2% FBS from single cell preparations of BM, added to Shandon Single Cytofunnels (Thermo Scientific #1102548) clipped to glass slides (FisherScientific #12–550-20), and centrifuged using a Cytospin 3 centrifuge (Shandon) set at 500 rpm for 5 min at medium acceleration. After drying, cells were stained with the Hema 3 stat pack (Fisher Scientific #23–123869) and images captured with a Nikon Eclipse E200 microscope equipped with an Infinity 2 color camera (Lumenera) controlled by Infinity Capture software (Lumenera).
For histopathology, mouse tibia and spleens were fixed in 10% neutral buffered formalin (Fisher Scientific #SF100–4) overnight at 4oC or 1 hr at room temperature, respectively. Spleens were inoculated in 35% sucrose (Fisher Scientific #525590A) overnight, whereas bones were decalcified (Calrite from Richard-allen Scientific #5501) for 12 days prior to overnight inoculation in 35% sucrose. Both tibias and spleens were rinsed with PBS and processed for paraffin embedding and sectioned at 5 μM. Both H&E and reticulin staining was performed by the Histology Lab of Washington University. Images were captured using an inverted microscope and analyzed with NIS-Elements software from Nikon.
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2

Hippocampal Assessment after Surgical Intervention

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At days 7 and 14 after surgery, the rats were deeply anesthetized with isoflurane for euthanasia, a cardiac blood sample was collected, and then all groups were divided into 2 subgroups: One for histological assessments and other for biochemical analysis. In subgroup 1, animals were intracardially perfused with cold 1xPBS (46-013-CM, Corning, NY, USA) followed by 10% buffered formalin phosphate (SF100-4, Fisher Chemical, Corning, NY, USA), their brains were removed, and coronal brain slices containing the dorsal hippocampus were cryoprotected with 30% sucrose (S0389, Sigma, St. Louis, MO, USA) and then frozen. Slices were cut into 10 µm sections, which were mounted on slides and stored at −20 °C. In subgroup 2, rats were decapitated, and their brains quickly removed. Hippocampi were dissected, rapidly frozen, and stored at −80 °C.
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3

Quantifying Bone Marrow Adiposity using microCT

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Long bones were dissected free of soft tissues and fixed in 10% neutral buffered formalin (Fisher #SF100-4) overnight at 4°C with gentle agitation. The next day, bones were washed in cool running tap water. The bones were decalcified in 4% EDTA for 15 days at 4°C, changing the EDTA every 3–4 days. The bones were then stained for lipid using a 1:1 mixture of 2% aqueous osmium tetroxide (Polysciences Inc, Warrington, PA) and 5% potassium dichromate for 48 hrs (34 (link)). The bones were then washed in cool running tap water for 2 hrs. Whole bones were imaged using micro-CT performed in water with energy of 55kVp, an integration time of 500 ms, and a maximum isometric voxel size of 10 μm (the “high” resolution setting with a 20mm sample holder) using a Scanco microCT-35. When creating volumes of interest (VOI), the interface between the decalcified bone and the marrow adipose tissue (MAT) is usually apparent, facilitating placement of graphical objects. When segmentation is applied, MAT can be visualized unencumbered by the surrounding bone. The data is a volumetric measurement analogous to the volumetric bone measurement, bone volume/total volume (BV/TV). As such, it is more sensitive and provides a better representation of the physical distribution of MAT than 2-dimentional data. The Yale micro-CT facility at Yale Medical School was used to perform the micro-CT analysis.
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Visualizing C2C12 Cell Cytoskeleton and Mitochondria

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C2C12 cells were seeded with 1.0 × 105 cells per well in a 35 mm MatTek microscopy glass dish (Fisher Scientific, PDCFOS30) and treated with 10 μM of CCG-1423 for 24 h, whereas 0.5% DMSO treatment was used as control. As described previously [24 (link)], cells were fixed with 3.7% formaldehyde (Fisher Scientific, SF100-4) for 10 min at room temperature and permeabilized with PBS containing 0.2% Triton X-100 for 5 min. Cells were washed with PBS and blocked with 3% BSA for 1 h at room temperature. Cells were then incubated with ActinGreen (ThermoFisher, Waltham, MA, USA, R37110) using rhodamine-phalloidin (1:200) for 20 min. Samples were then counterstained for 5 min with DAPI (1:1000) to label the nuclei (ThermoFisher, Waltham, MA, USA, D1306). Cells were stained with MitoTracker™ Red CMXRos (Invitrogen, Waltham, MA, USA, M7512) for 30 min following the manufacturer’s instructions. Fluorescent images were captured with a Zeiss LSM 880 confocal microscope with ZEN blue 3.2 software (Carl Zeiss Microscopy, White Plains, NY, USA). The collected images were analyzed, and fluorescence intensity was quantified using ImageJ software.
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5

Decalcification and Reticulin Staining of Mouse Tibias

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Mouse tibias were fixed in 10% neutral buffered formalin (Fisher Scientific #SF100-4) overnight at 4°C. Immediately after overnight fixation, tibias were decalcified in 14% EDTA for 12 days. This was followed by series of hydration steps: 20% EtOH for 1hr, 30% EtOH for 1hr, 50% EtOH for 1hr and 70% EtOH for hr. Tibias were rinsed with PBS and processed for paraffin embedding and sectioned at 5 μM. Reticulin staining was performed by the Washington University Musculoskeletal Histology and Morphometry Core. Images were captured using an AxioObserver D1 inverted microscope (Zeiss, Thrownwood, NY) equipped with an Axiocam 503 color camera. Images were acquired with Plan-Apochromat objective at 63X, 1.4 NA objective using the ZEN 2 (blue edition) software.
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Teratoma Formation from Engineered ESCs

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1×106 of WT or Klf5-overexpressing ESCs were injected into the dorsal flanks of 6–7-week-old immune-deficient NCr-nu/nu female mice (Taconic, Cat# NCRNU). After 4–5 weeks, resulting teratomas were collected by surgical removal, fixed overnight in 10% buffered formalin (Fisher Scientific, Cat. # SF100–4), dehydrated in a graded series of ethanol solutions, embedded in Paraplast X-TRA paraffin (Fisher Scientific, Cat. # 23–021-401), sectioned at 6 mm thickness, and stained with hematoxylin and eosin (H&E) using standard procedures (Choi et al., 2011 (link)). These paraffin sections will be subjected to immunohistochemistry
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7

Teratoma Formation from Engineered ESCs

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1×106 of WT or Klf5-overexpressing ESCs were injected into the dorsal flanks of 6–7-week-old immune-deficient NCr-nu/nu female mice (Taconic, Cat# NCRNU). After 4–5 weeks, resulting teratomas were collected by surgical removal, fixed overnight in 10% buffered formalin (Fisher Scientific, Cat. # SF100–4), dehydrated in a graded series of ethanol solutions, embedded in Paraplast X-TRA paraffin (Fisher Scientific, Cat. # 23–021-401), sectioned at 6 mm thickness, and stained with hematoxylin and eosin (H&E) using standard procedures (Choi et al., 2011 (link)). These paraffin sections will be subjected to immunohistochemistry
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8

Tissue Fixation and Histological Processing

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Tissues were dissected and fixed overnight in 10% neutral buffered formalin, pH 7.4 (NBF) (Fisher Scientific, #SF100-4), processed by standard procedures, and embedded in paraffin blocks. All the blocks were sectioned at 10 μm, and slides were stained by hematoxylin and eosin (H & E). In this analysis, lungs were inflated via trachea with 10% NBF prior to fixation; and sinuses were processed by post-fixation decalcification for 5 to 10 days in 10% EDTA, pH 7.0.
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9

Tumor Growth in NUAK2 KO Mice

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All mouse experiments were conducted in accordance with protocols approved by the animal facility at Toronto Centre for Phenogenomics as approved by the Canadian Council on Animal Care. MDA-MB231 cells (1.5 × 106) comprised a pool of three clones of NUAK2 KO (n = 8 mice per group) or empty vector controls (n = 7 mice per group) were inoculated into the right, fourth mammary fat pad of 10-week-old female C.B-17 severe combined immunodeficiency mice and tumor growth was measured weekly63 (link),64 (link). For immunofluorescent staining, MDA-MB231 tumors were harvested from mice sacrificed at 3 weeks and fixed in 10% buffered formalin phosphate (SF100-4, Fisher Scientific) prior to paraffin embedding. Tissue sectioning was performed at 4 mm thickness. The primary antibodies used for immunostaining were: rabbit anti-Yap (14074, Cell Signaling, 1:100) and mouse anti-human vimentin (M0725, Dako, 1:100) to identify MDA-MB231 cells.
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10

Comparative Laryngeal Anatomy Across Species

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Investigations were performed on six grasshopper mice (two O. arenicola, one O. torridus, three O. leucogaster and an F1 hybrid between O. arenicola and O. torridus), six laboratory mice (M. musculus, CD1 strain; four males and two females), 12 laboratory rats (R. norvegicus, Sprague–Dawley; eight males and four females) and four kangaroo rats (D. ordii; two males and two females). The animals were deeply anaesthetized with xylazine (8 mg kg−1) and ketamine (80 mg kg−1), cardially perfused with saline solution and subsequently with paraformaldehyde. Larynges were dissected and fixed in 10% buffered formalin phosphate (SF100-4; Fisher Scientific) for 24 h. All specimens were processed at Midwestern University, Glendale, AZ.
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