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21 protocols using 40 μm nylon filter

1

Transcriptional Insights into NPR-8 Longevity

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To gain molecular insights into the NPR‐8‐dependent longevity response to temperature, we employed RNA‐seq to compare gene expression in young and old wild‐type and npr‐8(ok1439) animals propagated at different temperatures. To this end, we collected five replicates of eight groups of RNA samples (young (1‐day‐old) and 9‐day‐old wild‐type and npr‐8(ok1439) adults propagated at 20 and 25°C) (Table 1). The temperature‐specific worm cultivation and synchronization steps were performed as described in the lifespan assay section. A portion of synchronized adult animals were collected at the age of 1 day old, and the remaining animals were grown till Day 9 before collection. These animals were washed every day using M9 buffer, and the adult animals were filtered using cell strainer (40‐μm nylon filter, Falcon) and transferred to E. coli OP50‐seeded NGM plates. Worms were washed and collected with M9 buffer then snap‐frozen in the TRIzol reagent (Thermo Fisher Scientific) and stored at −80°C until RNA isolation. RNA was extracted using the QIAzol lysis reagent (Qiagen) and purified with the RNeasy Plus Universal Kit (Qiagen).
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2

Tumor Tissue Disaggregation and Mononuclear Cell Isolation

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Tumor tissues were taken from the center of the cancer immediately after surgical removal and histologic confirmation. For preparation of single cell suspensions, tumor samples were mechanically dissected and incubated with 1% type IV collagenase supplemented with 100 U/ml penicillin and 100 mg/ml streptomycin at 37°C for 30 minutes. The cell suspension was passed through a sterile 40 μm nylon filter (BD Falcon, Heidelberg, Germany) and then was layered over an equal volume of Ficoll and centrifuged as per the manufacturer's instructions. Mononuclear cells were collected and suspended in PBS/culture medium.
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Single-Cell Isolation from Tumor Tissues

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Tumor samples were taken from each surgically removed specimen immediately following removal from the patient. Single-cell suspensions were prepared, and tumor tissues were mechanically dissected and suspended in phosphate-buffered saline (PBS). Enzymatic treatment was not used to dissociate tumors because it affected CIPS expression. Cell suspensions were subsequently passed through a sterile 40 μm nylon filter (BD Falcon, Heidelberg, Germany). Single cells were pelleted and suspended in RPMI 1640 (Life Technologies, Grand Island, NY, USA) containing 10% fetal bovine serum (FBS, Life Technologies), penicillin-streptomycin (WelGENE, Daegu, Korea), and L-glutamine (WelGENE). PBMCs were isolated by Ficoll (GE Healthcare, Piscataway, NJ, USA) density gradient centrifugation of whole blood from healthy donors and CRC patients. Cells were counted following trypan blue staining and the concentration adjusted to 0.5–1 × 106 viable cells/tube.
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4

Murine Splenic Cell Isolation

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Spleens were harvested and pooled from 8- to 10-week old C57BL/6 mice and poolied in RPMI 1640 medium (Mediatech, Manassus, VA, USA). Cell suspensions were prepared by dicing the spleens with a razor blade and digesting them with a solution containing 0.1 mg/mL DNase I (Roche, Indianapolis, IN, USA) and 1 mg/mL Collagenase D (Roche, Indianapolis, IN, USA) in HBSS (Cellgro, Manassas, VA, USA) for 30 min at 37 °C. Then, the cells were passed through a 40-μM nylon filter (BD Falcon, Bedford, MA, USA). Red blood cell lysis was performed using 2 ml of 1x red blood cell lysis buffer (BioLegend, USA) per spleen. The cells were then washed in PBS containing 5% heat-inactivated FBS and counted using a Countess automated cell counter (Invitrogen, Carlsbad, CA, USA). For flow cytometry immunophenotyping experiments, 1 × 106 cells per tube were stained as described below. For cell sorting, approximately 1 × 108 cells per cocktail were prepared in MACS buffer (Miltenyi Biotech) rather than staining buffer.
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5

Ovarian Cell Isolation and Culture

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Ovaries were collected from 8dpp CD1 mice, cleared of the surrounding tissues and incubated in 1 mg/mL collagenase type I (Sigma-Aldrich) in αMEM for 1 hr at 37°C in agitation. Following collagenase removal, the ovaries were suspended in the cultured medium (see below) and disaggregated by gently pipetting. Cell suspension was filtered through a 40 μm nylon filter (BD Falcon) while the retained tissue fragments were further incubated in 0.25% trypsin (Sigma-Aldrich) for 15 min at 37°C in agitation, disaggregated and filtered as above. The cellular suspensions were then mixed and finally plated at 30.000 cells/cm2. Culture was carried out in αMEM (Aurogene) supplemented with 10% FBS (Gibco), L-glutamine, penicillin-G and streptomycin, pyruvic acid, N-acetyl-L-cysteine (all from Sigma-Aldrich) and ITS liquid media supplement (Gibco), at 37°C in 5% CO2 in 95% humidified incubator. The day after ( = T0 time point), 0.5 μM EPI, 10 μM CS or 10 μM PM was added to the culture medium of the treated groups. Where indicated, 200 mIU/mL LH was also added to the medium 1 hr before drugs.
Images were acquired under phase contrast microscope (Leitz Diavert) equipped with a DS-Fi1 camera (Nikon).
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6

Cell Cycle Analysis of HL-60 Cells

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HL-60 cells (2 × 106/mL) were treated with vehicle or tricetin (0, 20, 40, and 80 μM) for 24 h and then cells were collected and fixed by 70% ethanol. Next, cells were incubated with propidium iodide (PI) buffer (4 μg/mL PI, 0.5 mg/mL RNase A, and 1% Triton X-100 in phosphate-buffered saline (PBS)) for 30 min at 37 °C in the dark followed by filtration through a 40-μm nylon filter (Falcon, San Jose, CA, USA). The cell cycle distribution was analyzed for 104 collected cells by a FACS Vantage flow cytometer that uses the Cellquest acquisition and analysis program (Becton-Dickinson FACS Calibur, San Jose, CA, USA). The proportion of nuclei in each phase of the cell cycle was determined, and apoptotic cells with hypodiploid DNA peak were catched in the sub-G1 region.
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7

Characterizing Ascites Immune Landscape

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Total ascites was collected when the mice were sacrificed. Erythrocytes in ascites were lysed using Red Blood Cells Lysis Buffer (Solarbio). Cells were washed using PBS with 1% FBS and passed through a 40 μm nylon filter (BD Biosciences, San Diego, CA, USA), then cells were Fc-blocked with anti-CD16/32, and stained with CD45-PE, CD11b-APC, and F4/80-APC/CY7 antibodies for detecting macrophages. MHC II-PERCP/Cy5.5 and CD206-FITC antibodies were used to differentiate M1- and M2-subtype macrophages. For detecting T cells and B cells, cells were stained with CD45-PE, CD3-FITC, CD4-APC, CD8-PE/CY7, and CD45R/B220-FITC antibodies. Cells were incubated with the antibodies for 30 min in the dark and washed twice using PBS with 1% FBS. LSRFORTESSA (BD Biosciences) was used to obtained the data, and FlowJo software (BD Biosciences) was used to analyze the data.
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8

Quantifying Bone Marrow BM Cell Subsets

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Whole BM flush were collected from tibia and femur into buffer containing PBS [3% (v/v) bovine serum albumin (BSA)] and filtered through 40-μm nylon filter (BD Biosciences, San Jose, CA). Red blood cells (RBCs) were lysed with RBC lysis buffer (Thermo Fisher Scientific) for 5 min at RT. Cells were stained with CD39 phycoerythrin (PE)/cyanine-7 (8 μg/ml; 143805, BioLegend, San Diego, CA), CD73 PE (1.25 μg/ml; 12-0731-82, Thermo Fisher Scientific), and CD45 allophycocyanin (APC) (1.25 μg/ml; 17-0451-82, Thermo Fisher Scientific) antibodies for 30 min at RT. Stained cells were analyzed with BD Accuri C6 flow cytometer and CFlow software. Analyses were performed by comparing to unstained cells and gated for singlets.
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9

Isolation and Analysis of Rat Muscle Stromal Cells

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Muscle stromal cells (containing satellite cells) were isolated, as described previously, with modifications [28 (link), 29 (link)]. Briefly, portions of the back muscles of rats were minced under a dissection microscope and enzymatically digested with 0.2% Collagenase Type I solution (Worthington Biochemical, Lakewood, NJ) in DMEM at 37°C for 30 min, and 0.25% Trypsin-EDTA for 15 min, the cell suspension was filtered through a 40 μm nylon filter (BD Biosciences). The suspended cells were cultured in 6-well plates with DMEM supplemented with 10% FBS (Invitrogen), and 1.0% penicillin-streptomycin for 24 hours. The isolated cells were then fixed and perforated with fixation and permeabilization solution (BD Biosciences). Then, the isolated cells were incubated with FITC labeled Anti-PAX7 antibody (Abcam) and underwent flow cytometry analysis (FACS Calibur™, BD Biosciences). The PAX7 positive cells were quantified.
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10

Isolation of Immune and Neural Cells

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Single-cell suspensions from naïve WT, Rag1−/−, and NRG mouse spleens and lymph nodes (LN; cervical) were prepared. Tissues were homogenized and strained through a 40-μm nylon filter (BD Biosciences, Germany). Homogenates were rinsed with washing medium (Dulbecco’s Modified Eagle’s Medium, DMEM, Invitrogen, USA) containing 1% FBS (ScienCell, USA), 1% glutamine (Gibco Life Technologies, USA), and 1% antibiotics (Sigma-Aldrich, USA) and shortly resuspended in erythrocyte lysis buffer (150 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA; pH 7.3).
Brain tissues were cut into pieces, homogenized in phosphate-buffered saline, layered on a density gradient using Lymphoprep™ (Fresenius, Germany), and separated by centrifugation for 16 min at 500 g. After isolating cells, they were washed and resuspended in the respective staining buffer. To quantify numbers of cells isolated from the central nervous system, beads (Beckman Coulter, USA) were added.
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