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344 protocols using sh800 cell sorter

1

Generation of TLR Reporter Cell Lines

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Retroviral expression constructs coding for TLR4, MD-2 and CD14 were described before (41 (link)). TLR4, MD-2 and CD14 were simultaneously transduced into TLR non-responder cells. Positive eGFP-expressing cells were sorted after stimulation with LPS (300 ng/mL) for 24 h using a Sony SH800 cell sorter. Single cell clones were established by limiting dilution culturing.
Sequences encoding human TLR2 and TLR1 were cloned into the retroviral expression vector pCJK2 (45 (link)). The TLR2 construct was expressed in TLR non-responder cells and TLR2-expressing cells were sorted on a Sony SH800 cell sorter using an AlexaFluor647-coupled anti-human CD282 (TLR2) antibody (BD Biosciences). Single cell clones were established and a clone with high reactivity towards Fsl-1 (TLR2/6 ligand) was chosen as TLR2/6 reporter cell line. Into the TLR2-positive sorted cell pool, TLR1 was transduced to establish TLR2/1/6 reporter cells. Cells were sorted for reactivity against Pam3CSK4 (TLR2/1 ligand) by sorting eGFP-expressing cells after activation with 100 nM Pam3CSK4 for 24 h on a Sony SH800 cell sorter. Single cell clones were established and a clone with high reactivity towards Fsl-1 (TLR2/6 ligand) and Pam3CSK4 (TLR2/1 ligand) was chosen as TLR2/1/6 reporter cell line.
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2

Flow Cytometry Analysis of Cell Surface Proteins

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The expression of surface proteins on cultured cells was measured with flow cytometry. Tumor cells were harvested upon incubation with Accutase (Nacalai Tesque). Cells were stained using CD133/1 (AC133) conjugated to allophycocyanin (APC; 130-090-826; Miltenyi Biotec, Auburn, CA) and CD44 conjugated to APC/Fire750 (33817; BioLegend, San Diego, CA). Relative fluorescent intensities were measured using an SH800 cell sorter (SONY, Tokyo, Japan). Single cells were sorted using an SH800 cell sorter (SONY). Data were analyzed with FlowJo 10.2 software (FlowJo LLC, Ashland, OR, USA).
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3

CRISPR-Mediated Genetic Knockout in THP-1 and iBMDM Cells

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sgRNAs were designed with CHOPCHOP or CRISPick, while other sgRNAs were picked based on data in the literature (Table S15). Oligos containing desired sgRNA sequences were annealed and assembled into the appropriate vector with the Golden Gate cloning protocols provided by the Zhang lab.
Bulk knockouts in THP-1 cells expressing lentiCRISPRv2-puro were selected with puromycin (2.5 μg/mL, 7 d), recovered (3–6 d), and immediately used for experiments. Bulk knockouts in THP-1s expressing lentiCRISPRV2-mCherry were sorted for mCherry-positive cells (using the parental line as a negative control) with a Sony SH800 Cell Sorter operating in purity mode. For each sorted cell line, 100,000 cells were obtained and expanded for experiments within 7 d. Cell pellets for western blots were taken on the same day as cells were plated for inflammasome assays. For clonal iBMDMs spinfected with lentiCRISPRv2-puro vectors, cells were selected with puromycin (5 μg/mL, 7 d) then single-cell cloned into 96-well dishes with a Sony SH800 Cell Sorter operating in single-cell mode. Clonal knockouts were first validated at the genomic level with Miseq using OutKnocker 2.0 [187 (link)] to align gDNA reads (see Table S15 for genomic primers). Subsequently, knockouts were validated at the protein level by Western Blot or immunofluorescence.
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4

Cell Cycle Analysis of Synchronized Cells

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Cells were synchronized at the G1 phase of the cell cycle by serum starvation for 96 hours and restimulated by changing medium containing 10% FBS as previously described.21 The restimulated cells were harvested, washed with PBS, and fixed in 70% ethanol at −20℃. The fixed cells were incubated in 0.25 mg/mL RNase for 30 minutes at 37℃. Samples were then washed with PBS and stained with propidium iodide (Sigma‐Aldrich). The cell cycle distribution was measured on an SH800 cell sorter (Sony Biotechnology).
An EdU assay was carried out using GET4 KO cells and WT cells in the medium containing 10% FBS. Cells were incubated with EdU for 2 hours before harvest. EdU was detected using a Click‐iT Plus EdU Alexa Fluor 488 Flow Cytometry Assay Kit (Thermo Fisher Scientific) following the manufacturer’s instructions. The cell cycle distribution was measured on an SH800 cell sorter (Sony Biotechnology).
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5

Apoptosis Assay for DATS Effects

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The Annexin V-FITC Apoptosis assay Kit from RayBiotech was used to determine DATS’s ability to induce apoptosis in MDA-MB-231 and MDA-MB-468 cells. Each experiment was done in triplicate and performed as described by the manufacturer. Briefly, both cell lines were seeded at 5×105 cells/well in a 6-well plate and incubated overnight. Cell-only samples were used as a negative control, while cells treated with 1 mM staurosporine were used as positive controls. DATS, TNF-α, and CoTx, as well as control samples, were brought to a final volume of 2 ml/well of experimental media to induce apoptosis. After a 72 h incubation period, cells were harvested, centrifuged, pelleted, and washed with PBS. Cell pellets were resuspended in 500 μl of 1X Annexin-V binding buffer, then 5 μl of Annexin V-FITC and propidium iodide (PI) was each added to the appropriate tube according to the manufacturer’s protocol. Finally, the apoptotic effect was quantified within 10 minutes by Sony SH800 Cell Sorter (San Jose, CA, USA). The Sony SH800 Cell Sorter was aligned with Sony SH800 and MA900 automatic setup beads, and the samples were analyzed within 1 h for data acquisition on Cell Sorter Software version 2.1.6. For each sample, 10×103 cells were analyzed separately.
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6

Evaluating Luteolin's Cytoprotective Effects

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PE-Annexin V/7-AAD staining was performed on HT-22 cells that were seeded in 6-well plates at a density of 100,000 cells per well and allowed to adhere for 18–24 h. The cells were pre-treated with luteolin (5 µM-25 µM) for 24 h. Following this pre-treatment, the cells were exposed to glutamate for 18 h. Subsequently, the cells were harvested from the plate, washed with PBS, and resuspended in 100 μL of 1X Annexin V binding buffer. They were then incubated in the dark at room temperature with 5 µL of PE Annexin V and 5 µL of 7-AAD viability staining solution for 15 min. Then, the cells were diluted with 400 μL of binding buffer. For each experiment, unstained and single-channel controls were used to calculate compensation. Flow cytometry analysis was performed using a Cell sorter SH800S (Sony Biotechnology, San Jose, CA, USA).
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7

Genome Editing Using ArciTect Cas9-eGFP

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For genome editing, the ArciTect Cas9-eGFP system was used according to the manufacturer’s conditions (STEMCELL Technologies, Köln, Germany). Briefly, ArciTect™ CRISPR-Cas9 RNP Complex solution was generated with 60 μM gRNA and tracrRNA and 3.6 µg ArciTect™ Cas9-eGFP Nuclease. Afterwards, 20 µM single-strand oligodeoxynucleotide (ssODN) was added to the RNP solution. The following gRNA was used to target TFR2 of HIF1α-AS1: 5ʹ-ACGTGCTCGTCTGTGTTTAG-3ʹ. The following ssODNs (Integrated DNA Technologies, Leuven, Belgium) were used to replace TFR2: MEG3, 5ʹ-GAG GCACAGCTGGGACGGGCTGCGACGCTCACGTGCTCGTCTGTGTTGTAATCGCTCCCTCTCTGCTCTCCGATGGGGGTGCGGCTCAGCCCGAGTCTGGGGACTCTGCGCCTTCTCCGAAGGAAGGCGG-3ʹ, negative control Luc 5ʹ-GCTGAGGCACAGCTGGGACGGGCTGCGACGCTCACGTGCTCGTCTGTGTTGTAATTATCACGCTCGTCGTTCGGTATGATGGGGGTGCGGCTCAGCCCGAGTCTGGGGACTCTGCGCCTTCTCCGAAGGAAG-3ʹ. 400.000 HUVECs were seeded in a 12-well plate and electroporated in E2 buffer with the NEON electroporation system (Invitrogen) (1,400 V, 1 × 30 ms pulse). A full medium exchange was done every 24 h and cells were incubated for 72 h. For FACS, eGFP-positive cells were sorted in PBS supplemented with 5% FCS with a Cell Sorter SH800S (Sony).
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8

Isolation and Culture of BEEC

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BEEC isolation and culture were performed according to a previously described protocol (16 (link)) with minor modifications. Cells were primed with pre-ovulatory levels of estradiol (E2) (1 ng ml−1) and progesterone (P4) (50 pg ml−1) until reaching confluence. Confluence and intact integrity were determined using area fraction (AF) output based on cellular translucence and boundaries (ImageJ software Version1.51j8). Epithelial cell purity >98% was evaluated using a monoclonal antibody against cytokeratin (anti-cytokeratin 8 + 18; ab53280, Abcam, Tokyo, Japan). Optimal viability of Annexin V-labeled cells was confirmed by FACS (Cell Sorter SH800S, Sony Biotechnology Inc., Bothell, WA, USA). Vimentin-negative staining indicated the absence of stromal cell contamination. Moreover, FACS analysis confirmed the absence of immune cell contamination using R-Phycoerythrin-conjugated mouse anti-CD45 hematopoietic cell marker (MA1–81458; Thermo Fisher Scientific, Waltham, MA).
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9

Intestinal Crypt Isolation and Cell Sorting

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The intestine was cut open longitudinally and incubated with 2 mM EDTA solution at 4 °C for 30 min to isolate intestinal crypts. To generate a single cell suspension, cells were incubated with Accutase (BD Biosciences, Cat#561527) at 37 °C for 10 min. Flow cytometry analysis was performed with CELL SORTER SH800S (SONY, Japan). Cells were gated for single cell based on the profiles of Forward-scatter area versus backward-scatter area (FSC-A vs. BSC-A) and forward-scatter height versus forward-scatter width (FSC-H vs. FSC-W). The size of the nozzle for all sorting is 100 µm.
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10

Yeast Cell Surface Display Screening

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For library sorting, 5 × 108 induced yeast cells were washed with PBS containing 0.1% BSA (PBS-B) and incubated with 250 nM TAMR-His6 for 30 min on ice. After washing with PBS-B, cells were stained with Goat F(ab’)2-anti-human-Kappa PE-conjugate (1:75 dilution, Southern Biotech) to detect surface presentation, with anti-His6 AlexaFluor647-conjugate (1:50 dilution, Thermo Fisher Scientific) for target binding and incubated for 15 min on ice. After a final washing step, cells were analysed by FACS using a Sony Cell Sorter SH800S. Sorting rounds were performed with decreasing target antigen concentrations. For subsequent rounds, TAMR-Fc was used as soluble antigen, staining with an anti-human IgG PE-conjugate (1:50 dilution, Thermo Fisher Scientific).
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