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82 protocols using matrix gel

1

Invasion and Migration Assay of Cal-27 Cells

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The invasion and migration ability of Cal-27 cells were analyzed by cell migration and invasion assays. For the invasion assay, matrix gel (BD Bioscience, Mount Kisco, NY, USA) was added to the upper chamber, whereas no matrix gel was used for the migration assay. Then, 2 × 105 cells were resuspended in 100 μL of medium without FBS, while the medium containing 10% FBS was added to the lower chamber and cultured for 24 h until the cells were attached to the wall. Then, 0.60 mM ICD was added to the upper and lower chambers. After incubation for 24 h, 48 h, and 72 h, respectively, the cells were fixed with 4% paraformaldehyde, stained with 2% crystal violet, photographed under a microscope, and counted.
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2

Xenograft Models of Cholangiocarcinoma

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All animal studies were approved by the Institutional Animal Care and Use Committee of Tulane University. Six-week-old male NOD-SCID mice (NOD.Cg-Prkdcscid/J) were obtained from The Jackson Laboratory. For subcutaneous inoculation, 1 × 106 control or METTL16-depleted CCA cells suspended in 100 µL PBS mixed with matrix gel (BD, 356,234) at 1:1 ratio was injected into the mice's flanks. Tumor sizes were measured at the relevant time intervals. At the end of the study, the mice were euthanized, and the tumors were dissected and weighed.
For intrahepatic inoculation, 1 × 106 control or METTL16-depleted CCLP1 cells suspended in 10 µL PBS mixed with matrix gel (BD, 356,234) at a 1:1 ratio was implanted into the livers of NOD-SCID mice. The mice were sacrificed 8 weeks after injection, their livers were surgically dissected, and the liver/body weight ratios were evaluated.
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3

Silencing ERLIN2 and CDK5RAP3 Impacts Proliferation and Migration

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The small interfering RNAs (siRNAs) of ERLIN2 and CDK5RAP3 were designed and synthesized by GenePharma Co. (China). For cell proliferation assay, 1000 cells were seeded into 96-well plates for 0–96 h, and 10 µL of the cell counting kit-8 (Keygen, China) solution was added per well. After a 2-h incubation at 37 °C, optical density (OD) at 450 nm was measured on a microplate reader (Bio-Tek, USA). Cells were inoculated onto 6-well plates for the wound-healing assay and treated with si-/nc-ERLIN2 and si-/nc-CDK5RAP3. The cell wound edge was marked and photographed under a microscope at the starting time point, and after 0–24 h, the cells’ migrated distances were measured and analyzed for the wound closure percentage. For migration assays, cells were inoculated into a 24-well transwell cell apical chamber containing matrix gel (BD, USA) for evaluating cell invasion. Cells that invaded the bottom chambers were fixed with 4% polyformaldehyde, stained with 0.1% crystal violet solution, counted, and photographed under a microscope.
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Cell Migration and Invasion Assays

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The cell migration and invasion assays were performed as previously described.17, 18 For the migration assay, HT29 or SW480 cells in serum‐free medium were seeded into a 24‐well Insert System with an 8‐μm pore size polyethylene terephthalate membrane (BD Biosciences). Complete medium was placed in the lower chambers. For the cell invasion assay, HT29 or SW480 cells in serum‐free medium were seeded into the chambers precoated with a matrix gel (BD Biosciences). Cells that had migrated or invaded through the membrane were fixed using 10% methanol, stained with 0.1% crystal violet, and quantified using a light microscope (Olympus). Migrated and invasive cells were counted from 5 randomly selected fields of each sample.
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5

Orthotopic Breast Cancer Mouse Model for PKM2 Evaluation

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All animal procedures were conducted under the guidelines approved by the Institutional Animal Care and Use Committee (IACUC) at MD Anderson Cancer Center. Female Nu/Nu nude and BALB/c mice were used as hosts for tumor xenografts and 4T1 syngeneic model, respectively. Briefly, orthotopic breast cancer mouse model was established as previously described (33 (link)). For MDA-MB-468 PKM2WT and PKM2Y148F cells (1 × 106 cells in 50 µL medium mixed with 50 µL Matrixgel™ (BD Biosciences) were injected into the left and right mammary fat pad, respectively. For 4T1 syngeneic model, PKM2WT- and PKM2Y148F-expressing mouse 4T1-luc cells (5 × 104 cells in 50 µL medium mixed with 50 µL Matrixgel™) were injected to the mammary fat pad. Tumor was measured weekly with a caliper, and tumor volume was calculated by the formula: π/6 × length × width2. For drug treatment, mice were treated with daily oral doses 500 mg/kg 2-DG and 10 mg/kg gefitinib for two weeks (5 days per week). Tumor infiltration lymphocyte profiles in excised tumors were analyzed as described in Supplementary Information.
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6

Xenograft Proliferation Effects of LNK

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In vivo cell proliferative effects after either gain or lost of LNK was studied in a murine xenograft model. 5–6 weeks old Nod-SCID mice were used for the study. 2 million (CAOV2 and A2008) or 6 million (OVCAR5) cells were resuspened in 100 μl FBS and 100 μl Matrix gel (BD Biosciences), and subcutaneously injected into both flanks of immune deficient Nod-SCID mice. The mice were sacrificed, and the tumors were excised and weighted at the end of the experiments (days 18–28).
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7

Xenograft Proliferation Effects of LNK

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In vivo cell proliferative effects after either gain or lost of LNK was studied in a murine xenograft model. 5–6 weeks old Nod-SCID mice were used for the study. 2 million (CAOV2 and A2008) or 6 million (OVCAR5) cells were resuspened in 100 μl FBS and 100 μl Matrix gel (BD Biosciences), and subcutaneously injected into both flanks of immune deficient Nod-SCID mice. The mice were sacrificed, and the tumors were excised and weighted at the end of the experiments (days 18–28).
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8

Transwell Invasion and Migration Assay

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We performed cell invasion and migration experiments using Transwell chambers with or without matrix gel (BD Biosciences, San Jose, CA, USA). After transfection, the cells were seeded in the upper chamber of the Transwell, and the lower chamber was filled with medium containing 20% FBS. After incubation for 48 h in the chamber, the cells on the upper and lower chambers were fixed with 4% paraformaldehyde solution, stained with 0.1% crystal violet staining solution, and photographed under a microscope. The number of migrated or invaded cells was calculated using ImageJ software.
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9

Breast Cancer Cell Invasion Assay

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Cell invasion assay was performed as previously described [22 (link)]. Briefly, the upper chamber of the trans-well membrane was coached with Matrix gel (BD). MCF-7-CT45A1 breast cancer cells were pre-treated with SP1 and SULF2 inhibitors for 72 hours. The cells were counted, and alive cells re-suspend in serum-free DMEM without inhibitors and 2 × 104 cells were seeded into the upper chamber in 200 μL medium. Then 500 μL DMEM (10% FBS) was added to the low chamber and cultured for 24 hours. The cells on bottom of the membrane of the chamber were stained by Wright-Giemsa solution and photographed. Three randomly chosen fields were analyzed for each trans-well.
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10

Quantifying Cell Migration and Invasion

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For the wound healing assay, cells were seeded with 10% fetal bovine serum culture until 80% confluent in 6-well plates. Then A2780 and SKOV3 cells were transfected with pcDNA3.1 or pcDNA3.1-LINC00152 while CAOV3 and ES-2 cells with either siControl or siLINC00152 siRNAs for 24 h. Then Cells were scraped off using a pipette tip and washed softly with PBS twice to remove the floating cells and debris. After washed by PBS, the cells were incubated with serum-free culture for 24 h to minimize the interference of cell proliferation. Representative images of cells migrating into the wounds were captured at 0 and 24 h in the same wounded region.
The Transwell assay was used to assess cell invasion (Corning Co. Ltd., USA). The lower chambers were pre-coated with 100 μL Matrix gel (#354234, BD Bioscience, USA) for 30 min. 24 h after transfection, cells were seeded on the upper chamber at 3.0 × 104/well in serum-free medium to minimize the interference of cell proliferation. Medium containing 20% fetal bovine serum medium was applied to the lower chamber as chemo-attractant. After 24 h incubation at 37° C, cells which invaded through the Matrix gel and adhered to the lower surface of the filter were fixed with ethanol, stained with 0.5% crystal violet, photographed at 200×, and counted at 400× in 10 different fields to determine the average number of cells (BX51, Olympus, Japan).
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