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11 protocols using nugc4

1

Characterization of Gastric Cancer Cell Lines

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Gastric cancer cell lines were purchased from ATCC (KATOIII, NCI-N87, SNU-16), KCLB (SNU-668, SNU-601, SNU-638), JCRB (MKN-45, NUGC-4) and ECACC (HGC-27). Microsatellite Instability (MSI) status was previously assessed for all cell lines and found negative for all but one cell line (SNU-638). Identity of each cell line was determined through independent karyotyping. Cells were checked for mycoplasma contamination. Cells were cultured in their recommended media conditions at 37°C. Afterward, the cells were processed into suspensions with standard procedures. Briefly, this process involved trypsinizing the cells, followed by inactivation by fetal bovine serum (FBS). We performed washes by centrifugation at 400 g in 1× phosphate-buffered saline with 0.04% bovine serum albumin. To remove cellular debris and cellular aggregates, we filtered cells through a Flowmi cell strainer (Wayne, NJ, USA) before proceeding to single-cell DNA and RNA sequencing.
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2

Gastric Cancer Cell Line Panel for Targeted Therapies

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Twelve gastric cancer cell lines (ECC10, GCIY, KATO‐III, MKN7, MKN74, NCI‐N87, NUGC3, NUGC4, OCUM‐1, SH‐10‐TC, SNU‐16, and SNU‐216) were used in this study. ECC10, GCIY, and MKN7 were provided by Riken BRC through the National Bio‐Resource Project of Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. NUGC3, MKN74, and OCUM‐1 were provided by Japanese Collection of Research Bioresources/Health Science Research Resources Bank (JCRB/HSRRB), Osaka, Japan. KATO‐III, NCI‐N87, NUGC4, SNU‐16, SH‐10‐TC were purchased from ATCC (Manassas, VA, USA), and SNU‐216 was obtained from the Korean Cell Line Bank. All the cells, other than GCIY and OCUM‐1, were cultured in RPMI‐1640 media supplemented with 10% FBS. GCIY and OCUM‐1 were cultured in minimum essential media (Sigma‐Aldrich) with 15% FBS and DMEM with 0.5 mmol/L sodium pyruvate and 10% FBS, respectively. Afatinib, neratinib, and PPP were purchased from Selleckchem and MedChem Express. Gefitinib was purchased from Sykkinase. Trastuzumab and pertuzumab were obtained from Chugai Pharmaceutical Co.
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3

Gastric Cancer Cell Culture Protocol

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Gastric cancer cell lines: AGS (ATCC CRL-1739), KatoIII (ATCC HTB-103), MKN7 (JCRB1025), MKN45 (JCRB0254), NCI-N87 (ATCC CRL-5822), NUGC-4 (JCRB0834), SNU1 (ATCC CRL-5971), St2957 (CVCL_9557) and St3051 (CVCL_9558) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) and supplemented with 10 % (v/v) FCS and 1% (v/v) Pen/Strep. Chinese hamster ovary cells (CHO) (ATCC CCL-61) and vector control CHO-CEACAM1-4L (CHO CC1) [21 (link)] were cultured in DMEM and supplemented with 10 % (v/v) FCS and 1% (v/v) Pen/Strep. Cells were kept in a humidified atmosphere at 37 °C and 5% (v/v) CO2. Regular mycoplasma testing was performed.
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4

Establishing Gastric Cell Lines and Fibroblasts

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Human gastric cancer cell lines (AGS, KATO III, MKN45, NUGC3, and NUGC-4) were purchased from the ATCC (AGS), the RIKEN BioResource Center Cell Bank (KATO III, MKN45), and the Japanese Collection of Research Bioresources Cell Bank (NUGC3, NUGC4). CAFs and normal fibroblasts (NF) were established from resected tissues from more than 100 patients with gastric cancer. CAFs were isolated from gastric walls infiltrated by tumors, and NFs were isolated from normal gastric walls. The detailed protocol used to establish these cell lines has been reported previously (12, 16) . All the cell lines tested negative for Mycoplasma using the e-Myco Mycoplasma PCR Detection Kit (catalog no. 25235, Cosmo bio) during the period of this study. These cell lines were cultured in RPMI1640 medium containing 10% FBS and maintained at 37 C in a humidified atmosphere containing 5% CO 2 .
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5

Cell Culture Protocols for Gastric Cancer and Endothelial Cells

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The GC cell line SGC-7901, HGC-27, MKN45, KATOIII, BGC-823, NUGC-4 were purchased from American Type Culture Collection (ATCC,USA), and cultured in RPMI-1640 medium (HyClone, Thermo Scientific, USA) supplemented with 10% fetal bovine serum (FBS, HyClone, Thermo Scientific, USA) and 1% penicillin/streptomycin (HyClone, Thermo Scientific, USA). HUVECs were purchased from the Sciencell and cultured in ECM consisting of 500 ml of basal medium, 25 ml of fetal bovine serum, 5 ml of endothelial cell growth supplement (ECGS) and 5 ml of penicillin/ streptomycin solution (P/S). SGC-7901 LV-YBX1 and LV-NC Cells were cultured in RPMI-1640 medium (HyClone, Thermo Scientific, USA) supplemented with 10% fetal bovine serum (FBS, HyClone, Thermo Scientific, USA) and 1% penicillin/streptomycin (HyClone, Thermo Scientific, USA). All cells were incubated in a standard humidified incubator in 5% CO2 at 37 °C.
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6

GC Cell Line Maintenance Protocol

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Seven GC cell lines (MKN1, MKN7, MKN45, MKN74, NUGC3, KatoIII, and NUGC4) were
obtained from the American Type Culture Collection (Manassas, VA) and the Japanese
Collection of Research Bioresources (Tokyo, Japan). All cell lines were maintained
in appropriate media containing 10% fetal bovine serum in plastic tissue
culture plates.
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7

Gastric Cancer Cell Line and Tumor Tissue Analysis

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Human GC cell lines, including MGC803, MKN1, HGC‐27, AGS, NUGC4, and AZ521 were purchased from the American Type Culture Collection (ATCC). All cell lines were cultured at 37 °C with 5% CO2 in RPMI‐1640 medium (GIBCO) supplemented with 10% fetal bovine serum (FBS, GIBCO, Thermo Scientific), penicillin (100 IU/ml), and streptomycin (100 mg/mL). The USP7 inhibitor FT671 and P5091 were purchased from TargetMol (FT671, cat#1959551‐26‐8; P5091, cat# 882257‐11‐6). The investigated compounds, including DHPO, were obtained from a natural product library established in Prof. Wei‐Dong Zhang's laboratory, with purity being >95%.[19 (link),
20 (link)
]A total of 128 pairs of fresh‐frozen GC tumor tissues and para‐tumor samples were collected from patients who underwent GC surgery in the Department of Gastric Surgery at Zhejiang Cancer Hospital (Hangzhou, China). Informed consent forms were signed in advance. Follow‐up was conducted in time to record the survival time of patients. All studies associated with clinical samples and data were carried out following the principles of the Declaration of Helsinki and were approved by the Ethics Committee of Zhejiang Cancer Hospital (study number: IRB‐2021‐456).
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8

Characterization of HER2 and miR-21 Expression in Gastric Cancer Cell Lines

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NUGC4, NCI-N87, SGC7901 and BGC823 were supplied by American Type Culture Collection (ATCC). We evaluated HER2 expression level in the cells by Western blot and immunohistochemistry as previously described [31 (link)]. HER2 was expressed positively in NCI-N87 and NUGC4 cells, and negatively in SGC7901 and BGC823, consistent with previous studies [13 (link), 32 (link)] (Supplementary Figure 2). The miR-21 expression in the cells showing HER2-positive expression was determined by real-time reverse-transcription polymerase chain reaction (RT-PCR) [13 (link)]. The expression of miR-21 was higher in NUGC4 SGC7901 than in NCI-N87 BGC823 cells (Supplementary Figure 3), which were therefore, selected for further study. All cells were cultured in RPMI 1640 medium, supplemented with 10% fetal bovine serum and incubated at 37°C at 5% CO2 and 95% humidity.
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9

Cell Line Culture for Gastric Cancer Research

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GC cell lines (AGS, NUGC4, and MKN74) and human normal epithelial cell line (GES-1) were purchased from the American Type Culture Collection (ATCC; Manassas, VA, USA). Cells were cultured in the RPMI1640 medium (CD-02168-ML, GIBCO, USA) added with 10% Fetal Bovine Serum (FBS; 10270-106, GIBCO) and 100 U/mL Penicillin/Streptomycin solution in humidified incubators. The air and temperature for the cell cultivation was required of 5% CO2 and 37 °C respectively.
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10

Gastric Cancer Cell Line Profiling

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Ten GC cell lines (AGS, KATOIII, MKN1, MKN45, MKN74, N87, NUGC2, NUGC3, NUGC4 and SC-6-JCK) and the non-tumourigenic epithelial cell line (FHs74) were obtained from the American Type Culture Collection (ATCC; Manassas, VA, USA), Tohoku University, Japan, or were established at our institute. Cell lines were
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