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About the product

The DLD-1 is a laboratory equipment product from Thermo Fisher Scientific. It is designed for DNA separation and analysis. The core function of the DLD-1 is to perform DNA electrophoresis, a technique used to separate and analyze DNA molecules based on their size and charge.

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246 protocols using dld 1

1

Colorectal Cancer Cell Line Cultivation

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CRC cell lines of SW480, HCT116, SW620, and DLD1 were supplied by Cell Bank, Chinese Academy of Sciences. Human normal colonic epithelial cells NCM460 were purchased from the American Type Culture Collection (Manassas, Virginia, USA). SW480 and SW620 cells were cultured in L‐15 (11415064, Gibco) medium containing 1% penicillin/streptomycin and 10% fetal bovine serum (Gibco, USA) at 37°C in an incubator. HCT116 cells were cultured in McCoy's 5a medium (12330031, Gibco) supplemented with 1% penicillin/streptomycin and 10% fetal bovine serum at 37°C in a 5% CO2 incubator. DLD1 cells were cultured in RPMI 1640 medium (11875093, Gibco) supplemented with 1% penicillin/streptomycin and 10% fetal bovine serum at 37°C in a 5% CO2 incubator. NCM460 cells were cultured in Dulbecco's modified Eagle's medium (KeyGEN BioTECH, Jiangsu, China) with 10% fetal bovine serum (Gibco, USA) at 37°C in a 5% CO2 incubator.
For experimental purposes, cells were transfected with overexpression vectors to upregulate target gene expression, siRNA to knockdown specific gene expression, block oligonucleotides to inhibit mRNA translation, and a negative control to ensure the specificity of the observed effects. All transfections were performed using the Lipo6000 transfection reagent, following the manufacturer's protocols for transient transfection.
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2

CRC Tissue and Cell Line Collection

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Six pairs of freshly frozen CRC tissues and adjacent normal tissues were obtained from patients who underwent surgery at the Sixth Affiliated Hospital of Sun Yat-sen University. This study was approved by the Institutional Review Board of the Sixth Affiliated Hospital of Sun Yat-sen University.
CRC cell lines HT29, SW480, DLD1, and RKO, along with normal human colorectal epithelial NCM460 cells, were generously provided by Dr. Ping Lan at the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China. The HCT116 cells were obtained from the National Collection of Authenticated Cell Cultures. HEK 293T cell lines were obtained from the American Type Culture Collection. HT29, DLD1, NCM460, and 293T cells were cultured in Dulbecco's modified eagle's medium medium (DMEM; Gibco, NY, USA) supplemented with 10% fetal bovine serum (FBS; Hyclone, USA) and 1% penicillin/streptomycin (Gibco, NY, USA). The RKO and SW480 cell lines were cultured in RPMI 1640 medium (Gibco, NY, USA) supplemented with 10% FBS. HCT116 cells were maintained in MycCoy's 5A medium (Gibco, NY, USA) supplemented with 10% FBS. All cell lines were incubated at 37°C in a cell incubator with a 95% air and 5% carbon dioxide mixture (Thermo Scientific, US) and detached using 0.25% trypsin-ethylenediaminetetraacetic acid solution with phenol red (Cat#C0203, Beyotime, China).
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3

Colorectal Cancer Cell Lines Cultivation

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The human colorectal carcinoma cell lines HCT116 and RKO were sourced from the Cell Bank of the Chinese Academy of Sciences (Shanghai, China), while the DLD-1 cell line was acquired from the BeNa Culture Collection (Beijing, China). The normal human colon epithelial cell line CCD 841 CoN and CRC cell line LoVo were obtained from iCell Bioscience Inc (Shanghai, China). LoVo, CCD 841 CoN, and HCT116 cells were propagated in RPMI-1640 medium (Gibco, Shanghai, China), whereas RKO and DLD-1 cells were cultivated in DMEM medium (Gibco, Shanghai, China). Both media were enriched with 10% fetal bovine serum (FBS; Biological Industries, Kibbutz Beit Haemek, Israel) and 1% penicillin/streptomycin (Gibco, Shanghai, China). All cell lines were maintained in a controlled environment with 5% CO2 at 37 °C under humidified conditions.
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4

Cell Line Validation and Culture Conditions

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Human CRC cell line DLD-1 [American Type Culture Collection (ATCC), CCL-221] was gifted by A. Shilatifard’s laboratory. CACO-2 (ATCC, HTB-37) was directly purchased from ATCC. All cell lines used in this study were subjected to short tandem repeat (STR) profiling to confirm the cellular identify. All cells were tested negative for Mycoplasma using Mycoplasma detection kit (SouthernBiotech, 13100-01).
DLD-1 cells were cultured in RPMI 1640 medium (Gibco, 11875093) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, 12440053) and 1% penicillin-streptomycin. CACO-2 cells were cultured in Eagle’s minimal essential medium (ATCC, 30-2003) with 20% fetal bovine serum (Thermo Fisher Scientific, 12440053) and 1% penicillin-streptomycin. All cells were cultured in a 37°C incubator with 5% CO2.
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5

Bacterial Infection of Colon Cancer Cells

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Colon cancer cell lines DLD-1 and HT-29 were acquired from Cell Bank, China Academy of Sciences (Shanghai, China). Immortalized human colonic epithelial cell NCM460 was kindly provided by BeNa Culture Collection (Henan, China). DLD-1, HT-29, and NCM460 cells were cultured in RPMI-1640, McCoy's 5A, and DMEM (Gibco, Thermo Fisher Scientific), respectively. Each media contained 10% (v/v) fetal bovine serum (FBS), and the cells were maintained in a humidified incubator at 37 °C with 5% CO2. Each cell line was recently authenticated by STR profiling and tested for mycoplasma contamination. For the bacterial infection study, cells were infected with S. moorei anaerobically or E. coli MG1655 at MOI (multiplicity of infection) of 100 for 2 h every 24 hours. Following incubation, then removed the bacteria and the bacteria-containing medium was substituted by a cell culture medium that contained 10% FBS, 20 µg/mL gentamycin, and 1% penicillin-streptomycin (PS) continue to culture cells in the carbon dioxide incubator. Cells were co-cultured with bacteria three times within 72 hours.
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6

Cell Culture Protocols for Cancer Research

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The female kidney cancer line A498, female ovarian cancer line OVCAR-8, male colon cancer line DLD-1 (ATCC), male kidney cancer line ACHN, female chronic myelogenous leukemia line K562 (ATCC), male acute T cell leukemia line Jurkat, male acute lymphocytic leukemia line Nalm-6 (DSMZ), male acute lymphocytic leukemia line SUP-B15 and male acute myeloblastic leukemia line Kasumi-1 were grown in L-glutamine containing RPMI (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Sigma Aldrich) and 1% Penicillin/Streptomycin (Sigma Aldrich) (cRPMI). The female breast cancer line MCF-7 (ATCC) was grown in L-glutamine containing RPMI supplemented (Gibco) with 10% heat-inactivated fetal bovine serum (Sigma Aldrich), 1% Sodium Pyruvate (Sigma Aldrich) and 1% Penicillin/Streptomycin (Sigma Aldrich). The female cervical cancer line HeLa (ATCC) was grown in L-glutamine containing DMEM (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Sigma Aldrich) and 1% Penicillin/Streptomycin (Sigma Aldrich). The male neuroblastoma line IMR-32 was grown in L-glutamine containing IMDM (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Sigma Aldrich) and 1% Penicillin/Streptomycin (Sigma Aldrich) (cIMDM). A549.Histone.mKate2 (A549), DLD-1-RFP and K562-GFP were cultured in cRPMI supplemented with 1 μg/mL Puromycin (Thermofisher). Adherent cell lines were split every 2–4 days using Trypsin/EDTA (Sigma Aldrich). Cell culture medium was renewed every 48 h in all cultures and experiments. The cell lines used in the study have not been authenticated.
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7

Culturing Colon Cancer and THP-1 Cells

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The human colon cancer cell lines DLD1 and HCT116 were obtained from the American Type Culture Collection (ATCC). The HCT116 cell line was cultured in DMEM medium (Gibco, Carlsbad, USA) supplemented with 10% fetal bovine serum, while the DLD1 cell line was maintained in RPMI-1640 medium (Gibco, Carlsbad, USA) with 10% fetal bovine serum. THP-1 cells were purchased from Procell (Wuhan, China). THP-1 cells were maintained in RPMI 1640 medium (Gibco, Carlsbad, USA) augmented with 0.05 mM 2-mercaptoethanol (Sigma-Aldrich) and 10% fetal bovine serum. All cell lines were kept in a cell incubator at 37 °C with a 5% CO2 atmosphere.
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8

Antiproliferative Potential of Plant Extracts

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The antiproliferative potential of EO and ES extracts against the colorectal adenocarcinoma cell line DLD-1 (CCL-221™, purchased from the American Type Culture Collection and provided by Dr. Eva Fisher-Fodor and Dr. Olga Șoritau at the Oncological Institute “Prof. dr. Ion Chiricuță” from Cluj-Napoca) was investigated using the CCK8 assay. DLD-1 cells were cultured in RPMI-1640 medium (Gibco Life Technologies, Paisley, UK) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO, USA), 1% glutamine (Sigma-Aldrich, St. Louis, MO, USA) and 1% antibiotics–antimycotics (Gibco Life Technologies, Paisley, UK). The cultures were maintained at 37 °C with 5% CO2 and 60% humidity. DLD-1 cells (1 × 104 cells/well) were exposed to each sample at five different concentrations (0.27 μmol GAE, 0.54 μmol GAE, 0.81 μmol GAE, 1.08 μmol GAE and 1.35 μmol GAE for EO and 0.22 μmol GAE, 0.44 μmol GAE, 0.66 μmol GAE, 0.88 μmol GAE and 1.10 μmol GAE for ES). These concentrations were calculated based on the TP concentration expressed in μmol GAE/μL. The positive control consisted of doxorubicin (reference compound) at a concentration of 20 μg/mL, while the negative control comprised cells maintained in standard culture medium. The potential inhibitory effect was also evaluated for the solvent used for preparing hydroalcoholic products. The extracts were incubated for a further 24 h. Following 24 h of incubation, CCK-8 solution (Sigma-Aldrich, St. Louis, MO, USA) was added to each well, and the cell cultures were further incubated for 4 h at 37 °C in the dark. CCK-8 contains a water-soluble tetrazolium salt that is reduced by viable cells to produce a colored formazan dye. The amount of formazan dye produced is directly proportional to the number of viable cells in the sample [53 (link),54 (link),55 (link)]. Subsequently, the absorbance of each well was measured at 450 nm using a microplate reader (Bio-Rad, Hercules, CA, USA). All experiments were performed in triplicate and expressed as mean  ±  SD. The calculation of cell survival (%) was performed based on the optical densities correlated with the optical density of the control.
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9

Cell Line Culturing and Transfection

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The mouse CRC cell line CT26 and human CRC cell lines HCT116, DLD1, and HT29 were purchased from Procell Life Science & Technology Company (Wuhan, Hubei,China). MC38 was a gift from the laboratory of Professor Penghui Zhou. SW620 cells were a gift from the laboratory of Professor Ranyi Liu. Cells (CT26, HCT116, DLD1 and SW620) were cultured and maintained in Roswell Park Memorial Institute-1640 (RPMI-1640, Gibco, Rockville, MD, USA) containing 10% heat-inactivated fetal bovine serum (FBS; WISENT [086-150], Pengchen Science&Technology Company, Guangzhou,Guangdong,China). MC38 cells were cultured and maintained in DMEM (10% FBS). HT29 cells were cultured in MyCo5A (10% FBS). All cells were incubated in 5% CO2 and 95% N2 at 37 °C and subjected to cell line authentication. Cells in the mid-log phase were used in the experiments. Small interfering RNA (siRNA) was used for gene silencing. siRNA targeting DDR1 (siDDR1 1-4) and negative control siRNA (siNC) were constructed by Tsingke Biotechnology Co., Ltd. (as presented in the Supplementary Table S1). A total of 3 × 105 cells were inoculated in each well of 6-well culture dishes, with one dish for each cell line. All transient transfections were performed with the TransIT-X2 Dynamic Delivery System (Mirus, #MIR6000, NeoBioscience Technology Co.,Ltd,Shenzhen,Guangdong,China) according to the manufacturer’s instructions. Specific target sequences are shown in Supplementary tables.
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10

Colorectal Adenocarcinoma Cell Line Viability

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The influence of CFA, CA, CTA, and CY was studied in relation to a colorectal adenocarcinoma DLD-1 cell line, which was obtained from the American Type Culture Collection (ATCC). DLD-1 cells were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco), penicillin (100 U/mL), and streptomycin (100 μg/mL) at 37 °C in a humified atmosphere of 5% CO2 in the air. The cells viability in tested cell lines was examined at the concentrations of 0.5 µM, 1 µM, 5 µM, 10 µM, 20 µM, 50 µM, 100 µM, 200 µM, 300 µM, and 500 µM for every studied compound.
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