The largest database of trusted experimental protocols
> Disorders > Neoplastic Process > Carcinoma

Carcinoma

Carcinomas are a type of cancer that originate from epithelial cells.
They can occur in a wide variety of organs, including the lungs, breasts, prostate, and colon.
Carcinomas are characterized by uncontrolled cell growth and the potential to invade surrounding tissues and metastasize to other parts of the body.
Early detection and appropriate treatment are crucial for improving patient outcomes.
Researchers utilize a variety of experimental protocols and products to study carcinoma biology and develop new therapies.
PubCompare.ai can help streamline this process by providing AI-powered access to relevant protocols and facilitating comparisions to identify the best approaches for carcionma research.

Most cited protocols related to «Carcinoma»

We developed a text-mining-based data parsing workflow and collected tumor scRNA-seq datasets of human from GEO (16 (link)) and ArrayExpress (17 (link)). We searched the single-cell-related keywords such as ‘single cell RNA sequencing’ or ‘scRNAseq’ or ‘single cell’ or ‘single-cell’, as well as the technology-related keywords like ‘microfluidics’, ‘10X Genomics’ and ‘SMARTseq’, and the tumor-related keywords such as ‘tumor’ or ‘cancer’ or ‘carcinoma’ in the description page of GEO or ArrayExpress. Each dataset was then manually confirmed and curated. A total of 118 cancer-related scRNA-seq datasets were obtained initially and were further filtered to keep the datasets with >1000 high-quality cells. To expand the utility of TISCH, we also included the scRNA-seq datasets of mice treated with immunotherapy and three scRNA-seq datasets of human peripheral blood mononuclear cells (PBMC) from 10X Genomics. Overall, the TISCH database contains 76 high-quality tumor datasets across 27 cancer types and three PBMC datasets (Supplementary Table S1). We downloaded the expression matrix of the raw count, TPM or FPKM (if available) for each dataset. We collected sample information from databases or the original studies, such as the patient ID, tissue origin, treatment condition, response groups and the original cell-type annotation. Notably, we processed each cancer type separately if a dataset contained multiple cancer types. The source code for processing all the collected scRNA-seq datasets are deposited at the Github repository (https://github.com/DongqingSun96/TISCH/tree/master/code)
Publication 2020
7-chloro-8-hydroxy-1-(3'-iodophenyl)-3-methyl-2,3,4,5-tetrahydro-1H-3-benzazepine Carcinoma Cells Homo sapiens Immunotherapy Malignant Neoplasms Mus Neoplasms Patients PBMC Peripheral Blood Mononuclear Cells Single-Cell RNA-Seq Tissues Trees
We analyzed whole-exome hybrid capture Illumina sequencing (WES) 36 (link) data from 214 ovarian carcinoma tumor-normal pairs previously analyzed by the TCGA consortium 33 (link). We used the program muTect (K. Cibulskis, et al., in preparation.) We have used a newer version of the program muTect than used in previous analysis of this data 33 (link). The primary improvement in the new version is a reduction in the prior that somatic mutations be at an allelic fraction of 0.5, allowing greater sensitive at low allelic-fraction mutations, such as clonal events in impure samples, or to subclonal mutations. This procedure resulted in 29,268 somatic mutations.
Publication 2012
Alleles Carcinoma Clone Cells Diploid Cell Hybrids Mutation Neoplasms Ovarian Cancer Ovarian Neoplasm

ChIP–chip dataset. A number of assays have been recently developed that use immunopercipitation-based enrichment of cellular DNA for the purpose of identifying binding or other chemical events and the genomic locations at which they occur. Location analysis, also known as ChIP–chip, is a technique that enables the mapping of transcription binding events to genomic locations at which they occur [1 (link),54 ]. The output of the assay is a fluorescence dye ratio at each spot of the array. If spots are taken to represent genomic regions, then we can regard the ratio and p-value associated with each spot as an indication of TF binding in the corresponding genomic region. We applied DRIM to S. cerevisiae genome-wide location data reported in Harbison et al. [25 (link)] and Lee et al. [28 (link)]. The first consists of the genomic occupancy of 203 putative TFs in rich media conditions (YPD). In addition, the genomic occupancy of 84 of these TFs was measured in at least one other condition (OC). In each of the experiments, the genomic sequences were ranked according to the TF binding p-value. Surprisingly, we observed that 69 of the 203 ranked sequence lists of YPD had significantly longer sequences at the top of the list (first 300 sequences) compared with the rest of the list with t-test p-value ≤ 10−3. We observed a similar phenomenon in 76 of the 148 ranked sequence lists of OC experiments (see Figure S1). In other words, for some TFs, longer sequences are biased toward stronger binding signals. This observation is unexpected since, although longer probes hybridize more labeled material than shorter probes, the increase should be proportional in both channels. This type of length bias may cause spurious results under our model assumptions and hence the final dataset, termed “Harbison filtered dataset,” refers to the remaining 207 experiments (135 YPD, and 72 OC) of 162 unique TFs that did not have length bias (Table S1).
An additional ChIP–chip dataset was constructed using the data reported in Lee et al. [28 (link)] containing 113 experiments in rich media. The data is partially exclusive to the data of Harbison et al. [25 (link)]. The same filtering procedure was performed, resulting in a set of 65 experiments, termed “Lee filtered dataset.”
Methylated CpG dataset. Using a technique similar to ChIP–chip, termed methyl-DNA immunoprecipitation (mDIP), enables the measurement of methylated CpG island patterns [2 (link),55 (link)]. The third dataset contains the CpG island methylation patterns of four different human cancer cell lines (Caco-2, Polyp, Carcinoma, PC3) where several replicate experiments were done for each of the cell lines. In each of these experiments, the CpG methylation signal was measured in ∼13,000 gene promoters as reported in [2 (link)].
Full text: Click here
Publication 2007
Biological Assay Carcinoma Cell Lines Cells ChIP-Chip CpG Islands DNA Replication Exanthema Fluorescent Dyes Genome Homo sapiens Immunoprecipitation Malignant Neoplasms Methylation Polyps Promoter, Genetic Transcription, Genetic
Artificial data sets were generated with negative binomial distributed counts for a fixed total number of 10 000 genes. The expected count size varied between genes according to a gamma distribution with shape parameter 0.5, an ad hoc choice that happened to mimic the size distribution of the carcinoma data. The average dispersion was set to 0.16 (BCV = 0.4). In one simulation, all genes had the same true dispersion. In the other simulation, true dispersions were randomly generated around 0.16 according to an inverse chisquare distribution with 20 degrees of freedom.
Publication 2012
Carcinoma Gamma Rays Genes
Both anchor-based and distribution-based approaches were used to estimate MIDs for the EQ-5D in the overall cancer cohort, and in the subgroup of lung cancer patients, when possible. Distribution-based criteria included: 1/2 standard deviation (SD) and the standard error of the measure (SEM) [22 (link)]. For consistency with past studies exploring MIDs, 1/3 SD was also reported, but it was not included in the summarized range of MIDs as there is less evidence to support that 1/3 SD represents an important difference. The SEM is calculated as σx1rx where r is reliability of the measure. It is debatable which type of reliability, internal consistency or test-retest (TRT) reliability, is most appropriate. Very limited evidence of TRT reliability is available on the EQ-5D in cancer [4 (link)]. Because the EQ-5D has single item dimensions, internal consistency reliability does not apply to each dimension. Although HRQL is considered a multi-dimensional construct, the aggregation of dimensional responses to create a single summary score is an implicit endorsement of HRQL as an overarching construct. However, item response theory-based analysis of the dimensional structure of the EQ-5D has indicated that the anxiety/depression dimension taps into a construct distinct from the other 4 items [23 ]. Calculation of internal consistency reliability using Cronbach's alpha was 0.68, regardless of whether or not anxiety/depression was included. Thus, for the purposes of our analysis, a reliability of 0.68 was used in the calculation of the SEM.
Anchors can be constructed using clinically-based criteria, such as response to treatment, or more subjective criteria, e.g. health status. We used ECOG grades, assessed by physician, to group patients into categories of performance status, and determined mean difference scores between ECOG grades. Distribution-based criteria were then applied to the statistics associated with each anchor-based category. A second anchor-based approach used FACT-G scores. The cohort was stratified into quintiles based on FACT-G summary scores. Grouping the cohort into quintiles approximated an appropriate threshold for stratifying patients based on MID estimates for the FACT-G, have been identified as close to 6 in previous studies: 6–7 in hepatobiliary carcinoma [13 (link)], and 5–6 in breast cancer [10 (link)]. Final results were summarized as a range of MID estimates and as an average MID across categories, weighted by the sample size within each category.
Full text: Click here
Publication 2007
Anxiety Carcinoma Electrocorticography Lung Cancer Malignant Neoplasm of Breast Malignant Neoplasms Patients Physicians

Most recents protocols related to «Carcinoma»

Example 5

In order to compare levels of adherence to HEp-2 epithelial cells in culture, we used an established model for evaluating adherence of EHEC O157:H7 (27). HEp-2, human laryngeal carcinoma epithelial cells, were a kind gift from Dr. Carlton Gyles (Department of Pathobiology, University of Guelph). Briefly, HEp-2 cells grown in EMEM supplemented with 10% (v/v) FBS were plated onto 24-well tissue culture plates at 2×105 cells ml−1 and incubated for 24 h in the presence of 5% CO2. The cells were then maintained during the assay in serum and antibiotic-free EMEM. Before inoculation with bacteria, 10% (v/v) of L. acidophilus CFSM selected fractions were added in triplicate to treatment group wells. Wells containing the negative control groups were inoculated with 105 E. coli O157:H7 strain VS94 with or without supplementation with 100 μM propanolol (Sigma-Aldrich Canada Ltd.). Following inoculation of 105 EHEC O157 into treatment and control group wells, the plates were incubated for 3 h at 37° C. in the presence of 5% CO2. The cell monolayers were then washed three times with PBS to remove non-adhering bacteria and fresh medium was added. Cells were incubated for another 3 h and then washed six times with PBS. Washed cells were lysed with 0.1% Triton X-100. Released bacteria present in the suspension were collected and appropriate dilutions were plated on LB agar. To evaluate if the percentage of adherence in the treatment groups was significantly different from that of the control group, where the recovered counts from the control group (2.2×107 CFU ml−1) were considered to be 100%, the percentage of adherence in the negative control and treatment groups were calculated using the following equation.

% of Recovery = Group _ 2.2 × 10 7 CFU ml - 1 × 100 _

Full text: Click here
Patent 2024
Agar Antibiotics Bacteria Bacterial Vaccines Biological Assay Carcinoma Cell Adhesion Cell Culture Techniques Cells Enterohemorrhagic Escherichia coli Epithelial Cells Escherichia coli O157 Homo sapiens Lactobacillus acidophilus Larynx Propranolol Serum Strains Technique, Dilution Tissues Triton X-100 Vaccination

Example 5

The human skin squamous carcinoma line (HSC) (Japanese Collection of Research Bioresources Cell Bank (JCRB)) was cultured in Dulbecco's minimal essential media (DMEM) containing 20% fetal bovine serum (FBS), (Thermofisher, Waltham, MA). Cells were plated at a density of 5,000 cells per well into a 96-well plate and allowed to attach for 24 h in a 37° C. humidified incubator with a 5% CO2 atmosphere. Media was replaced with that containing test agents or vehicle (0.1% dimethylsulphoxide) in 1% FBS and cells incubated for a further 72 h. Cell viability was assessed using CellTiter-Glo® (Promega). Non-linear regression analysis was performed using GraphPad PRISM®. FIG. 5 shows a representative experiment where the EC50 of COMPOUND A, was 5.2 nM and that of COMPOUND G was 9.2 nM.

Full text: Click here
Patent 2024
Atmosphere Carcinoma Cells Cell Survival Culture Media Cytotoxin Fetal Bovine Serum Homo sapiens inhibitors Japanese prisma Promega Skin Squamous Cell Carcinoma Squamous Epithelial Cells Sulfoxide, Dimethyl
We selected formalin-fixed, paraffin-embedded samples of UC, cystitis, and normal canine bladders from the archive at the Veterinary Pathology Diagnostic Services at the University of Sydney (New South Wales, Australia). An anatomic pathologist confirmed the diagnoses of UC, cystitis, and normal before immunohistochemical analysis was performed. Carcinoma cases had also been confirmed by histopathology for tumor origin in the kidney, bladder, or urethra. Samples without propria-submucosa were excluded. Information collected from the medical records included age, sex, breed, date of treatment initiation, treatment protocol, outcome, and, when available, cause of death. Cause of death was classified as: related to primary UC (such as acute renal failure, urinary obstruction, uremia), related to metastatic UC, or associated with other diseases unrelated to UC. All cases were assessed histologically and graded according to the World Health Organization (WHO) tumor classification system 201610 (link)
; tumors are differentiated into 3 grades: G1, G2, and G3. The lowest grade (G1) displays slim papilla with no atypia; the highest grade (G3) displays major atypia with marked loss of normal architecture. A classification of G2 covers the wide spectrum of lesions seen between G1 and G3 and includes increasing layers within the papilla and rare atypia.
Publication 2023
Canis familiaris Carcinoma Cystitis Diagnosis Formalin Kidney Failure, Acute Kidney Neoplasm Neoplasms Nipples Paraffin Embedding Pathologists Treatment Protocols Uremia Urethra Urinary Bladder Urine Vision
To generate the HNSCC PDX, the human HNSCC tissues were obtained without patient information from the Peking University School and Hospital of Stomatology. The tumor tissues were cut into small pieces, followed by implantation into the flanks of NOD-SCID mice (6 weeks old), according to a previously described method [8 (link)]. HNSCC specimens from 60 patients were obtained from the Peking University School and Hospital of Stomatology from September 2012 to October 2016. The inclusion criteria were as follows: 1) the tumor was in the tongue; 2) there was no distant metastasis; 3) removal of the primary carcinoma and neck dissection without preoperative radiotherapy or chemotherapy; and 4) patients who underwent postoperative follow-up for at least five years. Without conducting a pathological study, the clinical TNM staging approach was used to classify the tumor size and clinical stage for the 40 HNSCC samples among the 60 samples: 1) tumor size limited in T2 and T3; 2) clinically negative cervical lymph node (cN0); and 3) no distant metastasis (M0). Based on the histopathologic evaluation of the lymph nodes, these 40 patients were split into lymph node-negative and positive groups. These experiments were approved by the Institutional Review Board of the Peking University School and Hospital of Stomatology and all samples were obtained from patients who signed informed consent forms approving the use of their tissues for research purposes after surgery (Approval number: PKUSSIRB-2012010). The tissues were snap-frozen and placed at −80 °C until analysis.
Full text: Click here
Publication 2023
Carcinoma Ethics Committees, Research Freezing Homo sapiens Mice, Inbred NOD Neck Neck Dissection Neoplasm Metastasis Neoplasms Nodes, Lymph Ovum Implantation Patients Pharmacotherapy Radiotherapy SCID Mice Squamous Cell Carcinoma of the Head and Neck Tissues Tongue
We used a Dell Precision M4800 laptop and a SensoMotoric Instruments (Boston, MA) Remote Eye Tracking Device (RED; 250Hz, ≤ 0.5˚ gaze position accuracy) attached to a 22” color-calibrated Dell liquid crystal display (LCD) monitor (at 1920 × 1080 resolution). Images were displayed on a custom digital viewer software using the DeepZoom Silverlight application (Microsoft, Inc.) in the web browser. The viewer tool allowed participating pathologists to zoom (1× to 60×) and pan the digital whole slide images while maintaining high resolution, and make measurements and annotations. While a pathologist used the viewer tool, data were automatically logged (at approximately 10Hz) to a local SQL database, to include zoom, position, and annotation data.
To collect diagnostic information from participants after reviewing each image, we developed a histology form on the Qualtrics web-based platform; histology forms are commonly used by pathologists to record their observations and interpretations of images [31 (link), 41 (link)]. The histology form asked participating pathologists to provide the single most advanced diagnosis by selecting among the five diagnostic categories detailed above (ranging from benign to invasive carcinoma). They also rated the difficulty of interpreting the image and their confidence with their determination (both on scales from 1–7). Of less relevance to this paper, information was also gathered about histopathological features (e.g., nuclear grading, presence and nature of necrosis, mitotic activity), whether they believed the features indicated a borderline diagnosis (between two diagnostic categories), and whether the pathologist would seek a consultative second opinion if they encountered the image during ordinary clinical practice.
Full text: Click here
Publication 2023
Carcinoma Diagnosis Liquid Crystals Medical Devices Necrosis Pathologists

Top products related to «Carcinoma»

Sourced in United States, China, United Kingdom, Germany, Australia, Japan, Canada, Italy, France, Switzerland, New Zealand, Brazil, Belgium, India, Spain, Israel, Austria, Poland, Ireland, Sweden, Macao, Netherlands, Denmark, Cameroon, Singapore, Portugal, Argentina, Holy See (Vatican City State), Morocco, Uruguay, Mexico, Thailand, Sao Tome and Principe, Hungary, Panama, Hong Kong, Norway, United Arab Emirates, Czechia, Russian Federation, Chile, Moldova, Republic of, Gabon, Palestine, State of, Saudi Arabia, Senegal
Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
Sourced in United States, China, United Kingdom, Germany, France, Australia, Canada, Japan, Italy, Switzerland, Belgium, Austria, Spain, Israel, New Zealand, Ireland, Denmark, India, Poland, Sweden, Argentina, Netherlands, Brazil, Macao, Singapore, Sao Tome and Principe, Cameroon, Hong Kong, Portugal, Morocco, Hungary, Finland, Puerto Rico, Holy See (Vatican City State), Gabon, Bulgaria, Norway, Jamaica
DMEM (Dulbecco's Modified Eagle's Medium) is a cell culture medium formulated to support the growth and maintenance of a variety of cell types, including mammalian cells. It provides essential nutrients, amino acids, vitamins, and other components necessary for cell proliferation and survival in an in vitro environment.
Sourced in United States, China, Germany, United Kingdom, Japan, France, Canada, Australia, Italy, Switzerland, Belgium, New Zealand, Spain, Israel, Sweden, Denmark, Macao, Brazil, Ireland, India, Austria, Netherlands, Holy See (Vatican City State), Poland, Norway, Cameroon, Hong Kong, Morocco, Singapore, Thailand, Argentina, Taiwan, Province of China, Palestine, State of, Finland, Colombia, United Arab Emirates
RPMI 1640 medium is a commonly used cell culture medium developed at Roswell Park Memorial Institute. It is a balanced salt solution that provides essential nutrients, vitamins, and amino acids to support the growth and maintenance of a variety of cell types in vitro.
Sourced in United States, United Kingdom, Germany, China, France, Canada, Japan, Australia, Switzerland, Italy, Israel, Belgium, Austria, Spain, Brazil, Netherlands, Gabon, Denmark, Poland, Ireland, New Zealand, Sweden, Argentina, India, Macao, Uruguay, Portugal, Holy See (Vatican City State), Czechia, Singapore, Panama, Thailand, Moldova, Republic of, Finland, Morocco
Penicillin is a type of antibiotic used in laboratory settings. It is a broad-spectrum antimicrobial agent effective against a variety of bacteria. Penicillin functions by disrupting the bacterial cell wall, leading to cell death.
Sourced in United States, United Kingdom, Germany, China, France, Canada, Australia, Japan, Switzerland, Italy, Belgium, Israel, Austria, Spain, Netherlands, Poland, Brazil, Denmark, Argentina, Sweden, New Zealand, Ireland, India, Gabon, Macao, Portugal, Czechia, Singapore, Norway, Thailand, Uruguay, Moldova, Republic of, Finland, Panama
Streptomycin is a broad-spectrum antibiotic used in laboratory settings. It functions as a protein synthesis inhibitor, targeting the 30S subunit of bacterial ribosomes, which plays a crucial role in the translation of genetic information into proteins. Streptomycin is commonly used in microbiological research and applications that require selective inhibition of bacterial growth.
Sourced in United States, Germany, United Kingdom, China, Canada, France, Japan, Australia, Switzerland, Israel, Italy, Belgium, Austria, Spain, Gabon, Ireland, New Zealand, Sweden, Netherlands, Denmark, Brazil, Macao, India, Singapore, Poland, Argentina, Cameroon, Uruguay, Morocco, Panama, Colombia, Holy See (Vatican City State), Hungary, Norway, Portugal, Mexico, Thailand, Palestine, State of, Finland, Moldova, Republic of, Jamaica, Czechia
Penicillin/streptomycin is a commonly used antibiotic solution for cell culture applications. It contains a combination of penicillin and streptomycin, which are broad-spectrum antibiotics that inhibit the growth of both Gram-positive and Gram-negative bacteria.
Sourced in United States, China, United Kingdom, Germany, France, Canada, Japan, Australia, Italy, Switzerland, Belgium, New Zealand, Austria, Netherlands, Israel, Sweden, Denmark, India, Ireland, Spain, Brazil, Norway, Argentina, Macao, Poland, Holy See (Vatican City State), Mexico, Hong Kong, Portugal, Cameroon
RPMI 1640 is a common cell culture medium used for the in vitro cultivation of a variety of cells, including human and animal cells. It provides a balanced salt solution and a source of essential nutrients and growth factors to support cell growth and proliferation.
Sourced in United States, Germany, United Kingdom, Japan, Italy, China, Macao, Switzerland, France, Canada, Sao Tome and Principe, Spain, Australia, Ireland, Poland, Belgium, Denmark, India, Sweden, Israel, Austria, Brazil, Czechia, Netherlands, Portugal, Norway, Holy See (Vatican City State), New Zealand, Hungary, Senegal, Argentina, Thailand, Singapore, Ukraine, Mexico
FBS, or Fetal Bovine Serum, is a commonly used cell culture supplement. It is derived from the blood of bovine fetuses and provides essential growth factors, hormones, and other nutrients to support the growth and proliferation of a wide range of cell types in vitro.
Sourced in United States, United Kingdom, Germany, France, Canada, Switzerland, Italy, Australia, Belgium, China, Japan, Austria, Spain, Brazil, Israel, Sweden, Ireland, Netherlands, Gabon, Macao, New Zealand, Holy See (Vatican City State), Portugal, Poland, Argentina, Colombia, India, Denmark, Singapore, Panama, Finland, Cameroon
L-glutamine is an amino acid that is commonly used as a dietary supplement and in cell culture media. It serves as a source of nitrogen and supports cellular growth and metabolism.
Sourced in United States, China, Germany, United Kingdom, Canada, Japan, France, Italy, Switzerland, Australia, Spain, Belgium, Denmark, Singapore, India, Netherlands, Sweden, New Zealand, Portugal, Poland, Israel, Lithuania, Hong Kong, Argentina, Ireland, Austria, Czechia, Cameroon, Taiwan, Province of China, Morocco
Lipofectamine 2000 is a cationic lipid-based transfection reagent designed for efficient and reliable delivery of nucleic acids, such as plasmid DNA and small interfering RNA (siRNA), into a wide range of eukaryotic cell types. It facilitates the formation of complexes between the nucleic acid and the lipid components, which can then be introduced into cells to enable gene expression or gene silencing studies.

More about "Carcinoma"

Carcinomas are a type of malignant tumor that originate from epithelial cells, which line the surfaces of various organs in the body.
These cancerous growths can occur in a wide range of organs, including the lungs, breasts, prostate, and colon.
Carcinomas are characterized by uncontrolled cell division and the potential to invade surrounding tissues and spread (metastasize) to other parts of the body.
Early detection and appropriate treatment are crucial for improving patient outcomes in carcinoma cases.
Researchers utilize a variety of experimental protocols and products to study carcinoma biology and develop new therapies.
Common cell culture media used in carcinoma research include DMEM, RPMI 1640, and L-glutamine, often supplemented with antibiotics like Penicillin and Streptomycin.
Transfection reagents like Lipofectamine 2000 are also employed to introduce genetic material into carcinoma cells, enabling the study of specific genes and their role in cancer progression.
PubCompare.ai can streamline this research process by providing AI-powered access to relevant protocols and facilitating comparisons to identify the best approaches for carcinoma investigations.
By leveraging this tool, researchers can optimize their workflows and improve the accuracy and efficiency of their carcinoma studies.