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Uveal melanoma

Uveal melanoma is a rare and aggressive form of eye cancer that originates in the uveal tract, which includes the iris, ciliary body, and choroid.
This disease can be difficult to study and treat, but the AI-driven platform PubCompare.ai helps researchers optimize their Uveal melanoma research by locating the best protocols from published literature, preprints, and patents.
PubCompare.ai's comparisons enhance reproducibility and accuracy, ensuring researchers find the most effective approaches and take their Uveal melanoma studies to new heights.
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Most cited protocols related to «Uveal melanoma»

Results are based in part upon data generated by TCGA Research Network (http://cancergenome.nih.gov/). We aggregated TCGA transcriptomic and RPPA data from public repositories, listed in the “Data availability” section. RNA-seq expression data were processed by TCGA at the gene level, rather than at the transcript level. Tumors spanned 32 different TCGA projects, each project representing a specific cancer type, listed as follows: LAML, acute myeloid leukemia; ACC, adrenocortical carcinoma; BLCA, bladder urothelial carcinoma; LGG, lower grade glioma; BRCA, breast invasive carcinoma; CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma; CHOL, cholangiocarcinoma; CRC, colorectal adenocarcinoma (combining COAD and READ projects); ESCA, esophageal carcinoma; GBM, glioblastoma multiforme; HNSC, head and neck squamous cell carcinoma; KICH, kidney chromophobe; KIRC, kidney renal clear cell carcinoma; KIRP, kidney renal papillary cell carcinoma; LIHC, liver hepatocellular carcinoma; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma; DLBC, lymphoid neoplasm diffuse large B-cell lymphoma; MESO, mesothelioma; OV, ovarian serous cystadenocarcinoma; PAAD, pancreatic adenocarcinoma; PCPG, pheochromocytoma and paraganglioma; PRAD, prostate adenocarcinoma; SARC, sarcoma; SKCM, skin cutaneous melanoma; STAD, stomach adenocarcinoma; TGCT, testicular germ cell tumors; THYM, thymoma; THCA, thyroid carcinoma; UCS, uterine carcinosarcoma; UCEC, uterine corpus endometrial carcinoma; UVM, uveal melanoma. Cancer molecular profiling data were generated through informed consent as part of previously published studies and analyzed per each original study’s data use guidelines and restrictions.
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Publication 2019
4-carboxyphenylglyoxal Adenocarcinoma Adenocarcinoma of Lung Adrenocortical Carcinoma Breast Carcinoma Carcinoma, Thyroid Carcinoma, Transitional Cell Carcinosarcoma Cells Cholangiocarcinoma Chromophobia Chronic Obstructive Airway Disease Diffuse Large B-Cell Lymphoma Endocervix Endometrial Carcinoma Esophageal Cancer Familial Atypical Mole-Malignant Melanoma Syndrome Gene Expression Profiling Genes Glioblastoma Multiforme Glioma Hepatocellular Carcinomas Hypernephroid Carcinomas Kidney Leukemia, Myelocytic, Acute Lung Lymph Malignant Neoplasms Mesothelioma Neck Neoplasms Ovary Pancreas Paraganglioma Pheochromocytoma Prostate Renal Cell Carcinoma RNA-Seq Sarcoma Serous Cystadenocarcinoma Squamous Cell Carcinoma Squamous Cell Carcinoma of the Head and Neck Stomach Testicular Germ Cell Tumor Thymoma Urinary Bladder Uterus Uveal melanoma X-Ray Photoelectron Spectroscopy
Aligned RNA-seq bam files were analyzed using the ISB Cancer Genomics Cloud (https://isb-cgc.appspot.com/). These 33 cancer types included in this study are adrenocortical carcinoma [ACC], bladder urothelial carcinoma [BLCA], brain lower grade glioma [LGG], breast invasive carcinoma [BRCA], cervical squamous cell carcinoma and endocervical adenocarcinoma [CESC], cholangiocarcinoma [CHOL], colon adenocarcinoma [COAD], esophageal carcinoma [ESCA], glioblastoma multiforme [GBM], head and neck squamous cell carcinoma [HNSC], kidney chromophobe [KICH], kidney renal clear cell carcinoma [KIRC], kidney renal papillary cell carcinoma [KIRP], acute myeloid leukemia [LAML], liver hepatocellular carcinoma [LIHC], lung adenocarcinoma [LUAD], lung squamous cell carcinoma [LUSC], lymphoid neoplasm diffuse large B cell lymphoma [DLBC], mesothelioma [MESO], ovarian serous cystadenocarcinoma [OV], pancreatic adenocarcinoma [PAAD], pheochromocytoma and paraganglioma [PCPG], prostate adenocarcinoma [PRAD], rectum adenocarcinoma [READ], sarcoma [SARC], skin cutaneous melanoma [SKCM], stomach adenocarcinoma [STAD], testicular germ cell tumors [TGCT], thymoma [THYM], thyroid carcinoma [THCA], uterine carcinosarcoma [UCS], uterine corpus endometrial carcinoma [UCEC], and uveal melanoma [UVM]. The sample set consists of 10,337 total TCGA samples, 9,624 tumor samples, and 713 normal samples.
Level-3 gene expression (RSEM) and segment-based copy number data were downloaded from Broad GDAC firehose (https://gdac.broadinstitute.org) (version: 2016_01_28). Gene-based copy number data were obtained by intersecting with RefSeq gene annotation bed file (version: 2013-07-27). Mutation calls were provided by the Multi-Center Mutation Calling in Multiple Cancers (MC3) working group within TCGA (Key Resources Table; Ellrott et al., 2018 ).
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Publication 2018
Adenocarcinoma Adenocarcinoma of Lung Adrenocortical Carcinoma Brain Breast Carcinoma Carcinoma, Thyroid Carcinoma, Transitional Cell Carcinosarcoma Cells Cholangiocarcinoma Chromophobia Colon Adenocarcinomas Diffuse Large B-Cell Lymphoma Endocervix Endometrial Carcinoma Esophageal Cancer Familial Atypical Mole-Malignant Melanoma Syndrome Gene Annotation Gene Expression Genes Glioblastoma Multiforme Glioma Hepatocellular Carcinomas Hypernephroid Carcinomas Kidney Leukemia, Myelocytic, Acute Lung Lymph Malignant Neoplasms Mesothelioma Mutation Neck Neoplasms Ovary Pancreas Paraganglioma Pheochromocytoma Prostate Rectum Renal Cell Carcinoma RNA-Seq Sarcoma Serous Cystadenocarcinoma Squamous Cell Carcinoma Squamous Cell Carcinoma of the Head and Neck Stomach Testicular Germ Cell Tumor Thymoma Urinary Bladder Uterus Uveal melanoma

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Publication 2018
Adenocarcinoma Adenocarcinoma of Lung Adrenocortical Carcinoma Brain Breast Carcinoma Carcinoma, Thyroid Carcinoma, Transitional Cell Carcinosarcoma Cells Cholangiocarcinoma Chromophobia Colon Adenocarcinomas Diffuse Large B-Cell Lymphoma Endocervix Endometrial Carcinoma Esophageal Cancer Familial Atypical Mole-Malignant Melanoma Syndrome Gene Annotation Gene Expression Genes Glioblastoma Multiforme Glioma Hepatocellular Carcinomas Hypernephroid Carcinomas Kidney Leukemia, Myelocytic, Acute Lung Lymph Malignant Neoplasms Mesothelioma Mutation Neck Neoplasms Ovary Pancreas Paraganglioma Pheochromocytoma Prostate Rectum Renal Cell Carcinoma RNA-Seq Sarcoma Serous Cystadenocarcinoma Squamous Cell Carcinoma Squamous Cell Carcinoma of the Head and Neck Stomach Testicular Germ Cell Tumor Thymoma Urinary Bladder Uterus Uveal melanoma

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Publication 2017
Disease Progression Genes Genetic Heterogeneity Genome Uveal melanoma
A custom amplicon-based sequencing panel covering 29 genes (Supplemental Table 2) known to be recurrently
mutated in cutaneous and uveal melanoma was designed and prepared applying the GeneRead
Library Prep Kit from QIAGEN® according to the manufacturer's
instructions. For adapter ligation and barcoding of individual samples, the NEBNext Ultra
DNA Library Prep Mastermix Set and NEBNext Multiplex Oligos for Illumina from New England
Biolabs were applied. Twelve samples were sequenced in parallel on an Illumina MiSeq next
generation sequencer.
Sequencing analysis was performed applying the CLC Cancer Research Workbench
from QIAGEN®. In brief, the following steps were applied. The workflow
in CLC included adapter trimming and read pair merging before mapping to the human
reference genome (hg19). Insertions and deletions as well as single nucleotide variant
detection, local realignment and primer trimming followed. Additional information was then
obtained regarding potential mutation type, known single nucleotide polymorphisms and
conservation scores by cross-referencing varying databases (COSMIC, ClinVar, dbSNP, 1000
Genomes Project, HAPMAP and PhastCons-Conservation_scores_hg19). After the CLC processing,
resulting csv files were analyzed manually. Mutations affecting the protein coding portion
of the gene were considered if predicted to result in non-synonymous amino acid changes.
To eliminate questionable low frequency background mutations calls, not uncommon in our
experience with FFPE amplicon sequencing approaches [24 (link)], mutations were reported if the overall coverage of
the mutation site was ≥30 reads, ≥15 reads reported the mutated variant
and the frequency of mutated reads was ≥15 %.
Sanger-sequencing was performed for EIF1AX exon 1 applying the
primers F-CCTCCAGCACCTACTTGGTC and R-CTGGGTGACCTGCAATCTAC as previously described
[21 (link)].
Publication 2016
2',5'-oligoadenylate Amino Acids Cosmic composite resin DNA Library EIF1AX protein, human Exons Gene Deletion Genes Genome HapMap Insertion Mutation Ligation Malignant Neoplasms Mutation Nucleotides Oligonucleotide Primers Proteins Single Nucleotide Polymorphism Uveal melanoma

Most recents protocols related to «Uveal melanoma»

Human primary uveal melanoma cell lines (92.1, Mel270, and Mel285), human uveal melanoma liver metastasis cell lines (OMM2.3 and MM28), primary cutaneous melanoma cell lines (OCM3 and A375), and cutaneous melanoma lymph node metastasis cell lines (Hs294t and Sk‐Mel28) were studied. Cell lines mutational profile and original references are summarized on Table S1. OMM2.3, Mel 270, and Mel 285 cell lines were kindly provided by Dr Bruce R. Ksander (Schepens Eye Research Institute, Boston, MA, USA). MM28 and OCM3 cell lines were kindly provided by Dr Martine J. Jager (Leiden University Medical Center, Leiden, the Netherlands). SK‐Mel28, Hs294t, and A375 cell lines were purchased from ATCC (#HTB‐72, #HTB‐140, #CRL‐1619, ATCC, Manassas, VA, USA). Cell line 92.1 was purchased from Millipore Sigma (#13012458‐1VL, Millipore Sigma, Burlington, MA, USA). Cells were cultured in a 37 °C humidified incubator under 5% CO2 atmosphere. Mel285 and Mel270 were cultured in RPMI 1640 medium (#11875093, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 1% nonessential amino acids (#11140050, Thermo Fisher Scientific), 1% vitamin solution (#11120052, Thermo Fisher Scientific), 100 U·mL−1 penicillin, 100 U·mL−1 streptomycin (#15140122, Thermo Fisher Scientific), and 10% heat‐inactivated FBS (#10438026, Thermo Fisher Scientific). 92.1, OCM3, OMM2.3, and THP‐1 were cultured in RPMI 1640 medium supplemented with 100 U·mL−1 penicillin, 100 U·mL−1 streptomycin, and 10% heat‐inactivated FBS. MM28 was cultured in IMDM (#12440053, Thermo Fisher) supplemented with 200 U·mL−1 penicillin, 200 U·mL−1 streptomycin, and 20% heat‐inactivated FBS. Hs294t and A375 were cultured in DMEM medium (#11965092, Thermo Fisher Scientific) supplemented with 100 U·mL−1 penicillin, 100 U·mL−1 streptomycin, and 10% FBS. Sk‐Mel28 was cultured in EMEM medium (#30‐2003, ATCC) supplemented with 100 U·mL−1 penicillin, 100 U·mL−1 streptomycin, and 10% FBS. Cells were passaged by trypsinization with 0.25% EDTA trypsin (#25200056, Thermo Fisher Scientific) when they reached 90% confluency using sterile technique. Medium was changed every 2–3 days.
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Publication 2023
Amino Acids Atmosphere Cell Lines Cells Edetic Acid Familial Atypical Mole-Malignant Melanoma Syndrome Homo sapiens Liver Lymph Node Metastasis Mutation Neoplasm Metastasis Penicillins Sterility, Reproductive Streptomycin Trypsin Uveal melanoma Vitamins
Uveal melanoma (TCGA‐UVM) and cutaneous melanoma (TCGA‐SKCM) patients' tumor transcriptome profiling gene expression RNA sequencing data were downloaded from The Cancer Genome Atlas (TCGA) website (https://portal.gdc.cancer.gov/). NLRP3‐ and IL1B‐normalized gene expression values in transcripts per million were extracted from each case file to create a new data frame using rstudio [26 ]. Group medians were compared using the Mann–Whitney U test. Single‐cell transcriptomic data and graphs of RPE/choroid cells were acquired from spectacle website [27 (link)] (https://singlecell‐eye.org/app/spectacle/) based on Voigt et al. [28 (link)] dataset.
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Publication 2023
Cells Choroid Eyeglasses Familial Atypical Mole-Malignant Melanoma Syndrome Gene Expression Gene Expression Profiling Genome Interleukin-1 Malignant Neoplasms Neoplasms Patients Reading Frames RNA, Neoplasm Uveal melanoma
Manifests containing fragments per kilobase per million (FPKM) normalized RNA-seq data from 34 TCGA cohorts – Acute Myeloid Leukemia - (TCGA-LAML), Adrenocortical carcinoma (TCGA-ACC), Bladder Urothelial Carcinoma (TCGA-BLCA), Glioblastoma multiforme and Brain Lower Grade Glioma and (TCGA-GBMLGG), Breast Invasive Carcinomas (TCGA-BRCA), Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (TCGA-CESC), Cholangiocarcinoma (TCGA-CHOL), Chronic Myelogenous Leukemia (TCGA-LCML), Colon Adenocarcinoma (TCGA-COAD), Esophageal Carcinoma (TCGA-ESCA), Head and Neck Squamous Cell Carcinoma (TCGA-HNSC), pan-Kidney Cancer (TCGA-KIPAN), Liver Hepatocellular Carcinoma (TCGA-LIHC), Lung Adenocarcinoma (TCGA-LUAD), Lung Squamous Cell Carcinoma (TCGA-LUSC), Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (TCGA-DLBC), Mesothelioma (TCGA-MESO), Ovarian Serous Cystadenocarcinoma (TCGA-OV), Pancreatic Adenocarcinoma (TCGA-PAAD), Pheochromocytoma and Paraganglioma (TCGA-PCPG), Prostate Adenocarcinoma (TCGA-PRAD), Rectum Adenocarcinoma (TCGA-READ), Sarcoma (TCGA-SARC), Skin Cutaneous Melanoma (TCGA-SKCM), Stomach Adenocarcinoma (TCGA-STAD), Testicular Germ Cell Tumors (TCGA-TGCT), Thymoma (TCGA-TGCT), Thyroid Carcinoma (TCGA-THCA), Uterine Carcinosarcoma (TCGA-USC), Uterine Corpus Endometrial Carcinoma (TCGA-UCES), Uveal Melanoma (TCGA-UVM) were downloaded from the Broad Institute GDAC (TCGA data version 20150601). Patients were then sorted by increasing B7-H3 expression in each cohort.
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Publication 2023
4-carboxyphenylglyoxal Adenocarcinoma Adenocarcinoma of Lung Adrenocortical Carcinoma Brain Breast Carcinoma Cancer of Kidney Carcinoma, Thyroid Carcinoma, Transitional Cell Carcinosarcoma Cholangiocarcinoma Chronic Obstructive Airway Disease Colon Adenocarcinomas Diffuse Large B-Cell Lymphoma Endocervix Endometrial Carcinoma Esophageal Cancer Familial Atypical Mole-Malignant Melanoma Syndrome Glioblastoma Multiforme Glioma Hepatocellular Carcinomas Leukemia, Myelocytic, Acute Leukemias, Chronic Granulocytic Lung Lymph Mesothelioma Neck Neoplasms Ovary Pancreas Paraganglioma Patients Pheochromocytoma Prostate Rectum RNA-Seq Sarcoma Serous Cystadenocarcinoma Squamous Cell Carcinoma Squamous Cell Carcinoma of the Head and Neck Stomach Testicular Germ Cell Tumor Thymoma Urinary Bladder Uterus Uveal melanoma X-Ray Photoelectron Spectroscopy
Mouse mesothelioma cell lines were previously generated in our laboratory and cultured in Dulbecco’s Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12 + Glutamax; Gibco), supplemented with 4 μg/mL Hydrocortisone (Sigma), 5 ng/ml murine EFG (Sigma), insulin-transferrin-selenium solution (ITS; Gibco), 10% fetal calf serum (FCS; Capricorn), and 1% penicillin and streptomycin (Gibco).15 (link),52 (link) Human mesothelioma cell lines were obtained from the American Type Culture Collection (ATCC) and were cultured in mammalian cell culture medium as specified above. Uveal melanoma cell lines, also obtained from ATCC, were cultured in either RPMI 1640 (RPMI-1640; Gibco) or Dulbecco’s Modified Eagle Medium (DMEM; Gibco) supplemented with 10% or 20% FCS and 1% penicillin/streptomycin. All cell lines were maintained at 37°C in a humidified atmosphere containing 5% carbon dioxide (CO2) and were tested for mycoplasma contamination using MycoAlert Mycoplasma detection kit (Lonza). The human cell lines were authenticated using short tandem repeat STR DNA profiling.
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Publication 2023
Atmosphere Carbon dioxide Cell Culture Techniques Cell Lines Eagle Homo sapiens Hydrocortisone Insulin Mammals Mesothelioma Mus Mycoplasma Nutrients Penicillins Selenium Short Tandem Repeat Streptomycin Transferrin Uveal melanoma
The TCGA Research Network (https://portal.gdc.cancer.gov/) has analyzed clinical and molecular data from over 10,000 oncology patients in 33 countries, covering 33 different tumor types and over 10,000 oncology patients. Transcriptomic RNA-seq data for 33 cancers were extracted from TCGA database. 33 cancer types were included: adrenocortical carcinoma (ACC), bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), colon adenocarcinoma (COAD), lymphoid neoplasm diffuse large B cell lymphoma (DLBC), esophageal carcinoma (ESCA), glioblastoma multiforme (GBM), head and neck squamous cell carcinoma (HNSC), kidney chromophobe (KICH), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), acute myeloid leukemia (LAML), brain lower grade glioma (LGG), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), ovarian serous cystadenocarcinoma (OV), pancreatic adenocarcinoma (PAAD), prostate adenocarcinoma (PRAD), pheochromocytoma and paraganglioma (PCPG), rectum adenocarcinoma (READ), skin cutaneous melanoma (SKCM), stomach adenocarcinoma (STAD), testicular germ cell tumors (TGCT), thyroid carcinoma (THCA), thymoma (THYM), uterine corpus endometrial carcinoma (UCEC), cholangiocarcinoma (CHOL), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), mesothelioma (MESO), sarcoma (SARC), uveal melanoma (UVM), and uterine carcinosarcoma (UCS).
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Publication 2023
Adenocarcinoma Adenocarcinoma of Lung Adrenocortical Carcinoma Brain Breast Carcinoma Carcinoma, Thyroid Carcinoma, Transitional Cell Carcinosarcoma Cells Cholangiocarcinoma Chromophobia Colon Adenocarcinomas Diffuse Large B-Cell Lymphoma Endocervix Endometrial Carcinoma Esophageal Cancer Familial Atypical Mole-Malignant Melanoma Syndrome Gene Expression Profiling Glioblastoma Multiforme Glioma Hepatocellular Carcinomas Hypernephroid Carcinomas Kidney Leukemia, Myelocytic, Acute Lung Lymph Malignant Neoplasms Mesothelioma Neck Neoplasms Ovary Pancreas Paraganglioma Patients Pheochromocytoma Prostate Rectum Renal Cell Carcinoma RNA-Seq Sarcoma Serous Cystadenocarcinoma Squamous Cell Carcinoma Squamous Cell Carcinoma of the Head and Neck Stomach Testicular Germ Cell Tumor Thymoma Urinary Bladder Uterus Uveal melanoma

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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.
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Penicillin is a type of antibacterial drug that is widely used in medical and laboratory settings. It is a naturally occurring substance produced by certain fungi, and it is effective against a variety of bacterial infections. Penicillin works by inhibiting the growth and reproduction of bacteria, making it a valuable tool for researchers and medical professionals.
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More about "Uveal melanoma"

Uveal melanoma is a rare and aggressive form of eye cancer that originates in the uveal tract, which includes the iris, ciliary body, and choroid.
This ocular malignancy can be challenging to study and treat, but the AI-driven platform PubCompare.ai helps researchers optimize their uveal melanoma research by locating the best protocols from published literature, preprints, and patents.
PubCompare.ai's comparisons enhance reproducibility and accuracy, ensuring researchers find the most effective approaches and take their uveal melanoma studies to new heights.
Uveal melanoma is a type of melanoma that arises from melanocytes, the pigment-producing cells in the uveal tract of the eye.
This rare form of eye cancer accounts for approximately 5% of all melanoma cases and can be difficult to detect and manage.
The disease can spread to other parts of the body, including the liver, lungs, and bones, making it a serious and life-threatening condition.
Researchers studying uveal melanoma often utilize a variety of cell culture techniques and reagents to understand the underlying mechanisms of the disease and develop new treatments.
Commonly used materials include RPMI 1640 medium, a cell culture medium that provides essential nutrients for the growth and maintenance of cells, and penicillin/streptomycin, an antibiotic combination used to prevent bacterial contamination in cell cultures.
Additionally, researchers may employ the Cell Titer Glow assay, a luminescent-based method for determining the number of viable cells in a population, and the QIAmp DNA Mini Kit, a tool for extracting and purifying DNA from various samples.
By harnessing the power of PubCompare.ai, researchers can streamline their uveal melanoma research, optimizing their protocols and enhancing the reproducibility and accuracy of their findings.
This AI-driven platform helps researchers discover the most effective approaches, taking their uveal melanoma studies to new heights and advancing the understanding and treatment of this rare and aggressive form of eye cancer.