Affymetrix data was downloaded from a total of ten datasets from published studies listed in Table 2 from the Gene Expression Omnibus [3 (link)] or Array Express [1 (link)] repositories. Raw .cel files were not available for the Wang et al. dataset, so all other datasets were normalized as in this study using the MAS 5.0 algorithm with a target intensity of 600 as implemented in the Simpleaffy package [50 (link)], using R [31 (link)] within BioConductor [48 (link)]. NetAffx [9 (link)] was used to identify Affymetrix probesets representing the 'intrinsic gene set' previously used to classify human breast tumours [8 (link)]. Centered average linkage clustering was performed using the Cluster [35 (link)] and TreeView programs as described previously [7 (link)]. Supervised principal components analysis using the Superpc for R package was used as previously described [29 ,30 (link)], in order to compare the predictive power of combining different published datasets. The follow up endpoints for the Loi et al., Pawitan et al. and Sotoriou et al. datasets were recurrence-free survival, for Desmedt et al. and Ivshina et al. datasets it was disease-free survival and for the Minn et al. and Wang et al. datasets it was distant metastasis-free survival.
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Mammary Neoplasms, Human
Mammary Neoplasms, Human
Mammary Neoplasms are tumors or abnormal growths that develop in the breast tissue.
These can include benign conditions like fibroadenomas as well as malignant cancers like breast carcinoma.
Proper identification and classification of mammary neoplasms is crucial for effective treatment and management.
PubCompare.ai offers a powerful platform to discover optimized research protocols that enhance reproducibility and accuracy in the study of these complex conditions.
These can include benign conditions like fibroadenomas as well as malignant cancers like breast carcinoma.
Proper identification and classification of mammary neoplasms is crucial for effective treatment and management.
PubCompare.ai offers a powerful platform to discover optimized research protocols that enhance reproducibility and accuracy in the study of these complex conditions.
Most cited protocols related to «Mammary Neoplasms, Human»
Gene Expression
Genes
Mammary Neoplasms, Human
Neoplasm Metastasis
Recurrence
miRNA profiling from total RNA was performed using Agilent Technologies “Human miRNA Microarray Kit (V2)” according to manufacturer's protocol. Scanning on Agilent Scanner G2565A and Feature Extraction (FE) v9.5 was used to extract signals. Excluding two samples, experiments were performed using duplicate hybridizations (99 samples) on different arrays and time points. miRNA signal intensities for replicate samples were averaged and log2 transformed. The expression levels were normalized to the 75th percentile. That is, the expression levels in each sample, i, were multiplied by a constant, ci, such that the 75th percentile of the expression levels in that sample will equal to a constant c – the 75th percentile in the entire dataset. miRNA expression status was scored as present or absent for each gene in each sample by default settings in FE v9.5. miRNAs in samples that were run in replicates were considered present if scored in one of the two arrays. The microarray contains probes for 76 viral and 723 human miRNAs (based on miRBASE v10.1). We filtered out all miRNAs that were detected in less than 10% of the samples. This filtering resulted in 489 miRNAs considered to be expressed in this set of human breast tumors and used in further analysis steps. For these miRNAs, all expression values were used for further analysis. Thus, no missing values were used. The miRNA expression data is MIAME compliant and have been submitted to the Gene Expression Omnibus (GEO) with accession number GSE19536.
Acid Hybridizations, Nucleic
DNA Replication
Gene Expression
Genes
Homo sapiens
Mammary Neoplasms, Human
Microarray Analysis
Strains
For all human breast tumor studies, intrinsic subtype classification was performed using the PAM50 predictor [9 (link)]. Human claudin-low tumor samples were identified using either SigClust [22 (link)] or the nine-cell line claudin-low predictor. Samples identified by SigClust [22 (link)] or the nine-cell line claudin-low predictor were called claudin-low, regardless of the PAM50 call. For breast cancer cell lines, the claudin-low subtype classification was based on unsupervised hierarchical clustering using the intrinsic list of Parker et al. [9 (link)] and the node identified in Figure S4 in Additional file 1 . The complete gene list of the nine-cell line claudin-low predictor can be found in Supplemental Data in Additional file 2 .
Cell Lines
Claudins
Genes
Homo sapiens
Mammary Neoplasms, Human
MCF-7 Cells
Neoplasms
Expression profiles of human breast tumors were downloaded from GEO series GSE3165. In order to standardize on one microarray platform, only the 94 arrays of platform GPL887 (Agilent Human 1A Microarray V2) were included in the analysis. Each tumor was classified to one of six molecular subtypes, namely basal-like, luminal A, luminal B, Her2, normal-like and claudin-low (30 (link)). Expression values were normalized and filtered as described previously (31 (link)).
Claudins
ERBB2 protein, human
Homo sapiens
Mammary Neoplasms, Human
Microarray Analysis
Neoplasms
Phenobarbital
Autopsy
Cells
Corticosterone
Heterografts
Homo sapiens
Immunocompetence
Injections, Intraperitoneal
Institutional Animal Care and Use Committees
Lentivirus
Lung
Lung Cancer
Lung Neoplasms
Malignant Neoplasms
Mammary Neoplasms, Human
Mice, 129 Strain
Mice, Nude
Mus
Neoplasms
Patients
Poly A
polyethylene glycol 300
Ritonavir
Somatostatin-Secreting Cells
Sulfoxide, Dimethyl
Tumor Burden
Most recents protocols related to «Mammary Neoplasms, Human»
Metabolomic profiling of human breast tissues was performed using an untargeted approach. Untargeted metabolic profiling of known and unknown metabolites was performed in 67 human breast tumors and 65 tumor-adjacent noncancerous tissues by Metabolon Inc, as described previously [18 (link), 19 (link)]. The TNBC cohort includes patients recruited in Baltimore (Maryland, USA) hospitals between 1993 and 2003, as previously described [18 (link), 19 (link)]. Clinical and pathological information (e. g. hormone receptor status) was obtained from medical records and pathology reports. Triple-negative tumors were negative for estrogen, progesterone, and HER2 receptor expression. In total 17 triple-negative tumors where the metabolic analysis was available were identified [18 (link), 19 (link)]. Survival analysis was performed in these 17 patients, who had long-term follow up for breast cancer-specific survival.
Breast
Breast Carcinoma
ERBB2 protein, human
Estrogens
Homo sapiens
Hormones
Mammary Neoplasms, Human
Neoplasms
Patients
Progesterone
Tissues
The protocol (#BC2015-013) for human breast tumor biopsy collection was approved by the Ethics Board of Jiangxi Provincial People’s Hospital. All enrolled patients provided written informed consent. In total, 73 ER-negative and 102 ER-positive breast tumors and their adjacent normal tissues were collected. All patients were diagnosed and underwent surgery from 2015 to 2019 in the Department of Oncology, Jiangxi Provincial People’s Hospital, Nanchang, China. The basic information (ages and tumor stages) of these patients are provided in Table S1.
Biopsy
Breast Neoplasm
Mammary Neoplasms, Human
Neoplasms
Operative Surgical Procedures
Patients
Tissues
Human breast tumor cells (MDA-MB-231, ATCC HTB-26) were cultured in DMEM culture medium, supplemented with FBS (10% v/v), penicillin (1% w/v) and streptomycin (1% v/v), and maintained in a humidified incubator containing 5% CO2 at 37 °C. Upon reaching the confluence stage, the cells were trypsinized, and an aliquot was transferred to another flask containing a complete culture medium for subculture.
Cells
Culture Media
Mammary Neoplasms, Human
Penicillins
Streptomycin
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-2000 (DSPE-PEG2000) were supplied by Lipoid GmbH (Ludwigshafen, Germany). Cholesterol hemisuccinate (CHEMS), phosphate-buffered saline (PBS), sodium hydroxide, 4-(2-hydroxyethyl)piperazine-1-ethane sulfonic acid (HEPES), ammonium sulfate, and sodium bicarbonate were obtained from Sigma-Aldrich (St. Louis, MI, USA). Polysorbate 80 (Tween™ 80) was provided by Croda Inc (Edison, NJ, USA). Chloroform and dimethylsulfoxide (DMSO) were provided from Synth (São Paulo, Brazil). Sodium chloride and HPLC-grade methanol were purchased from Merck (Frankfurt, Germany). Doxorubicin hydrochloride (DOX) was purchased from ACIC Chemicals (Brantford, ON, Canada). SIM was acquired from Fagron (São Paulo, Brazil) with a purity greater than 98.0%. The water used in the experiments was purified using the Milli-Q® distillation and deionization equipment (Millipore, MA, USA). The other substances used were of analytical grade.
Human breast tumor cell lines (MDA-MB-231, MCF-7, SK-BR-3) were purchased by American Type Culture Collection (Manassas, VA, USA). Culture media (Dulbecco’s Modified Eagle’s Medium, DMEM; Minimum Essential Medium, MEM and McCoy), Fetal bovine serum (FBS), penicillin, and streptomycin were obtained from Gibco Life Technologies (Carlsbad, USA). Sulforhodamine B (SRB), tris(hydroxymethyl)aminomethane (Tris base), and trypsin were obtained from Sigma-Aldrich (St. Louis, MI, USA) and Hoechst 33258 (Thermo Fisher Scientific—Waltham, MA, USA).
Human breast tumor cell lines (MDA-MB-231, MCF-7, SK-BR-3) were purchased by American Type Culture Collection (Manassas, VA, USA). Culture media (Dulbecco’s Modified Eagle’s Medium, DMEM; Minimum Essential Medium, MEM and McCoy), Fetal bovine serum (FBS), penicillin, and streptomycin were obtained from Gibco Life Technologies (Carlsbad, USA). Sulforhodamine B (SRB), tris(hydroxymethyl)aminomethane (Tris base), and trypsin were obtained from Sigma-Aldrich (St. Louis, MI, USA) and Hoechst 33258 (Thermo Fisher Scientific—Waltham, MA, USA).
1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-methoxy-poly(ethylene glycol 2000)
Acic
Bicarbonate, Sodium
Cell Lines
Chloroform
cholesterol-hemisuccinate
croda
dioleoyl cephalin
Distillation
Eagle
ethane sulfonate
Fetal Bovine Serum
HEPES
High-Performance Liquid Chromatographies
Hoechst 33258
Hydrochloride, Doxorubicin
lissamine rhodamine B
Mammary Neoplasms, Human
Methanol
methylamine
Penicillins
Phosphates
phosphoethanolamine
Piperazine
polyethylene glycol 2000
Polysorbate 80
Saline Solution
Sodium Chloride
Sodium Hydroxide
Streptomycin
Sulfate, Ammonium
Sulfoxide, Dimethyl
Tromethamine
Trypsin
Tween 80
Cell Culture. Tumor cell lines from human mammary adenocarcinoma MCF-7 and human glioblastoma T98G were cultured in IMDM and EMEM medium, respectively, supplemented with 10% fetal bovine serum (FBS) (Invitrogen), penicillin (100 units/mL), and streptomycin (100 μg/mL) at 37 °C with 5% CO2 in a humid atmosphere.
The inhibition of cell proliferation was determined using a colorimetric assay based on the cleavage of MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) by mitochondrial dehydrogenases in viable cells, leading to formazan formation [67 (link)]. Briefly, exponentially growing cells were plated in a 96-well plate (2000 cells per well). After overnight incubation, the cells were treated with media containing albumin conjugates. The solutions of conjugates were applied into the media for 72 h at 37 °C. A 10 μL aliquot of MTT solution (25 mg/mL in PBS) was added to each well, and the plates were incubated at 37 °C for 3 h. The medium was removed, and the dark blue crystals of formazan were dissolved in 0.1 mL of isopropanol. The absorbance at 570 nm (peak) and 620 nm (baseline) was read using a microplate reader, Multiscan EX (Thermo Electron Corporation). The results were expressed as a percentage of the control values. All values in the present study are given as the mean ± standard deviation (SD) values, and all measurements were repeated three times.
The inhibition of cell proliferation was determined using a colorimetric assay based on the cleavage of MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) by mitochondrial dehydrogenases in viable cells, leading to formazan formation [67 (link)]. Briefly, exponentially growing cells were plated in a 96-well plate (2000 cells per well). After overnight incubation, the cells were treated with media containing albumin conjugates. The solutions of conjugates were applied into the media for 72 h at 37 °C. A 10 μL aliquot of MTT solution (25 mg/mL in PBS) was added to each well, and the plates were incubated at 37 °C for 3 h. The medium was removed, and the dark blue crystals of formazan were dissolved in 0.1 mL of isopropanol. The absorbance at 570 nm (peak) and 620 nm (baseline) was read using a microplate reader, Multiscan EX (Thermo Electron Corporation). The results were expressed as a percentage of the control values. All values in the present study are given as the mean ± standard deviation (SD) values, and all measurements were repeated three times.
Adenocarcinoma
Albumins
Atmosphere
Biological Assay
Bromides
Cell Culture Techniques
Cell Lines
Cell Proliferation
Cells
Colorimetry
Cytokinesis
Electrons
Fetal Bovine Serum
Formazans
Glioblastoma
Homo sapiens
Isopropyl Alcohol
Mammary Neoplasms, Human
Mitochondrial Inheritance
Oxidoreductase
Penicillins
Psychological Inhibition
Streptomycin
Top products related to «Mammary Neoplasms, Human»
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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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MDA-MB-231 is a cell line derived from a human breast adenocarcinoma. This cell line is commonly used in cancer research and is known for its aggressive and metastatic properties.
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MCF-7 is a cell line derived from human breast adenocarcinoma. It is an adherent epithelial cell line that can be used for in vitro studies.
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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.
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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.
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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.
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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.
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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.
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SKBR3 is a cell line derived from a breast adenocarcinoma. It is a commonly used model for breast cancer research.
Sourced in United States, Germany, United Kingdom, Japan, Sweden
The BT474 is a cell line derived from a human breast carcinoma. It is a well-characterized model for studying breast cancer biology and is commonly used in research and drug development.
More about "Mammary Neoplasms, Human"
Mammary Neoplasms, also known as breast tumors or breast cancers, are abnormal growths that develop in the breast tissue.
These can range from benign conditions like fibroadenomas to malignant cancers like breast carcinoma.
Proper identification and classification of these neoplasms is crucial for effective treatment and management.
Breast cancer cell lines like MDA-MB-231, MCF-7, SKBR3, and BT474 are commonly used in research to study mammary neoplasms.
These cell lines are typically cultured in media like RPMI 1640 or DMEM, often supplemented with penicillin and streptomycin antibiotics.
Understanding the complex biology and behavior of mammary neoplasms is an active area of research.
Discovering optimized research protocols that enhance reproducibility and accuracy is key to advancing the field.
PubCompare.ai offers a powerful platform to help researchers find the best protocols from literature, pre-prints, and patents through intelligent comparisons, enabling them to achieve reliable results in the study of these conditions.
These can range from benign conditions like fibroadenomas to malignant cancers like breast carcinoma.
Proper identification and classification of these neoplasms is crucial for effective treatment and management.
Breast cancer cell lines like MDA-MB-231, MCF-7, SKBR3, and BT474 are commonly used in research to study mammary neoplasms.
These cell lines are typically cultured in media like RPMI 1640 or DMEM, often supplemented with penicillin and streptomycin antibiotics.
Understanding the complex biology and behavior of mammary neoplasms is an active area of research.
Discovering optimized research protocols that enhance reproducibility and accuracy is key to advancing the field.
PubCompare.ai offers a powerful platform to help researchers find the best protocols from literature, pre-prints, and patents through intelligent comparisons, enabling them to achieve reliable results in the study of these conditions.