Tag: MCF10A

Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction | Nucleic Acids Research

Abstract RNA In situ imaging through DNA self-assembly is advantaged in illustrating its structures and functions with high-resolution, while the limited reaction efficiency and time-consuming operation hinder its clinical application. Here, we first proposed a new strand displacement reaction (SDR) model (Cas12a thrusting SDR, CtSDR), in which Cas12a could overcome…

Continue Reading Rapid in situ RNA imaging based on Cas12a thrusting strand displacement reaction | Nucleic Acids Research

capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

Cell culture All cell lines were grown in 6 cm dishes at 37 °C in a 5% CO2 incubator. The K562, MDA-MB-231 and HCT 116 cell lines were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics (pen-strep). NCM460 cells were cultured in RPMI 1640 medium supplemented…

Continue Reading capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements

Problem while working with sequenza

Problem while working with sequenza – Chromosomes out of order 1 Hi, I’m trying to work with sequenza in order to calculate HRD score of a sample using WES data. When I run sequenza, I get a message saying that “chromosomes are out of order”, and I don’t know how…

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Error using sequenza-utils with WES

Hi! I’m trying to calculate the homologous recombination deficiency score of a cell line (MDA-MB-231) using whole exome sequencing data. To do this, I pretend to use the scarHRD package in R, but I first need a “*.seqz.gz” archive, which is made using sequenza-utils, but I have the following error…

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Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model

Cell culture Mammary epithelial, non-transformed MCF10A cells (ATCC CRL-10317) were grown in DMEM:F-12 (Dulbecco’s Modified Eagle Medium:Nutrient Mixture F-12) (1:1) medium (Gibco, 11330057) supplemented with 5% Horse Serum (HS), 2 mM l-glutamine and 1% penicillin/streptomycin (Sigma-Aldrich, G6784), 10 µg/ml insulin (Sigma-Aldrich, I9278) and 0.5 µg/ml hydrocortisone (Sigma-Aldrich, H0888). Human Epidermal Growth Factor (hEGF,…

Continue Reading Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model

Ras-induced EpCAM and several other membrane proteins.

A. Microarray data (GSE12777) for 51 breast cancer cell line was analyzed using Gene-E software. E-cadherin correlated 121 genes are enriched in first step followed by EpCAM close (correlated). These genes are presented in normal and Ras-transduced cells (right panel). B-C. Two independent microarray data sets from MCF10A and Ras-transduced…

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PRR15 deficiency facilitates malignant progression by mediating PI3K/Akt signaling and predicts clinical prognosis in triple-negative rather than non-triple-negative breast cancer

Cell culture and reagents Non-cancerous mammary epithelium cell (MCF10A), breast cancer cells including luminal (MCF7, MDA-MB-361, T47D, and BT474), HER2amp (SKBR3), and triple-negative (MDA-MB-231, CAL51, BT20, and MDA-MB-468) subtypes, as well as human embryonic kidney 293T (HEK-293T) cells, were purchased from the American Type Culture Collection (Manassas, VA, USA). MDA-MB-231,…

Continue Reading PRR15 deficiency facilitates malignant progression by mediating PI3K/Akt signaling and predicts clinical prognosis in triple-negative rather than non-triple-negative breast cancer

Chromosomal instability as central hallmark of Breast Cancer

Introduction In recent years, CIN has gained great importance due to its implications for both, the diagnosis and prognosis of cancer. Recent studies have suggested that both CIN and clonal heterogeneity, influence cancer progression, aggressiveness, prognosis, and response to therapy.1–4 The above because both, CIN and clonal heterogeneity, lead to…

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ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation

ANKLE1 is the causal gene for breast and ovarian cancer risk in the chr19p13.1 region Expression quantitative trait loci (eQTL) data have revolutionized how geneticists identify candidate causal genes from genome-wide association study (GWAS) loci. We integrated the most recent meta-analysis of breast cancer GWAS10 and Genotype-Tissue Expression (GTEx) project…

Continue Reading ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation

MYO10 drives genomic instability and inflammation in cancer

INTRODUCTION Genomic instability often refers to the existence of a variety of DNA alterations, ranging from single nucleotide changes (such as base substitution, deletion, and insertion) to chromosomal rearrangements (e.g., gain or loss of a segment or the whole chromosome) (1). Loss of genome stability can lead to early onset…

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