Search Results - EGA European Genome-Phenome Archive

Single-cell RNA sequencing of breast cancer lung metastasis and adjacent normal tissue

This dataset contains single-cell RNA sequencing data from two samples: L1 (breast cancer metastasis to lung) and N3 (adjacent normal lung tissue) from a female patient. The samples were processed using 10X Chromium 3' technology and sequenced on Illumina NextSeq 500. This data supports the study "Endocrine therapy reprogramming of breast cancer facilitates metastatic escape via upregulation of P-Rex1/Rac1 signalling" which investigates how endocrine therapy reprograms breast cancer cells, leading to upregulation of P-Rex1/Rac1 signalling pathways that facilitate metastatic escape. The single-cell analysis reveals cellular reprogramming mechanisms in endocrine therapy-resistant breast cancer cells that form metastases in the lung.

Dataset EGAD00001015769

Resolution of tumour cell populations enhances specificity of treatment options for precision cancer medicine

This dataset comprises FASTQ files for single-cell RNA-seq and single-cell ATAC-seq data. These data were generated using 10x Genomics' multiome kit. In this cohort, there are 25 samples from 17 human cancer patients.

Dataset EGAD00001015782

MethylScan data of plasma samples

10ng from each cfDNA sample was used as the input material. For gDNA samples, 1.5-2ug each was first sonicated by Covaris R230 system (Woburn, MA). Next, size-selection with 0.8x-1.5x two-step Ampure XP beads was performed to enrich the 150-200bp fragments. 200ng of the size-selected gDNA was used as input material. The pre-capture library construction was performed with NEB UltraII DNA library prep kit for Illumina (Ipswich, MA) and the adapter was the methylated EM-seq adapter. Before the first PCR amplification, the gDNA samples were subjected to bisulfite conversion by QIAGEN Epitect kit, and cfDNA samples were subjected to enzymatic conversion by NEBNext enzymatic methyl-seq kit if the hybrid capture panel designed for converted DNA was used downstream. Twist panel hybrid capture was performed with their standard protocol (Twist Bioscience, South San Francisco, CA). The concentration of the post-capture library after the second PCR amplification was measured by Qubit 1xdsDNA HS kit (ThermoFisher, Waltham, MA). Their quality was examined by TBE-UREA PAGE and Bioanalyzer before sequencing. Libraries were then sequenced with 150bp paired-end reads on Illumina machines by Genewiz, Inc. (South Plainfield, NJ, USA). This dataset contains MethylScan data of the plasma samples from 248 noncancer individuals and 27 cancer patients (17 liver and 10 GI-tract cancers).

Dataset EGAD00001015815

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Single-cell RNA sequencing of breast cancer lung metastasis and adjacent normal tissue

Resolution of tumour cell populations enhances specificity of treatment options for precision cancer medicine

MethylScan data of plasma samples

Genome and transcriptome sequence data from a recurrent odontogenic ghost cell carcinoma of the left maxilla patient

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

Genome and transcriptome sequence data from a breast ductal carcinoma patient

Genome and transcriptome sequence data from a breast cancer patient

Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

Genome and transcriptome sequence data from a breast cancer patient

Genome and transcriptome sequence data from a ovarian cancer patient

Genome and transcriptome sequence data from a melanoma patient

Genome and transcriptome sequence data from a breast cancer patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a retroperitoneal leiomyosarcoma patient

Genome and transcriptome sequence data from a breast cancer patient

Genome and transcriptome sequence data from a primary unknown patient

Genome and transcriptome sequence data from a adenocarcinoma of the lung patient

Genome and transcriptome sequence data from a metastatic neuroendocrine carcinoma patient

Genome and transcriptome sequence data from a neuroendocrine tumor likely pancreatic origin patient

Genome and transcriptome sequence data from a pancreatic ductal adenocarcinoma patient

Genome and transcriptome sequence data from a medullary thyroid carcinoma patient

Genome and transcriptome sequence data from a pancreatic cancer (likely pnet) patient

Genome and transcriptome sequence data from a adenocarcinoma of unknown primary patient

Genome and transcriptome sequence data from a metastatic lymphoepithelial-like thymic carcinoma patient

Genome and transcriptome sequence data from a serous endometrial cancer patient