12312 results for "cancer rna-seq"

in 18.25 milliseconds.

• Determining genome-wide binding of ETS2 by CUT&RUN in primary human macrophages

  This dataset consists of sequencing data from an ETS2 CUT&RUN experiment in primary inflammatory (TPP) macrophages (n = 2). Pre-cultured TPP macrophages were harvested and processed immediately using the CUT&RUN Assay kit (Cell Signaling) according to the manufacturer’s instructions with the following modifications (essentially, avoiding the use of ConA-coated beads). Anti-ETS2 (ThermoFisher) or IgG control (Cell Signaling) antibodies were used for targeted digestion of chromatin. For each donor, 5x10^5 cells were pelleted, washed in Wash Buffer, and resuspended in Antibody Binding buffer. Cells were incubated with antibodies (1:100 dilution for anti-ETS2) for 2h at 4°C. After washing in Digitonin Buffer, cells were incubated with pA/G-MNase for 1h at 4°C. Cells were washed twice in Digitonin Buffer, resuspended in the same buffer and cooled for 5 minutes on ice. Calcium chloride was added to activate pA/G-MNase digestion and cells were incubated for 30 minutes at 4°C before Stop Buffer was added, and cells were incubated for 10 min at 37°C to release cleaved chromatin fragments. Supernatants were collected by centrifugation and DNA extracted using DNA Purification Buffers and Spin Columns (Cell Signaling). Library preparation was performed according to a protocols.IO protocol (dx.doi.org/10.17504/protocols.io.bagaibse) using the NEBNext Ultra II DNA Library Prep Kit. Size selection was performed using AMPure XP beads (Beckman Coulter) and fragment sizes were determined using an Agilent 2100 Bioanalyzer (High Sensitivity DNA kit). Equimolar pools of indexed libraries were sequenced on an Illumina NovaSeq 6000 (100bp PE reads). Raw data are provided as 100 bp paired-end Illumina reads.

  Dataset EGAD00001011349

• Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma

  This study expands our understanding of aggressive chromophobe renal cell carcinoma (ChRCC), provides insight into molecular mechanisms of tumor progression, and informs pathologic classification and diagnostics. Tumor and adjacent normal samples were collected from 11 patients treated in affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital. Seven of the eleven patients consented to depositing their genomic data to public repository.

  Study EGAS50000000287

• Inherited damaging mutations in immune-related genes favour the development of genetically heterogeneous synchronous colorectal cancer.

  Synchronous colorectal cancers are physically separated tumours that develop simultaneously in the intestine. To understand how common genetic and environmental backgrounds influence the development of multiple tumours, we conduct a genome-wide comparative analysis of somatic alterations of 20 syCRCs from 10 patients. We show that syCRCs have independent genetic origins, acquire discordant somatic alterations, and follow different clonal developments.

  Study EGAS00001001461

• Pseudotime_ordering_of_cell_cycle_state

  We will be using G&T method to sequence single cell genome and transcriptome derived from FS13B iPSCs cell line. The cell cycle state of each of the single cells is known. Hence, we will be analysing the genome and transcriptome of single cells from each of the cell cycle state to generate a copy number profile and transcriptome profile per given cell cycle stage: G1, S, G2, S.

  Study EGAS00001003293

• Whole-exome sequencing (WES) data of papillary thyroid cancer and adjacent normal tissues

  High-coverage WES sequencing of DNA samples from 50 PTCs was performed on the Illumina HiSeq 2500 or 4000 System

  Dataset EGAD00001003262

• Whole Genome Sequencing of Liver Cancers

  Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogeneous cellular processes. With a diversity of risk factors including viral infection, carcinogenic exposures and metabolic diseases, liver cancer is an ideal model to study these interactions. Whole genome sequencing of liver tumors identified 10 mutational signatures showing distinct relationships with environmental exposures, replication and transcription. Transcription-coupled damage was specifically associated with the liver-specific signature 16 and alcohol intake. Flood of indels were identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture revealed mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin-B1 signature in African migrants. These findings shed new light on the natural history of liver cancers.

  Dataset EGAD00001003281

• Genetic characterization patients affected by Cancer of Unknown Primary

  The genetic changes sustaining the development of human Cancers of Unknown Primary (CUP) remain elusive. Here we report the genomic profiling of 14 rigorously selected CUP samples. Although no specific recurring mutation in known driver genes was found, a comparison of the mutational landscape of CUPs with that of most other human tumor types revealed a consistent change in diverse genes belonging to the axon guidance KEGG pathway.

  Study EGAS00001006621

• RNAseq - Colorectal organoids and tumoroids (2015-08-05)

  Transcriptome sequencing of tumour tissue, adjacent normal tissue and derived organoids/tumoroids from colorectal cancer. This dataset contains all the data available for this study on 2015-08-05.

  Dataset EGAD00001001459

• BIG MS Pilot

  Testing logistics and infrastructure of molecular screening program. Core biopsies taken from invasive recurrent or metastatic breast cancer to evaluate and identify molecular traits rendering them suitable for clinical trials

  Dataset EGAD00001000870

• Spatial whole exome sequencing of metastatic melanoma

  We performed whole exome sequencing of 8 samples derived from a patient with metastatic melanoma. These represent six different regions of a metastatic melanoma biopsy that was treated with anti-PD-1 inhibitor, one pre-treatment biopsy that was treatment naive and one post-PD-1 inhibitor treated lesion. Exome sequencing data was generated using methods as previously described, including library preparation using the Agilent SureSelect XT Target Enrichment protocol (#5190-8646) prior to sequencing on an Illumina HiSeq 2000/2500 v3 system using 76bp paired-end reads. Raw sequencing data was then processed using Saturn V, the next generation sequencing data processing and analysis pipeline developed by the Department of Genomic Medicine at the UT MD Anderson Cancer Center.

  Dataset EGAD00001005819