9931 results for "cancer rna-seq"

in 49.45 milliseconds.

• Reference epigenome Pancreas-Islet06 miRNA-Seq data generated from KEP study

  Pancreas-Islet06 miRNA-Seq single end data

  Dataset EGAD00001007187

• Reference epigenome Pancreas-Islet07 miRNA-Seq data generated from KEP study

  Pancreas-Islet07 miRNA-Seq single end data

  Dataset EGAD00001007188

• Reference epigenome Pancreas-Islet08 miRNA-Seq data generated from KEP study

  Pancreas-Islet08 miRNA-Seq single end data

  Dataset EGAD00001007189

• Reference epigenome Fat-adipocyte03 miRNA-Seq data generated from KEP study

  Fat-adipocyte03 miRNA-Seq single end data

  Dataset EGAD00001007190

• Reference epigenome Fat-adipocyte04 miRNA-Seq data generated from KEP study

  Fat-adipocyte04 miRNA-Seq single end data

  Dataset EGAD00001007191

• Reference epigenome Fat-adipocyte05 miRNA-Seq data generated from KEP study

  Fat-adipocyte05 miRNA-Seq single end data

  Dataset EGAD00001007192

• scRNA-seq of placental immune cells

  scRNA-seq analysis of 384 placental immune cells

  Dataset EGAD00001010040

• Reference epigenome Islet-derived_MSC08 mRNA-Seq data generated from KEP study

  Islet-derived_MSC08 mRNA-Seq paired end data

  Dataset EGAD00001007879

• Reference epigenome Islet-derived_iPSC04 mRNA-Seq data generated from KEP study

  Islet-derived_iPSC04 mRNA-Seq paired end data

  Dataset EGAD00001007880

• Reference epigenome Islet-derived_MSC06 miRNA-Seq data generated from KEP study

  Islet-derived_MSC06 miRNA-Seq single end data

  Dataset EGAD00001007881

• Reference epigenome Islet-derived_MSC08 miRNA-Seq data generated from KEP study

  Islet-derived_MSC08 miRNA-Seq single end data

  Dataset EGAD00001007882

• Reference epigenome Islet-derived_iPSC04 miRNA-Seq data generated from KEP study

  Islet-derived_iPSC04 miRNA-Seq single end data

  Dataset EGAD00001007883

• STAG1-ChIP-Seq of STAG2-mutated and cohesin wildtype adult AMLs

  ChIPseq targeting the cohesin subunit STAG1 in STAG2-mutated AMLs or cohesin wildtype AMLs

  Dataset EGAD00001011206

• Genomic Characterization of Duke Melanoma Brain Metastases

  Previous work has shown that melanoma brain metastases (MBM) have a unique molecular profile compared to extracranial metastases (ECM). Description of the biology of MBM and associations between biological features and clinical outcomes will facilitate the design of rational therapies for patients with MBM. To better characterize the molecular profile of MBM, we conducted whole exome sequencing (WES) and total RNA sequencing on MBM tissues obtained from an independent cohort of 14 patients from Duke University Medical Center. This cohort adds valuable patient samples to the field and enables strengthened investigation of somatic mutations and gene expression profiles within and between cohorts. The mutational landscape and gene expression of MBM from the Duke cohort resembled those previously reported in a previously published dataset of WES and RNA sequencing in MBM and matched ECM tissues from UT MD Anderson Cancer Center (Fischer et al., 2019 30787016). Duke MBM demonstrated similar rates of mutations in genes associated with melanoma, including BRAF, NRAS, and PTEN, as the MD Anderson cohort. Immune populations in MBM were similar between Duke and MD Anderson MBM, though Duke samples demonstrated more resting CD4+ memory T cells. The ratio of M2 to M1 macrophages in the Duke cohort was similar to that of the MD Anderson cohort. In MBM, a higher M2:M1 ratio may contribute to an immune-suppressive tumor microenvironment. Sequencing data and sample attributes from MBM tissues obtained from 14 patients from Duke University Medical Center will be available through dbGaP.

  Study phs003009

• Dataset for upper_gastrointestinal_tumor-RNA

  Rare cancer sequencing data of 44 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008853

• Tumor-derived cell lines as pharmacogenomic models to predict therapeutic vulnerabilities in hepatocellular carcinoma

  Hepatocellular carcinoma (HCC) is a heterogeneous aggressive malignancy with low efficacy of current therapies at advanced stages. We integrated molecular and pharmacological profiling of a large panel of liver cancer cell lines (LCCL) to assess their clinical relevance as HCC preclinical models and identify new effective therapies and biomarkers of response. Here, we performed multi-omic analysis including whole-exome, RNA and microRNA sequencing in a series 34 LCCL. Molecular profiles of LCCL and primary HCC were compared and we searched for molecular features associated with drug response. Our panel of LCCL faithfully recapitulated the most aggressive molecular “proliferation class” of HCC.

  Dataset EGAD00001004938

• Spatial transcriptomic data of breast cancer

  Fastq files from spatial transcriptomic of breast cancer coming from 8 Breast cancer sections. Sample preparation: frozen BC samples were chosen based on tissue structure and RNA quality (RIN > 8). The “Visium Spatial Tissue Optimization Slide and Reagent Kit” (10X Genomics; #PN-1000193) was then used to optimize permeabilization conditions for BC tissues. Briefly, sections were fixed, stained and then permeabilized at different time points to capture mRNA, and the reverse transcription was performed to generate fluorescently labeled cDNA. The permeabilization time that resulted in the highest fluorescence signal with the lowest background diffusion was chosen. The best permeabilization time for BC tissue was 18 min. Cryostat sections of 10 μm of thickness were cut and placed on Visium Spatial Gene Expression slides (10X Genomics, PN-1000184). The slide was incubated for 1 min at 37°C, then fixed with methanol for 30 min at -20°C followed by Hematoxylin and Eosin (H&E) staining and images were taken under a high-resolution microscope. After imaging, the coverslip was detached by holding the slide in water and the slide was mounted in a plastic slide cassette. The spatial gene expression process, including tissue permeabilization, second strand synthesis and cDNA amplification, was performed according to the manufacturer’s instructions (10X Genomics; #CG000239). cDNA quality was next assessed using Agilent High sensitivity DNA Kit (Agilent, #5067-4626). The spatial gene libraries were constructed using Visium Spatial Library Construction Kit (10X Genomics, PN-1000184).

  Dataset EGAD50000000322

• Dataset for B-ALL scRNA-seq

  10x Genomics 5' library scRNA-seq data for 85 B-ALL patients with different subtypes

  Dataset EGAD00001011327

• McGill EMC Release 4 for assay "Bisulfite-seq"

  McGill EMC Release 4 for assay "Bisulfite-seq": Methylation profiling by high-throughput sequencing

  Dataset EGAD00001001289

• McGill EMC Release 4 for assay "mRNA-seq"

  McGill EMC Release 4 for assay "mRNA-seq": Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001001291

• McGill EMC Release 4 for assay "smRNA-seq"

  McGill EMC Release 4 for assay "smRNA-seq": Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001001292

• Reference epigenome CKD24_C_Podo_mRNA-Seq data generated from KEP study

  A CKD24_C_Podo_mRNA-Seq paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003482

• Reference epigenome CKD25_C_Podo_mRNA-Seq data generated from KEP study

  A CKD25_C_Podo_mRNA-Seq paired end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003483

• Reference epigenome OB57_D_PreA_mRNA-Seq data generated from KEP study

  A OB57_D_PreA_mRNA-Seq paired end data for Preadipocyte(fat)

  Dataset EGAD00001003487

• Reference epigenome OB56_N_PreA_smRNA-Seq data generated from KEP study

  A OB56_N_PreA_smRNA-Seq single end data for Preadipocytes(fat)

  Dataset EGAD00001003495

• Reference epigenome OB57_D_PreA_smRNA-Seq data generated from KEP study

  A OB57_D_PreA_smRNA-Seq single end data for Preadipocyte(fat)

  Dataset EGAD00001003496

• Reference epigenome CKD24_C_Podo_smRNA-Seq data generated from KEP study

  A CKD24_C_Podo_smRNA-Seq single end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003498

• Reference epigenome CKD25_C_Podo_smRNA-Seq data generated from KEP study

  A CKD25_C_Podo_smRNA-Seq single end data for Podocytes(CD90(-) Podocalyxin(+), kidney)

  Dataset EGAD00001003499

• Histone marks

  EZH2, H3K4me3, H3K27ac and H3K27me3 ChIP-seq data consisting of fastq single-end reads from peripheral blood CLL cells

  Dataset EGAD00001004063

• Reference epigenome Fat-adipocyte03 mRNA-Seq data generated from KEP study

  Fat-adipocyte03 mRNA-Seq paired end data

  Dataset EGAD00001007157

• Reference epigenome Fat-adipocyte04 mRNA-Seq data generated from KEP study

  Fat-adipocyte04 mRNA-Seq paired end data

  Dataset EGAD00001007158

• Reference epigenome Fat-adipocyte05 mRNA-Seq data generated from KEP study

  Fat-adipocyte05 mRNA-Seq paired end data

  Dataset EGAD00001007159

• Reference epigenome Pancreas-Islet06 mRNA-Seq data generated from KEP study

  Pancreas-Islet06 mRNA-Seq paired end data

  Dataset EGAD00001007166

• Reference epigenome Pancreas-Islet07 mRNA-Seq data generated from KEP study

  Pancreas-Islet07 mRNA-Seq paired end data

  Dataset EGAD00001007167

• Reference epigenome Pancreas-Islet08 mRNA-Seq data generated from KEP study

  Pancreas-Islet08 mRNA-Seq paired end data

  Dataset EGAD00001007168

• Reference epigenome SMC01 h3k4me3 ChIP-Seq data generated from KEP study

  SMC01 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007311

• Reference epigenome SMC05 h3k9me3 ChIP-Seq data generated from KEP study

  SMC05 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007336

• Reference epigenome ADMSC05 h3k27me3 ChIP-Seq data generated from KEP study

  ADMSC05 h3k27me3 ChIP-Seq paired end data

  Dataset EGAD00001007375

• oxBS-seq for APL

  Oxidative bisulfite sequencing (oxBS-Seq) for APL

  Dataset EGAD00001008135

• Single-cell DNA-seq

  Single-cell DNA sequencing (scDNA-seq) data.

  Dataset EGAD00001008779

• Reference epigenome Islet-derived_MSC06 mRNA-Seq data generated from KEP study

  Islet-derived_MSC06 mRNA-Seq paired end data

  Dataset EGAD00001007878

• CITE-seq raw count matrix

  Raw count matrix for CITE-seq data of PBMC collected from 113 patients.

  Dataset EGAD50000000141

• Raw count matrix scRNA-seq

  Raw count matrix for scRNA-seq data of PBMC collected from 113 patients.

  Dataset EGAD50000000142

• Paired-end ATAC-seq analysis of the 3D spatially mapped GBM samples.

  Dataset contains 70 paired-end ATAC-seq samples from 8 patients.

  Dataset EGAD00001010311

• BLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples

  BLLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001001596

• H3K27ac ChIP-seq of human acute leukemias and healthy donors

  H3K27ac ChIP-seq of 79 primary samples derived from human acute leukemias, namely AML, T-ALL and mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, 4 samples derived from CD34+ cord blood cells of healthy donors were included.

  Dataset EGAD00001011060

• Reference epigenome SMC01_smRNA-Seq data generated from KEP study

  A SMC01_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003858

• Reference epigenome SMC02_smRNA-Seq data generated from KEP study

  A SMC02_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003859

• Reference epigenome SMC03_smRNA-Seq data generated from KEP study

  A SMC03_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003860

• Reference epigenome SMC04_smRNA-Seq data generated from KEP study

  A SMC04_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003861

• Reference epigenome SMC05_smRNA-Seq data generated from KEP study

  A SMC05_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003862

• Reference epigenome SMC06_smRNA-Seq data generated from KEP study

  A SMC06_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003863

• Reference epigenome SMC07_smRNA-Seq data generated from KEP study

  A SMC07_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003864

• Reference epigenome SMC08_smRNA-Seq data generated from KEP study

  A SMC08_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003865

• Reference epigenome SMC09_smRNA-Seq data generated from KEP study

  A SMC09_smRNA-Seq single end data for skeletal muscle cells

  Dataset EGAD00001003866

• ATAC-seq for placental and buffycoat cells.

  We performed ATAC-seq experiments using 2 placental samples and 2 buffycoat samples.

  Dataset EGAD00001004291

• ChIP-Seq files for RMS.

  ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".

  Dataset EGAD00001004312

• ChIP-Seq files for PCGP ATRX study

  ChIP-Seq files for PCGP ATRX study paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"

  Dataset EGAD00001004429

• Reference epigenome KNIH007 mRNA-seq data generated from KEP study

  A KNIH007 mRNA-seq paired end data for adipocytes

  Dataset EGAD00001002173

• Reference epigenome KNIH008 mRNA-seq data generated from KEP study

  A KNIH008 mRNA-seq paired end data for adipocytes

  Dataset EGAD00001002174

• Reference epigenome KNIH009 mRNA-seq data generated from KEP study

  A KNIH009 mRNA-seq paired end data for preadipocytes

  Dataset EGAD00001002175

• Reference epigenome KNIH007 miRNA-seq data generated from KEP study

  A KNIH007 miRNA-seq single end data for adipocytes

  Dataset EGAD00001002766

• Reference epigenome KNIH008 miRNA-seq data generated from KEP study

  A KNIH008 miRNA-seq single end data for adipocytes

  Dataset EGAD00001002767

• Reference epigenome KNIH009 miRNA-seq data generated from KEP study

  A KNIH009 miRNA-seq single end data for preadipocytes

  Dataset EGAD00001002768

• ChIP-Seq files for RMS.

  ChIP-Seq files accompanying the paper titled "Identification of Therapeutic Targets in Rhabdomyosarcoma Through Integrated Genomic, Epigenomic, and Proteomic Analyses".

  Dataset EGAD00001006398

• Reference epigenome Islet-derived-MSC01 miRNA-Seq data generated from KEP study

  Islet-derived-MSC01 miRNA-Seq single end data

  Dataset EGAD00001007181

• Reference epigenome Islet-derived-MSC02 miRNA-Seq data generated from KEP study

  Islet-derived-MSC02 miRNA-Seq single end data

  Dataset EGAD00001007182

• Reference epigenome Islet-derived-MSC03 miRNA-Seq data generated from KEP study

  Islet-derived-MSC03 miRNA-Seq single end data

  Dataset EGAD00001007183

• Reference epigenome Islet-derived-MSC04 miRNA-Seq data generated from KEP study

  Islet-derived-MSC04 miRNA-Seq single end data

  Dataset EGAD00001007184

• Reference epigenome Islet-derived-iPSC01 miRNA-Seq data generated from KEP study

  Islet-derived-iPSC01 miRNA-Seq single end data

  Dataset EGAD00001007185

• Reference epigenome Islet-derived-iPSC02 miRNA-Seq data generated from KEP study

  Islet-derived-iPSC02 miRNA-Seq single end data

  Dataset EGAD00001007186

• Reference epigenome SMC01 h3k27ac ChIP-Seq data generated from KEP study

  SMC01 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007308

• Reference epigenome SMC01 h3k36me3 ChIP-Seq data generated from KEP study

  SMC01 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007309

• Reference epigenome SMC01 h3k4me1 ChIP-Seq data generated from KEP study

  SMC01 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007310

• Reference epigenome SMC01 h3k9me3 ChIP-Seq data generated from KEP study

  SMC01 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007312

• Reference epigenome SMC01 input ChIP-Seq data generated from KEP study

  SMC01 input ChIP-Seq paired end data

  Dataset EGAD00001007313

• Reference epigenome SMC02 h3k27ac ChIP-Seq data generated from KEP study

  SMC02 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007314

• Reference epigenome SMC02 h3k36me3 ChIP-Seq data generated from KEP study

  SMC02 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007315

• Reference epigenome SMC02 h3k4me1 ChIP-Seq data generated from KEP study

  SMC02 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007316

• Reference epigenome SMC02 h3k4me3 ChIP-Seq data generated from KEP study

  SMC02 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007317

• Reference epigenome SMC02 h3k9me3 ChIP-Seq data generated from KEP study

  SMC02 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007318

• Reference epigenome SMC02 input ChIP-Seq data generated from KEP study

  SMC02 input ChIP-Seq paired end data

  Dataset EGAD00001007319

• Reference epigenome SMC03 h3k27ac ChIP-Seq data generated from KEP study

  SMC03 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007320

• Reference epigenome SMC03 h3k36me3 ChIP-Seq data generated from KEP study

  SMC03 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007321

• Reference epigenome SMC03 h3k4me1 ChIP-Seq data generated from KEP study

  SMC03 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007322

• Reference epigenome SMC03 h3k4me3 ChIP-Seq data generated from KEP study

  SMC03 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007323

• Reference epigenome SMC03 h3k9me3 ChIP-Seq data generated from KEP study

  SMC03 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007324

• Reference epigenome SMC03 input ChIP-Seq data generated from KEP study

  SMC03 input ChIP-Seq paired end data

  Dataset EGAD00001007325

• Reference epigenome SMC04 h3k27ac ChIP-Seq data generated from KEP study

  SMC04 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007326

• Reference epigenome SMC04 h3k36me3 ChIP-Seq data generated from KEP study

  SMC04 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007327

• Reference epigenome SMC04 h3k4me1 ChIP-Seq data generated from KEP study

  SMC04 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007328

• Reference epigenome SMC04 h3k4me3 ChIP-Seq data generated from KEP study

  SMC04 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007329

• Reference epigenome SMC04 h3k9me3 ChIP-Seq data generated from KEP study

  SMC04 h3k9me3 ChIP-Seq paired end data

  Dataset EGAD00001007330

• Reference epigenome SMC04 input ChIP-Seq data generated from KEP study

  SMC04 input ChIP-Seq paired end data

  Dataset EGAD00001007331

• Reference epigenome SMC05 h3k27ac ChIP-Seq data generated from KEP study

  SMC05 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007332

• Reference epigenome SMC05 h3k36me3 ChIP-Seq data generated from KEP study

  SMC05 h3k36me3 ChIP-Seq paired end data

  Dataset EGAD00001007333

• Reference epigenome SMC05 h3k4me1 ChIP-Seq data generated from KEP study

  SMC05 h3k4me1 ChIP-Seq paired end data

  Dataset EGAD00001007334

• Reference epigenome SMC05 h3k4me3 ChIP-Seq data generated from KEP study

  SMC05 h3k4me3 ChIP-Seq paired end data

  Dataset EGAD00001007335

• Reference epigenome SMC05 input ChIP-Seq data generated from KEP study

  SMC05 input ChIP-Seq paired end data

  Dataset EGAD00001007337

• Reference epigenome SMC07 h3k27ac ChIP-Seq data generated from KEP study

  SMC07 h3k27ac ChIP-Seq paired end data

  Dataset EGAD00001007338