9296 results for "cancer rna-seq"

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• SF11949 scRNA-Seq primary oligodendroglioma G3 IDH1 Mutant Male

  SF11949 Primary oligodendroglioma G3 IDH1 Mutant. Male, 40 Single Cell RNA seq from primary astrocytoma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005397

• SF11979 scRNA-Seq Primary GBM IDHR132H Wild-type Female

  Single Cell Prmary high grade glioma IDHR132H Wild-type Female 76 Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005429

• Human data for chromatin accessibility (ATAC-Seq and scATAC-Seq) and transcriptome (RNA-Seq and scRNA-Seq) in eight B-cell precursors, from HSC to Naive B cells

  We generated paired transcriptomic (RNA-Seq) and chromatin accessibility (ATAC-Seq) profiles from 8 immune cell populations representing the early lymphoid hematopoietic differentiation stages along the B cell lineage: HSC, CLP, pro-B, pre-B, Immature B, Transitional B, Naive B CD5-, Naive B CD5+. Cell populations were isolated from healthy adult human bone marrow precursors and peripheral blood (n=13) following a predefined sorting strategy. For each donor, a subset of different cell type populations was obtained. Additionally, to explore the continuous dynamic of RNA and ATAC, we generated a single-cell sample of human CD34+ B cell precursors.

  Study EGAS00001007296

• WES and RNA-seq of triple-negative breast cancers from the MyBrCa cohort

  The dataset contains a genomics characterization of 35 triple-negative Asian breast tumours from the Malaysian Breast Cancer cohort. This includes whole-exome sequencing of tumour tissue at 80X, whole-exome sequencing of matched normal (blood) tissue at 40X, and RNA-seq of tumour tissue at 40X coverage (>15 million reads). Whole-exome libraries were prepared using the Nextera Rapid Capture Exome Kit; exome capture was performed in pools of 3 and subjected to paired end 75 sequencing on a NovaSeq 6000 platform. RNA libraries were prepared using the TruSeq Stranded Total RNA HT kit with Ribo-Zero Gold as per manufacturer’s instructions and also subjected to paired end 75 sequencing on a NovaSeq 6000 platform. Uploaded bam files have been mapped to the hs37d5 human genome and processed using the standard GATK pipelines. Paired clinical, demographic, genotyping, and overall survival data for these patients are available from the associated publications or by request.

  Dataset EGAD00001009311

• The Finland-United States Investigation of NIDDM Genetics (FUSION) Study - Islet Expression and Regulation by RNAseq and ATACseq

  This study evaluates gene expression and its regulation in human pancreatic islets, a tissue relevant in the study of genetic risk factors contributing to diabetes. We obtained islets from deceased donors and generated data from genome-wide SNP chip, bulk RNA-Seq, microRNA (miRNA)-Seq, whole genome sequence, DNA methylation (methyl)-Seq, transcription initiation profiles using cap analysis of gene expression (CAGE)-Seq, single cell RNA-seq, and single nuclei ATAC-seq. These data include ATAC-seq of two islet subjects, RNA-seq of 31 additional subjects, genome-wide chip genotypes, and imputed genotypes of the 33 subjects released with phs001188.v1. For genotyping, 500-1000 islet equivalents (IEQ) were cultured as in Gershengorn (Science, 2004, PMID: 15564314); genomic DNA isolated from islet cultures. For RNA analyses, 2500-5000 IEQ from each islet source were used for bulk or single-cell RNA isolation. Messenger RNA was isolated with trizol extraction and 12-plex libraries were generated using the Illumina TruSeq directional mRNA-seq library protocol. Bulk RNA sequencing was performed on HiSeq2000/HiSeq2500 sequencers using paired-end reads at the NIH Intramural Sequencing Center (NISC). miRNA libraries were prepared from total RNA from 68 samples, pooled and sequenced 50bp single-end reads on Illumina HiSeq2500. CAGE libraries were prepared from total RNA samples using the nAnT-iCAGE protocol at DNAFORM, Japan. CAGE libraries were sequenced at the NIH Intramural Sequencing Center (NISC) on the HiSeq2000 sequencer. Genotyping on the Illumina Omni2.5M array was performed at the NHGRI Genomics Core facility. Genotypes were imputed using the HRC.r1.1.2016 reference panel. In order to assess regions of open chromatin in islets, we performed bulk ATAC-seq on HiSeq2000 sequencers using paired-end reads at NISC. Single-nuclei ATAC-seq libraries were prepared using single-cell-combinatorial-indexing (sci-) ATAC-seq protocol and sequenced on Illumina NextSeq using paired-end reads. scRNA-seq libraries were generated using the 10X Genomics platform and sequenced on Illumina HiSeq3000 at the Genomics Technology Core of the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS). Greater than 90% of the loci associated with T2D through genome-wide association studies occur in non-coding regions, suggesting a strong regulatory component to disease susceptibility. Therefore, there is a critical need to understand the full spectrum of genetic variation and regulatory element usage in T2D-relevant tissues. To that end, this study contains whole genome sequence and whole genome bisulfite sequence, and/or Illumina MethylationEPIC Array data, providing a comprehensive survey of both individual genetic variation as well as DNA methylation across different tissues from multiple individuals. In addition, we carried out sequencing of single cell RNAs (two subjects) and single cell nuclei (one subject) to characterize gene expression and chromatin accessibility of islets.

  Study phs001188

• Dissecting Cell Composition and Drug Sensitivity in Human Adenoid Cystic Carcinomas (ACCs)

  The study reports the results of single-cell RNA sequencing (scRNA-seq), RNA sequencing (RNA-seq), and whole-exome sequencing (WES) experiments performed on malignant cells isolated by flow cytometry from seven patient-derived xenograft (PDX) lines established from human Adenoid Cystic Carcinomas (ACCs). Of these seven lines, five are characterized by well differentiated histology (ACCX5M1, ACCX6, ACCX14, ACCX22, SGTX6) and two by solid histology (ACCX9, ACCX11). Analysis by scRNA-seq of the well-differentiated PDX line ACCX22 led to identification of cell-surface markers (CD49f, KIT) that enabled the differential purification of the two major cellular components contained in well-differentiated ACCs: myoepithelial-like (CD49f-high/KIT-negative) and ductal-like (CD49f-low/KIT-positive) cells. The study reports the analysis by RNA-seq and WES of purified preparations of myoepithelial-like and ductal-like cells from well-differentiated PDX lines (ACCX5M1, ACCX6, ACCX14, ACCX22, SGTX6) and of ductal-like (CD49f-low/KIT-positive) cells from solid PDX lines (ACCX9, ACCX11).

  Study phs002764

• RNA Seq Data

  Human melanoma samples were collected pre, on, and progression on BRAF inhibitor therapy. RNA was extracted and run on RNA-seq. This has provided insights into different categories of BRAF inhibitor resistance mechanisms.

  Dataset EGAD00001001306

• RNA-Seq data of VDH15 cells with and without deletion of NSUN3

  paired RNA-Seq data of VDH15 cells with and without deletion of NSUN3. The 11 samples were sequenced on HiSeq 4000 and prepared with SmarTer low input RNA and Chip NEBNext kit.

  Dataset EGAD00001006560

• Single RNA-Seq of fCAB treated tRNAs from VDH01

  Single RNA-seq of fCAB treated tRNAs from vdh01 samples (5 replicates). tRNAs were extracted using Mirvana° Invitrogen kit. The samples were prepped with Il TruSeq Small RNA and sequenced on Illumina NextSeq550.

  Dataset EGAD00001008743

• RNA-seq colorectal adenomas NKI-AvL TGO series NGS-ProToCol

  The dataset "RNA-seq colorectal adenomas NKI-AvL TGO series NGS-ProToCol" includes 2 x 30 fastq files from paired-end total RNA sequencing on Illumina HiSeq2500 for 30 snap-frozen colorectal adenomas.

  Dataset EGAD00001004055