9295 results for "cancer rna-seq"

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• Results of scRNA-seq analysis of a PBMC collected from a male with a mosaic 45,X/48,XYYY karyotype

  Results of scRNA-seq analysis of a PBMC collected from a male with a mosaic 45,X/48,XYYY karyotype

  Dataset EGAD00001008645

• CLL ATAC Seq of Untreated and IBET762 treated samples

  CLL PBMC cells were isolated using ficoll gradient. They have been treated with IBET762 or DMSO as solvent control and ATAC Seq has been performed on them.

  Dataset EGAD00001008723

• CITE-seq

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell CITE-seq Experiments, as well as the demultiplexed cell-donor identities matrices which were generated with Vireo (Analysis).

  Dataset EGAD00001009820

• scRNA-seq dataset for AD and Pso patients

  This dataset contains scRNA-seq fastq files to the paper entitled "Single-cell profiles reveal distinctive immune response in atopic dermatitis in contrast to psoriasis". The details of experiment setup was described in the paper.

  Dataset EGAD00001010106

• Identifying Novel Small RNA Biomarkers Unique to Patients with Gastric Cancer

  The biomarker development study consisted of two parts: discovery and validation. The first part was the discovery and verification phase of biomarkers using two different platforms: transcriptomic and miRNA. The salivary transcriptomes of 63 GC samples and 31 non-GC controls were profiled using Affymetrix HG U133+2.0 microarrays (Affymetrix, Santa Clara, CA). The identified exRNA candidates were verified by quantitative real-time PCR (RT-qPCR) using all 94 of the original samples. In the discovery phase for the miRNA biomarkers, 10 early-stage GC samples and 10 non-GC controls were selected. The salivary miRNAs of these samples (n=20) were profiled using the TaqMan MicroRNA Array (Applied Biosystems, Foster City, CA). MicroRNA candidates were verified using TaqMan miRNA Assay (Thermo Scientific, Grand Island, NY). The second part of the study was to validate these verified exRNA biomarker candidates with exRNA samples extracted from an independent cohort of 100 GC and 100 non-GC saliva samples. The cohort was not balanced for demographics on gender and smoking history but more accurately reflected the diagnostic setting where our proposed final model could be implemented. Reprinted from "Li F, Yoshizawa MJ, Kim K, Kanjanapangka J, Grogan T, Wang X, Elashoff D, Ishikawa S, Chia D, Liao W, Akin D, Yan X, Lee M, Choi R, Kim S, Kang S, Bae J, Sohn T, Lee J, Choi M, Min B, Lee J, Kim J, Kim Y, Kim S, Wong D. (2018) Development and Validation of Salivary Extracellular RNA Biomarkers for Noninvasive Detection of Gastric Cancer. Clin Chem. PMID: 30097497 DOI: 10.1373/clinchem.2018.290569", with permission from American Association for Clinical Chemistry (United States).

  Study phs001767

• RNA Sequencing of Colorectal Liver Metastases

  Reverse-stranded paired-end 75 base-pair RNA sequencing libraries of 93 metastatic FFPE samples were constructed using Illumina Total RNA Stranded Kits. Ribosomal RNAs (rRNAs) were depleted by using the Ribo-Zero rRNA Removal Kit (Illumina). Libraries were sequenced on a HiSEQ2500 machine. Five samples were re-sequenced using paired-end 50 base-pair libraries due to the smaller insert sizes.

  Dataset EGAD00001004111

• Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing in Familial amyotrophic lateral sclerosis (ALS)

  To identify the genetic cause and modifiers of Familial amyotrophic lateral sclerosis (ALS), we performed Whole-exome-sequencing and Whole-genome-sequencing and RNA-sequencing of Familial amyotrophic lateral sclerosis (ALS) patients.

  Study JGAS000358

• The immunological characterization of expanded tumor-infiltrating lymphocytes in renal cell carcinoma patients

  In this study, we comprehensively characterized the non-expanded and expanded tumor-infiltrating lymphocytes (TILs) from treatment-naïve RCC patients, as well as the corresponding “young” TILs (pre-REP TILs) and “rapidly expanded” TILs (REP TILs) following a clinical-grade TIL production protocol. From our scRNA+TCRαβ-seq and TCRβ-seq analyses, we show that the REP protocol preferentially favors the expansion CD4+ T-cells that originate from small T-cell clones in the tumor microenvironment (TME), indicating that the large, exhausted T-cell clones in the tumor do not expand during the protocol. We further identified RCC-associated TCR motifs that were validated in multiple TCRαβ-seq and scRNA+TCRαβ-seq datasets, as well as quantified the RCC-associated TCRs from the REP protocol. Overall, the T-cells carrying the RCC-associated TCRs remained high in the tumors and corresponding pre-REP TILs, but the frequency was reduced in the REP TILs. Furthermore, the overall anti-viral TCRs remained low throughout the REP protocol. Our results provide an in-depth understanding of the origin, phenotype, and specificity of the TCRs in RCC TILs.

  Study EGAS00001006952

• Nanobody-Tethered Transposition Allows for Multifactorial Chromatin Profiling at Single-Cell Resolution

  Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods are unable to measure more than one aspect of chromatin state in a single experiment, limiting our ability to accurately measure chromatin states. Here we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), a new assay capable of measuring the genome-wide presence of multiple histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq utilizes recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk- and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and cells of the human immune system, demonstrating the high accuracy and sensitivity of the method. We further extend NTT-seq to enable simultaneous profiling of cell-surface protein expression alongside multimodal chromatin states to study cells of the immune system.

  Study phs003068

• Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts

  Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts

  Dataset EGAD00001001609