11931 results for "cancer rna-seq"

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• Childhood Cancer Data Initiative (CCDI): Single-Cell Atlas of NF1 Nerve Sheath Tumors

  The worst outcome of NF1 is the development of the aggressive and highly metastatic malignant peripheral nerve sheath tumors (MPNST), which transform from benign plexiform neurofibroma (PN) and lack effective treatment. In this study, we performed single-cell RNA sequencing of 63 clinically annotated NF1-associated peripheral nerve sheath tumors, including 24 PN, 34 premalignant atypical neurofibromas, and 5 MPNSTs. These results improve the ability of identifying high-risk neurofibromas and provide a unique opportunity for early detection of MPNST.

  Study phs003519

• The genetic analysis of circulating tumor DNA in blood of the digestive cancer patients to investigate the prognostic factors of metastasis and reccurence.

  A Darwinian evolutionary shift occurred early in the neutral evolution of advanced colorectal carcinoma (CRC) and copy number aberrations (CNA) were essential in the transition from adenoma to carcinoma. Subsequent to the primary evolution, we now focus on the evolutionary principle of the genome to foster postoperative recurrence of CRC. SO, We compared CNA, single nucleotide variance (SNV), RNA sequences between 8 primary and 11 metastatic sites from 10 CRCR cases.

  Study JGAS000221

• RNAseq SCLC Cell lines MYC

  RNAseq data set (Mollaoglu et al., MYC drives progression of small cell lung cancer to a variant neuroendocrine subtype with vulnerability to Aurora kinase inhibition) RNA isolation from primary tumors and healthy lungs was performed using RNeasy Mini Kit (Qiagen) with the standard protocol. RNA was subjected to library construction with the Illumina TruSeq Stranded mRNA Sample Preparation Kit (cat# RS-122-2101, RS-122-2102) according to manufacturer’s protocol. Chemically denatured sequencing libraries (25 pM) are applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot. Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001). Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002).

  Dataset EGAD00001003099

• DNA-Sequencing of Baseline Plasma From the Phase III Alliance A031201 Trial

  Liquid biopsy assays tailored for metastatic castration-resistant prostate cancer (mCRPC) patients are needed to identify molecular alterations and predict survival in the context of androgen receptor (AR) inhibitors. We developed a novel plasma cell-free DNA (cfDNA) sequencing assay to detect circulating tumor DNA (ctDNA) and alterations in key mCRPC driver genes, and tested associations with clinical features and survival outcomes in a phase III trial. cfDNA was isolated from evaluable baseline plasma specimens of untreated mCRPC patients (n=790) enrolled in the Alliance A031201 randomized phase III trial (NCT01949337) prior to enzalutamide therapy with or without abiraterone acetate and prednisone. A customized targeted cfDNA sequencing assay was used to detect AR and non-AR alterations in mCRPC. For this, DNA-seq libraries were constructed from cfDNA using Takara ThruPLEX Tag-Seq or Plasma-Seq kits, and subjected to hybridization enrichment using a custom-designed Agilent SureSelect bait panel. Post-capture DNA-seq libraries were pooled and sequenced on an Illumina HiSeq 2500 using 2x150 bp settings. ctDNA positivity was defined as >20% ctDNA using an aneuploidy-based estimate derived from ichorCNA (Group 1) or a novel definition of ≤20% ctDNA, but with detection of any alteration in AR, or gain of MYC and/or MYCN (Group 2). cfDNA sequencing data was obtained from 776 patients. There were 480/776 (62%) ctDNA-positive patients, with 324 (42%) in Group 1 and an additional 156 (20%) in Group 2 with AR or MYC/MYCN alterations detected. ctDNA-positive patients in Groups 1 and 2 had similarly poor median overall survival (OS) of 25.4 months (95% CI: 21.8-29.0) and 29.7 months (95% CI: 27.3-35.5), respectively, as compared to ctDNA-negative patients who had a median OS of 49.1 months (95% CI: 42.3-53.5). Relative to ctDNA-negative patients, OS was inferior in ctDNA-positive patients in Group 1 (HR 2.3, 95% CI: 1.9-2.9, P AR inhibitors in a contemporary phase III trial.

  Study phs003325

• Oesophageal adenocarcinoma scRNAseq from LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19)

  This dataset contains single-cell RNA-seq generated from the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19) and additional donors with Barrett's oesophagus using the 5' Single Cell Gene Expression assay from 10x Genomics. Samples were generated from oesophageal tumours, Barrett's oesophagus, and normal oesophagus and gastric tissues, with the aim of generating a reference atlas for cell types found in normal and disease-associated tissue states in the upper GI tract. This reference atlas was used as the basis for a deconvolution workflow to estimate the cell composition of bulk transcriptomes from these tissues, and to assess cell type-specific expression patterns of potential predictive biomarkers for immunochemotherapy regimens in this setting.

  Dataset EGAD00001009401

• Dataset for study Genome-wide gene expression analysis following CRISPRi of transposable elements

  Transposable elements (TEs), once regarded as parasitic genomic remnants, are now recognized as key regulators of gene expression and genome evolution, yet the functional specificity of individual TE subfamilies remains largely unexplored. This dataset investigates the transcriptional consequences of targeted repression of MER57E3 and LTR10B2 elements using CRISPR interference (CRISPRi) in human induced pluripotent stem cells (hiPSCs). hiPSCs expressing CRISPRi machinery (n = 2 biological replicates) were transduced with guide RNAs targeting individual or grouped copies of MER57E3 and LTR10B2, as well as the ZNF678 promoter or a lacZ non-targeting control. Transduced cells were subsequently differentiated into neural progenitor cells (NPCs), and total RNA was extracted for mRNA library preparation and sequencing. The dataset comprises 24 single-end mRNA-seq FASTQ files generated from these NPCs and wild-type controls.

  Dataset EGAD00001015689

• Transcriptome analysis of a novel human iPSC-derived 3D cortical tissue model - WT, APP KI, Abeta-treated, Abeta/Aducanumab-treated

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model. Samples include distinct conditions (each as biological duplicates): - wild-type cells from cultures after 1 month (WT_1mo, cell lines: A18, KOLF) and 3 months (WT_3mo, cell lines: SA2, KOLF, A18) of culturing - knock-in cells from cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (KI_3mo, cell lines: SA2, A18) - subset of WT 1 month-old samples were exposed to 500nM synthetic Abeta42 for 2 consecutive feeds, and a subset of these subsequently treated with 1µg/ml Aducanumab antibody for 14 days

  Dataset EGAD50000002031

• NGS data of human NES cells and tumors

  Raw RNA-seq data for WT and 2 Gorlin NES cells, tumors derived from MYCN mis-expressed WT NES cells, tumors derived from Gorlin NES cells, and tumors derived from Gorlin NES cells transduced with mutant DDX3X (R351W and R534S) and CRISPR/Cas9 targeting GSE1 (each sample has 3 replicates/tumors except Gorlin NES cell tumors have 4). Raw whole exome sequencing data for WT and Gorlin 1 NES cells, tumors derived from MYCN mis-expressed WT NES cells, and tumors derived from Gorlin NES cells (each sample has 3 replicates/tumors except Gorlin NES cell tumors have 4). Raw data for amplicon sequencing of GSE1 and KDM3B at regions targeted by CRISPR/Cas9 in Gorlin NES cells.

  Dataset EGAD00001004990

• RNA-seq study of longitudinal blood cell samples drawn from children at risk of type 1 diabetes

  The appearance of type 1 diabetes (T1D)-associated autoantibodies is the first and only measurable parameter to predict progression toward T1D in genetically susceptible individuals. However, autoantibodies indicate an active autoimmune reaction, wherein the immune tolerance is already broken. Therefore, there is a clear and urgent need for new biomarkers that predict the onset of the autoimmune reaction preceding auto-antibody positivity or reflect progressive b-cell destruction. Here we report the mRNA sequencing-based analysis of 306 samples including fractionated samples of CD4+ and CD8+ T cells as well as CD4, CD8 cell fractions and unfractionated PBMC samples longitudinally collected from seven children who developed beta-cell autoimmunity (case subjects) at a young age and matched control subjects.

  Dataset EGAD00001005767

• RNA-seq of non-LPS treated (N), non-tolerized (NT), and tolerized (T) IFNg-primed macrophages pretreated with or without HDAC3i

  In this experiment we investigated the effect of HDAC3 inhibition on the transcriptome of IFNg-primed macrophages under different tolerization conditions. Peripheral blood mononuclear cells (PBMCs) were isolated from 3 healthy donors. PBMCs were isolated from whole blood of healthy donors using Ficoll gradient (Invitrogen). Monocytes (CD14+ cells) were positively selected from PBMCs using CD14 Microbeads according to the manufacturer’s instructions (Miltenyi Biotec). Monocytes were subsequently treated with or without 500 nM HDAC3i (ITF3100) for 30 minutes prior to overnight IFNg priming (50 ng/mL). Cells were then kept without LPS (non-LPS; N), treated with 10 ng/mL LPS once (non-tolerized; NT), or treated with LPS twice (tolerized; T; second LPS concentration: 100 ng/mL). In total, there were 18 samples included.

  Dataset EGAD00001005959