The effect of anti-HER2/CD3 TDB on transcription in human CD8 T cells (bulk)
ABSTRACT: RNA was isolated from purified human CD8 cells that were incubated with anti-HER2/CD3 TDB in the presence of SK-BR-3 cells. This dataset only contains the metadata and processed data. Raw data can be accessed via the EGA accession EGAS00001003734
Project description:Single-cell RNA-seq libraries were generated from human PBMCs that were incubated with anti-HER2/CD3 TDB in the presence of KPL-4 cells. This dataset only contains the metadata and processed data. Raw data can be accessed via the EGA accession EGAS00001003734
Project description:Mice of indicated ages and genotypes were perfused and their brains dissected and dissociated. Cells were fixed, immunolabeled and FACS sorted. RNA was extracted from neuron, astrocyte, and microglial cell populations. Typical RIN=4-5 for neurons, 6-8 for astrocytes, and 5-7 for microglia. Typical RNA yields ~100ng for neurons, ~20ng for microglia, and ~10ng for astrocytes. cDNA was generated from up to 25 ng of total RNA using Nugen's RNA-Seq method for low-input RNA samples, Ovation RNA-Seq System V2 (NuGEN). (Per manufacturers instructions, total RNA was neither depleted of rRNA nor polyA-selected.) 1 ug of sheared cDNA was taken into further processing, starting at end repair step, using Illumina's TruSeq RNA Sample Preparation Kit v2 (Illumina). The 'SAMPLE_ID'; sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0006149 Astrocytes, microglia and neurons were sorted from 7- or 13-month old PS2APP or non-transgenic mice, 4 <= n <= 7 per group.
Project description:Cancer cell lines can provide robust and facile biological models for the generation and testing of hypothesis in the early stages of drug development and caner biology. Although clinical trials remain the ultimate scientific testing ground for anticancer therapies, the use of appropriate model systems to explore the molecular basis of drug activity and to identify predictive biomarkers during their development can have a profound effect on the design, cost and ultimate success of new cancer drug development. In order to capture the high degree of genomic diversity in cancer and to identify rare molecular subtypes, we have assembled a collection of >1000 cancer cell lines. These lines have been characterised using whole exome sequencing, genome wide analysis of copy number, mRNA gene expression profiling and DNA methylation analysis (http://cancer.sanger.ac.uk/cell_lines). To further characterise this panel of cell lines we have now compiled data for RNA sequencing. The current study represent data for ~450 of the cell lines in the panel, data for the remaining lines can be accessed via the CGHUB data browser hosted at UCSC. <br>This ArrayExpress record contains only meta-data. Raw data files have been archived at the European Genome-Phenome Archive (EGA, www.ebi.ac.uk/ega) by the consortium, with restricted access to protect sample donors' identity. The relevant accessions of the EGA data set is EGAD00001001357 under EGA study accession EGAS00001000828.
Project description:Bone marrow derived macrophages 1 µM CpG or 20 µg/ml TDB, an analogon to the mycobacterial cord factor TDM for 8h, 24h, 48h and 72h respectively. Keywords: CpG, TDB, macrophage, time series Overall design: time series; 8h, 24h, 48h and 72h CpG or TDB
Project description:The expression profile and sequence variants of 476 early stage urothelial carcinoma were studied using whole transcriptome sequencing. RNA-Seq libraries were prepared by Ribo-Zero treatment of total-RNA (to reduce the rRNA content) followed by library preparation using ScriptSeq. RNA-Seq libraries were paired-end sequenced (2x 101 bp) on Illumina HiSeq 2000 and the resulting fastq files were processed using tools from the Genome Analysis Toolkit (GATK and from the Tuxedo suite. Access to the sequence data (bam and vcf files), containing person identifying information, needs signature on a controlled access form, and can be accessed at The European Genome-phenome Archive (EGA) using the study ID EGAS00001001236 following request. An expression matrix of FPKM values are available without restriction at ArrayExpress.
Project description:Bone marrow derived macrophages from wt and card9 KO mice were stimulated with CpG, Curdlan or TDB, an analogon to the mycobacterial cord factor TDM for 48h, respectively. Keywords: card9 knockout, macropphage, TDB Overall design: wt or card9 KO macrophages stimulated for 48h
Project description:Bone marrow derived macrophages from wt and card9 KO mice were stimulated with CpG, Curdlan or TDB, an analogon to the mycobacterial cord factor TDM for 48h, respectively. Keywords: card9 knockout, macropphage, TDB wt or card9 KO macrophages stimulated for 48h
Project description:Bone marrow derived macrophages 1 µM CpG or 20 µg/ml TDB, an analogon to the mycobacterial cord factor TDM for 8h, 24h, 48h and 72h respectively. Experiment Overall Design: time series; 8h, 24h, 48h and 72h CpG or TDB
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national induced pluripotent stem cell (iPS cell) resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the using RNAseq of fibroblasts, peripheral blood mononuclear cells (PBMCs) and induced pluripotent stem cells (iPS cells) generated from the skin biopsies or blood of healthy volunteers. This experiment includes the data and expands the metadata from two obsolete ArrayExpress accessions (E-ERAD-216 and E-ERAD-327) for use in the Expression Atlas. For samples derived from E-ERAD-216 the raw data is stored in the European Genome-Phenome Archive (EGA) and is subject to access control. Data from E-ERAD-327 is stored in the European Nucleotide Archive (ENA) and is publicly available.
Project description:The availability of human genome sequence has transformed biomedical research over the past decade. However, an equivalent map for the human proteome with direct measurements of proteins and peptides was lacking. To this end, Akhilesh Pandey's lab reported a draft map of the human proteome based on high resolution Fourier transform mass spectrometry-based proteomics technology, which included an in-depth proteomic profiling of 30 histologically normal human samples including 17 adult tissues, 7 fetal tissues and 6 purified primary hematopoietic cells ( http://dx.doi.org/10.1038/nature13302 ). The profiling resulted in identification of proteins encoded by greater than 17,000 genes accounting for ~84% of the total annotated protein-coding genes in humans. This large human proteome catalog (available as an interactive web-based resource at http://www.humanproteomemap.org) complements available human genome and transcriptome data to accelerate biomedical research in health and disease. Pandey's lab and collaborators request that those considering use of this primary dataset for commercial purposes contact email@example.com. The full details of this study can be found in the PRIDE database: www.ebi.ac.uk/pride/archive/projects/PXD000561/. This ArrayExpress entry represents a top level summary of the metadata only which formed the basis of the reanalysis performed by Joyti Choudhary's team ( firstname.lastname@example.org ), results of which are presented in the Expression Atlas at EMBL-EBI : http://www.ebi.ac.uk/gxa/experiments/E-PROT-1.