Filters
Technology
Platform
Pseudomonas aeruginosa
10 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: The goal of this study was to use RNA Seq to explore whether and to what extent genetic heterogeneity would shape the transcriptional profile in the environment of the CF lung Methods : mRNA profiles were generated for Pseudomonas aerugionsa samples derived from explanted lung tissue or pure cultures isolated from the same lung regions by deep sequencing. To enrich the bacterial RNA MicrobeEnrich Kit (Ambion) was used. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina) . The samples were sequenced in single end mode on an Illumina HiSeq 2500 device and mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using Stampy pipeline with defaut settings. Overall design: mRNA profiles either from Pseudomonas aeruginosa containing explanted lung tissue from a single patient from various regions of the lung or pure P. aeruginosa liquid cultures grown in LB at 37C from the same lung regions as the ex vivo samples were generated and deep sequenced using Illumina HiSeq 2500.
Publication Title
Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung.
Sample Metadata Fields
Subject
View Samples- Pseudomonas aeruginosa
- 167 Downloadable Samples
- Illumina NovaSeq 6000, Illumina HiSeq 2500
Description
Purpose : The goal of this study was to use RNA-seq to compare transcriptional profiles under biofilm conditions with planktonic growth and explore the correlation of gene expression of a collection of clinical P. aeruginosa isolates to various phenotypes, such as biofilm structure or virulence. Methods : mRNA profiles were generated for Pseudomonas aeruginosa clinical samples derived from various geographical locations by deep sequencing. The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina). The samples were sequenced in single end mode on an Illumina HiSeq 2500 device or paired end mode on an Illumina Novaseq 6000. mRNA reads were trimmed and mapped to the NC_008463.1 (PA14) reference genome from NCBI using bowtie2 with default settings. Overall design: mRNA profiles from Pseudomonas aeruginosa derived from static biofilm cultures grown for 12h to 48h in 96-well microtiter plates or planktonic LB cultures grown to an OD600 = 2 and deep sequenced using Illumina HiSeq 2500/NovaSeq 6000.
Publication Title
Parallel evolutionary paths to produce more than one <i>Pseudomonas aeruginosa</i> biofilm phenotype.
Sample Metadata Fields
Subject
View Samples- Pseudomonas aeruginosa
- 16 Downloadable Samples
- NextSeq 500
Description
Purpose : The goal of this study was to use RNA Seq to validate transcriptional data of two clinical isolates focussing on a subset of 74 transcript that were selected specifically for Nanostring analysis. Methods : mRNA profiles were generated for the clinical isolates FRD1 and CI224_M, in duplicate, by deep sequencing. Strains were grown for 8 hours in LB medium at 37C prior to RNA harvest. Ribosomal RNA was removed using the Ribi-Zero rRNA Removal Kit (Epicentre). mRNA reads were trimmed and mapped to the PAO1 NC_002516 reference genome from NCBI using the ClC Genomics Workbench platform and defaut parameters. Overall design: mRNA profiles of liquid cultures grown for 8 hours in LB at 37C were generated for P. aeruginosa clinical isolates FRD1 and CI224_M, each in duplicate, by deep sequencing using Illumina NextSeq.
Publication Title
Use of a Multiplex Transcript Method for Analysis of Pseudomonas aeruginosa Gene Expression Profiles in the Cystic Fibrosis Lung.
Sample Metadata Fields
Disease, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
- IlluminaHiSeq2000
Description
This experiment aims to identify the biological pathways and diseases associated with the cytokine Interleukin 13 (IL-13) using gene expression measured in peripheral blood mononuclear cells (PBMCs). Overall design: The experiment comprised of samples obtained from 3 healthy donors. The expression profiles of in vitro IL-13 stimulation were generated using RNA-seq technology for 3 PBMC samples at 24 hours. The transcriptional profiles of PBMCs without IL-13 stimulation were also generated to be used as controls. An IL-13R-alpha antagonist (Redpath et al. Biochemical Journal, 2013) was introduced into IL-13 stimulated PBMCs and the gene expression levels after 24h were profiled to examine the neutralization of IL-13 signaling by the antagonist.
Publication Title
Combining multiple tools outperforms individual methods in gene set enrichment analyses.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 84 Downloadable Samples
- Illumina HiSeq 2500
Description
Database of gene expression in different haematopoietic cell types at haemosphere.org Overall design: Comparison of gene expression in different haematopoietic cell types
Publication Title
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
Illumina MouseWG-6 v2.0 expression beadchip
Description
G-CSF is a hemopoietic growth factor that has a role in steady state granulopoiesis, as well as in mature neutrophil activation and function. We developed a neutralizing monoclonal antibody to the murine G-CSF receptor (G-CSFR), which antagonizes binding of murine G-CSF and inhibits G-CSFR signalling. Anti-G-CSFR rapidly halts the progression of established disease in collagen antibody-induced arthritis (CAbIA). Neutrophil accumulation in joints is inhibited, without rendering animals neutropenic, suggesting an effect on homing to inflammatory sites. Neutrophils in the blood and arthritic joints of anti-G-CSFR treated mice show alterations in cell adhesion receptors, while anti-G-CSFR suppresses local production of proinflammatory cytokines and chemokines known to drive tissue damage. Our aim in this study was to use differential gene expression analysis of joint and blood neutrophils to more thoroughly understand the effect of G-CSFR blockade on the inflammatory response following anti-G-CSFR therapy in CAbIA.
Publication Title
Therapeutic Targeting of the G-CSF Receptor Reduces Neutrophil Trafficking and Joint Inflammation in Antibody-Mediated Inflammatory Arthritis.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Treatment
View Samples- Gallus gallus
- 12 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
A systematic survey of the transcriptional status of individual segments of the developing chick hindbrain (r1-5) and the adjacent region of the embryonic midbrain (m) during the HH11 stage of chick development
Publication Title
Transcriptomic analysis of midbrain and individual hindbrain rhombomeres in the chick embryo.
Sample Metadata Fields
Specimen part
View Samples- Caenorhabditis elegans
- 21 Downloadable Samples
- Affymetrix C. elegans Genome Array (celegans)
Description
C. elegans GLD-2 forms an active PAP with multiple RNA-binding partners to regulate diverse aspects of germline and early embryonic development. One GLD-2 partner, RNP-8, was previously shown to influence oocyte fate specification. To identify transcripts selectively associated with both GLD-2 and RNP-8, we employ a genomic approach using the method of RNA immunoprecipitation followed by microarray analysis (RIP-chip).
Publication Title
GLD-2/RNP-8 cytoplasmic poly(A) polymerase is a broad-spectrum regulator of the oogenesis program.
Sample Metadata Fields
Sex, Specimen part, Disease
View Samples
SRP189590- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA-seq with male and female juvenile and adult spinal cords Overall design: RNA was isolated from 4 week and 8 week spinal cords for sequencing
Publication Title
Age and Sex-Related Changes to Gene Expression in the Mouse Spinal Cord.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Subject
View Samples- Triticum aestivum
- 41 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
Different wheat cultivars may be classified as either winter or spring varieties depending on whether they require exposure to an extended period of cold in order to become competent to flower. Using a growth regime that mimics the conditions that occur during a typical winter in Britain, we wished to survey the genes that are involved in phase transition as well as those involved in cold-acclimation.
Publication Title
Cold- and light-induced changes in the transcriptome of wheat leading to phase transition from vegetative to reproductive growth.
Sample Metadata Fields
No sample metadata fields
View Samples