Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-sequencing of the mRNA transcriptome in blood, across three time-points in severe psoriasis patients treated with the tumor necrosis factor (TNF) inhibitor, etanercept

ABSTRACT: Blood (mRNA and miRNA) and skin mRNA transcriptomes were investigated across three time-points in a pilot investigation of ten severe psoriasis patients, treated with the tumor necrosis factor (TNF) inhibitor, etanercept. We used illumina RNA-sequencing to analyse the mRNA transcriptome in blood

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Barnes

PROVIDER: E-MTAB-6555 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-sequencing of the mRNA transcriptome in lesional and non-lesional skin, across three time-points in severe psoriasis patients treated with the tumor necrosis factor (TNF) inhibitor, etanercept

Project description:Blood (mRNA and miRNA) and skin mRNA transcriptomes were investigated across three time-points in a pilot investigation of ten severe psoriasis patients, treated with the tumor necrosis factor (TNF) inhibitor, etanercept. We used illumina RNA-sequencing to analyse the small-RNA transcriptome in blood

2018-09-21 | E-MTAB-6556 | biostudies-arrayexpress

Molecular Hallmarks of Experimentally Acquired Immunity to Malaria [Pilot Study]

Project description:Sterile immunity to Plasmodium falciparum infection can be induced experimentally in humans after few exposures. An example is the induction of immunity using whole parasites by exposure of malaria-naive volunteers to infectious mosquito bites while using chloroquine prophylaxis (CPS immunization). Chloroquine kills blood-stage parasites but leaves liver-stage parasites unaffected, thereby exposing the liver-stage and early blood-stage antigens to the immune system. Upon subsequent challenge, volunteers are completely protected from infection, but protective efficacy decreases when fewer infectious mosquito bites are used for CPS immunization. Efforts to understand the mechanisms of this immunity, and how it differs from naturally-acquired immunity, may provide critical insights that could aid malaria vaccine development. In this pilot study, transcriptomic features are derived from blood samples collected before and after challenge with infectious mosquito bites. 12 samples; paired pre- and post-challenge for 5 individuals, plus two controls

2013-09-18 | E-GEOD-50957 | biostudies-arrayexpress

RNAseq data of blood samples from children with pneumonia, M. pneumoniae pneumonia and Healthy Controls used to validate transcriptomic signatures of M.pneumoniae penumonia

Project description:Pneumonia remains the leading cause of death in children under five, but existing diagnostic methods frequently lead to innecessary or mistaken treatment. M. pneumoniae lacks cellular wall so it does not respond to common firs-line antibiotic. Our study aims to guide the diagnosis and treatment by identifying host transcriptomic biomarkers in the blood of children with Mycoplasma pneumoiae pneumonia. Using RNA sequencing, we identified and validated 8 different n-transcript signature that accurately differentiates M. pneumoniae pneumonia from the rest of pneumonias. A strand specific library preparation was completed using NEBNext® Ultra™ II mRNA kit (NEB) and NEB rRNA/globin depletion probes following manufacturer’s recommendations. Individual libraries were normalized using Qubit, pooled together and diluted. The sequencing was performed using a 150 or 75 paired-end configuration in a Novaseq6000 or HiSeq 4000 platforms. Quality control of raw data was carried out using FastQC, alignment and read counting were performed using STAR, alignment filtering was done with SAMtools and read counting was carried out using FeatureCounts. RNAseq data was processed for batch correction using control samples and COMBAT-Seq package.

2024-12-08 | E-MTAB-14588 | biostudies-arrayexpress

Yeast X-Chromosome Associated Protein 5 (Xap5) Functions with H2A.Z to Suppress Aberrant Transcripts [RNA-seq]

Project description:Functional characterization of the Xap5 protein using epistatic genetic interaction analysis (E-MAP), RNA-seq and ChIP-chip along with other growth experiments. wild type and mutant cells were grown at 37C in EMM50 and RNA was extracted from exponentially growing cells. Strand specific libraries were constructed with random primers. Ribo zero was used to remove r-RNA. For ChIP-chip Agilent 60mer array was used to analyze DNA recovered by chromatin immunoprecipitation of Xap5 from fission yeast culture.

2014-07-01 | E-GEOD-46382 | biostudies-arrayexpress

RNA-sequencing of the small-RNA transcriptome in blood, across three time-points in severe psoriasis patients treated with the tumor necrosis factor (TNF) inhibitor, etanercept

2018-09-21 | E-MTAB-6428 | biostudies-arrayexpress

Pustular psoriasis: molecular pathways and effects of spesolimab in generalized pustular psoriasis

Project description:pre- and post spesolimab treatment gene expression analysis of blood as well as skin biopsy samples.

2023-06-04 | E-MTAB-11144 | biostudies-arrayexpress

RNA-seq of Plasmodium vivax derived from clinical isolates

Project description:This project contains RNA-sequencing reads of Plasmodium vivax derived directly from clinical patients. Here, we aim to characterize the gene expression patterns in patients with various parasite compositions. Patients (n=10) were recruited from two malaria endemic areas in Thailand. Ten RNA samples were treated with DNase, followed by Epicentre Globin-Zero Gold kit to deplete rRNA and globin transcript. The RNA-seq libraries were sequenced on an Illumina HiSeq4000 platform to generate approximately 60 million paired-end reads of 150 bp for each sample.

2019-06-30 | E-MTAB-6753 | biostudies-arrayexpress

RNA profiling for mouse B10+ cells and B10- B cells

Project description:we used genome-wide transcriptome analysis to profile the mRNA, long noncoding RNA (lncRNA), and microRNA (miRNA) expression of B10 cells, an antigen-specific Cd1dhiCd5+Cd19hiIl10 competent regulatory B cell. Potential key upstream regulators (including transcription factors, cytokines, trans-membrane receptors, and kinases) for Breg biogenesis and function were identified. B10+ B cells (Cd1dhiCd5+Cd19hiIl10+) and B10- cells (Cd1d-Cd5-Cd19hiIl10-) from mouse splenic B cell were sorted for RNA preparation. Two independent repeats were prepared for RNA-seq

2015-10-29 | E-GEOD-63426 | biostudies-arrayexpress

RNA-Sequencing of whole blood samples from children with a range of acute febrile illnesses

Project description:RNA sequencing data were generated from the whole blood of children with a range of acute febrile illnesses. These data were used as the validation cohort for a multiclass diagnostic gene expression signature for the discrimination of 18 infectious and inflammatory diseases which was discovered using publicly available microarray datasets.

2022-11-22 | E-MTAB-11671 | biostudies-arrayexpress

Xanthomonas campestris pv. Campestris 8004 far-red light irradiation and XccBphP overexpression transcriptional analysis

Project description:RNA isolation and RNA-Seq: Wild-type Xcc or pXccBphP strains were cultured in far-red light or dark conditions up to logarithmic phase (0.7 to 0.8 OD600) at 28C in PYM broth. Total bacterial RNA was isolated using the MasterPureTM RNA Purification Kit (Epicentre, Illumina). Samples corresponding to two biological replicates of each condition were submitted to Genome Qubec for rRNA removal with Ribo-Zero (Illumina) and TruSeq RNA-seq library preparation. 50 bp single-end sequencing of the libraries was performed using an Illumina HiSeq 2000 platform (Genome Qubec). Removal of low-quality reads and Illumina adapters, and assessment of the quality of the reads was performed using Trimmomatic (Bolger et al, 2014) and FastQC (www.bioinformatics.babraham.ac.uk/ projects/fastqc/), respectively. Rads were aligned to the Xcc genome obtained from GenBank (accession number: NC_007086.1) using SAMtools and the BurrowsWheeler Alignment software (BWA) (Li et al, 2009). Alignments were visualized using the software Integrated Genome Viewer (IGV) (http://broadinstitute.org/igv). RNA-Seq differential expression analysis: Read counts corresponding to annotated ORFs were quantified with the software FeatureCounts (Liao et al, 2014) using the strand specific mode. Differential expression analysis was performed using the software DESeq (Anders & Huber, 2010). Genes displaying adjusted p-value < 0.05.

2016-12-03 | E-MTAB-4958 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data