Project description:Shotgun sequencing of sleeping sickness patient blood. WARNING: these results cannot be compared with those from trypanosome poly(A)+ mRNA, because the poly(A) selection introduces substantial bias, including loss of long mRNAs. Details will appear in the publication. These are additional sequencing runs that match some from E-MTAB-5293
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 mRNA transcriptome in blood
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.
Project description:Subjects are children from Kilifi District Hospital, Kenya, recruited in 2001 malaria season. total RNA extracted from PaxGene tubes, total RNA and Stratagene Universal reference RNA underwent linear amplification (Message Amp, Ambion). Amplified RNA directly labelled Cy5 and Cy3 and hybridised to 'lymphochip' arrays (print run - lc36n). Scanned on Axon 4000B scanner using GenePix 4.0 software. Clinical sample ID provided in 'Disease State Description' corresponds with Sample ID in Table 1 "Clinical Information for the micro-array samples" in the associated publication.
Project description:We aimed to identify how loss of the cap methyltransferase RNMT affected the ribosomes and ribosome-associated proteins in activated CD4 T cells.
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.
Project description:Whole blood transcriptional profiles of patients with (1) active pulmonary ['AdjuVIT active TB' and 'New active pulmonary'] and (2) extrapulmonary TB ['New active-extrapulmonary'] at time of diagnosis, (3) long-term recovery after treatment for active pulmonary TB ['AdjuVIT active TB'], (4) febrile illnesses presenting to hospital ['Fever mixed infection'] and (5) febrile pneumonia ['Fever pneumonia'] before antibiotic treatment, and (6) healthy vounteers. Each array sample represents a separate individual in each group. This submission includes two human whole genome Agilent Array Designs: A-MEXP-2104 and A-AGIL-28. Each of the individual raw array files are included as well as a single processed file representing the data matrix of all the merged and normalised data for the probes that are shared by the two array designs.
Project description:The cohort comprised patients recruited between Sept 2014- June 2020. It includes patients with bacteremia and positive viral diagnostic test in the context of acute admission. All patients with definite infection were used for signature discovery. Whole blood was collected at the time of recruitment in Tempus Blood RNA tubes and total RNA was isolated with the Tempus Spin RNA Isolation Kit (ThermoFisher Scientific) according to the manufacturer’s instructions. RNA samples were stored at −80 °C until further analysis. After additional DNAse treatment, library preparation and sequencing of 30 million 150bp, paired end reads were conducted using the Illumina's TruSeq® RNA Sample Preparation Kit; ribosomal and globin RNA depletion was performed using the Illumina Ribo-Zero Gold kit and HiSeq 4000 at The Wellcome Centre for Human Genetics in Oxford UK.
Project description:Subjects are children from Kilifi District Hospital, Kenya, recruited in 2001 malaria season. total RNA extracted from PaxGene tubes, total RNA and Stratagene Universal reference RNA underwent linear amplification (Message Amp, Ambion). Amplified RNA directly labelled Cy5 and Cy3 and hybridised to 'lymphochip' arrays (print run - lc36n). Scanned on Axon 4000B scanner using GenePix 4.0 software. Clinical sample ID provided in 'Disease State Description' corresponds with Sample ID in Table 1 "Clinical Information for the micro-array samples" in the associated publication. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Keywords: disease_state_design