Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

76 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analysis of immune response in healthy controls and COVID-19 cases using the NanoString Human Immunology Panel

ABSTRACT: Daily transcriptomic profiling was conducted on whole blood collected from COVID-19 cases. Whole blood was collected in Tempus Blood RNA tubes, and RNA was extracted from whole blood using the Tempus Spin RNA Isolation Kit. Healthy controls consisted of participants of a measles, mumps and rubella re-vaccination study. Pre-vaccination whole blood was collected and processed and analyzed as above.

ORGANISM(S): Homo sapiens

SUBMITTER: Eugenia Ong

PROVIDER: E-MTAB-8871 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Daily transcriptomic profiling of immune response in COVID-19 cases and healthy controls using the NanoString Human Immunology Panel

Project description:Daily transcriptomic profiling was conducted on whole blood collected from COVID-19 cases. Whole blood was collected in Tempus Blood RNA tubes, and RNA was extracted from whole blood using the Tempus Spin RNA Isolation Kit. Healthy controls consisted of participants of a measles, mumps and rubella re-vaccination study. Pre-vaccination whole blood was collected and processed and analyzed as above.

2021-02-24 | E-MTAB-9719 | biostudies-arrayexpress

NanoString profiling of host response in healthy volunteers vaccinated with ARCT-021 self-amplifying mRNA vaccine or placebo

Project description:Transcriptomic profiling was conducted on whole blood collected from study participants (NCT04480957). A total of 106 healthy participants were randomized into single and two-injection cohorts. Gene transcript levels were determined at baseline (pre-dose 1), day 2, 3, and 8 for all vaccinees. In addition, gene expression was profiled at day 29 (pre-dose 2), 30 and 36 among vaccinees in the two-injection cohort. Whole blood was collected in Tempus Blood RNA tubes, and RNA was extracted from whole blood using the Tempus Spin RNA Isolation Kit.

2022-11-30 | E-MTAB-11315 | biostudies-arrayexpress

Microarray analysis of healthy volunteers that received measles, mumps and rubella vaccination

Project description:RNA was extracted from whole blood of subjects collected in Tempus tubes on day 0 (immediately prior to vaccination), day 1 and 3 post-vaccination. We performed gene expression analysis of subjects with similar baseline antibody titres to rubella virus (RV) that experienced an increase in anti-RV IgG titre (>= 2-fold) or not (< 2 fold) at one month post-vaccination.

2019-04-03 | E-MTAB-7055 | biostudies-arrayexpress

Baseline expression of symptomatic and asymptomatic subjects after YF17D vaccination in Trial 2

Project description:This study investigates how the baseline expression level of genes impact symptomatic outcome of flaviviral infection. Before given the YF17D vaccine, whole blood was extracted into tempus tubes from vaccinated subjects. Thereafter, the subjects were assessed if they experienced adverse events (or symptoms). 35 subjects (n=12 symptomatic, n=23 asymptomatic) were processed according to manufacturer's protocol. Transcript expression was then evaluated by nCounter RNA Cancer Metabolism (#VRXC-CM1-12) or a custom Unfolded Protein Response codeset and its respective probesets.

2019-05-11 | E-MTAB-7931 | biostudies-arrayexpress

Microarray analysis of healthcare workers that received the COVID-19 mRNA vaccination

Project description:RNA was extracted from whole blood of subjects collected in Tempus tubes prior to COVID-19 mRNA booster vaccination. D01 and D21 correspond to samples collected at pre-dose 1 and pre-dose 2 respectively. RNA was also extracted from blood collected at indicated time points post-vaccination. DB1, DB2, DB4 and DB7 correspond to booster day 1 (pre-booster), booster day 2, booster day 4 and booster day 7 respectively. The case subject experienced cardiac complication following mRNA booster vaccination. We performed gene expression analysis of case versus controls over time.

2023-03-20 | E-MTAB-12829 | biostudies-arrayexpress

Transcription profiling of human peripheral blood samples incubated for 3 hours at room temperature with or without addition of PHA

Project description:RNA isolation and purification steps greatly influence the results of gene expression profiling. There are two commercially available products for whole blood RNA collection, PAXgene and Tempus blood collection tubes, and each comes with their own RNA purification method. We examined the impact of RNA isolation methods on gene expression profiles. We demonstrated that peripheral blood RNA isoaltion can critically impact differential expression results, particularly in the clinical setting where fold-change differences are typically small and there is inherent variability within biological corhorts Experiment Overall Design: Whole blood from 7 healthy individuals was collected using Li Heparin tubes, and was incubated for 3 hours at room temperature with or without addition of 25 ug/mL of PHA. After incubation, samples were subsequently transferred to either Tempus or PAXgene tubes.

2008-11-13 | E-GEOD-12709 | biostudies-arrayexpress

RNA-seq of whole blood samples from healthy adults randomized to receive either placebo or metformin followed by live-attenuated YF-17D vaccination

Project description:RNAseq was carried out to identify the transcriptomic changes that occur in healthy adult volunteers given either placebo or metformin from 3-days before to 3-days after live-attenuated YF-17D vaccination. Whole blood was collected at baseline (before placebo/metformin therapy), before YF-17D vaccination, Day 1, Day 3, Day 7 and Day 10 post YF-17D vaccination for RNAseq.

2025-01-01 | E-MTAB-13265 | biostudies-arrayexpress

Transcription profiling of human peripheral blood samples collected into PAXgene or Tempus tubes vs. the same 5 healthy control samples drawn in Li Heparin Differential gene expression profiles are dependent upon method of peripheral blood RNA isolation (direct, heparin

Project description:RNA isolation and purification steps greatly influence the results of gene expression profiling. There are two commercially available products for whole blood RNA collection, PAXgene and Tempus blood collection tubes, and each comes with their own RNA purification method. We examined the impact of RNA isolation methods on gene expression profiles. We demonstrated that peripheral blood RNA isoaltion can critically impact differential expression results, particularly in the clinical setting where fold-change differences are typically small and there is inherent variability within biological corhorts Experiment Overall Design: Comparison of 5 healthy control samples drawn directly in PAXgene or Tempus tubes vs. the same 5 healthy control samples drawn in Li Heparin tubes with no PHA stimulation.

2008-11-13 | E-GEOD-12710 | biostudies-arrayexpress

Next generation sequencing of human immune cell subsets across diseases

Project description:This study compared whole transcriptome signatures of 6 immune cell subsets and whole blood from patients with an array of immune-associated diseases. Fresh blood samples were collected from healthy subjects and subjects diagnosed type 1 diabetes, amyotrophic lateral sclerosis, and sepsis, as well as multiple sclerosis patients before and 24 hours after the first treatment with IFN-beta. At the time of blood draw, an aliquot of whole blood was collected into a Tempus tube (Invitrogen), while the remainder of the primary fresh blood sample was processed to highly pure populations of neutrophils, monocytes, B cells, CD4 T cells, CD8 T cells, and natural killer cells. RNA was extracted from each of these cell subsets, as well as the whole blood samples, and processed into RNA sequencing (RNAseq) libraries (Illumina TruSeq). Sequencing libraries were analyzed on an Illumina HiScan, with a target read depth of ~20M reads. Reads were demultiplexed, mapped to human gene models (ENSEMBL), and tabulated using HTSeq. Read count data were normalized by the TMM procedure (edgeR package). We performed whole genome RNAseq profiling of immune cell subsets and whole blood from subjects with an array of immune-associated diseases.

2015-01-06 | E-GEOD-60424 | biostudies-arrayexpress

Blood RNA sequencing was performed on a cohort of adults attending the Emergency Department with suspected infection who had subsequently-confirmed viral, bacterial, COVID19 and healthy controls

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.

2024-09-23 | E-MTAB-13307 | 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