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SRP126691
Homo sapiens
162 Downloadable Samples
Illumina HiSeq 4000
Description
Whole blood transcriptional signatures distinguishing patients with active tuberculosis from asymptomatic latently infected individuals have been described but, no consensus exists for the composition of optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Overall design: We undertook RNA Sequencing (RNA-Seq) of our earlier Berry et al. 2010 (GSE19444 and GSE19442) cohorts and additionally set up a prospective cohort study at Leicester (UK) in subject groups of incident TB and recent TB contacts, respectively. In the Leicester cohort, we performed systematic longitudinal sampling and clinical characterisation first, to validate our TB signature using RNA-Seq in a new and independent cohort of individuals with active TB and LTBI, and secondly to provide longitudinal data in a low TB incidence setting.
Publication Title
A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection.
Sample Metadata Fields
Sex, Specimen part, Race, Subject
View Samples- Homo sapiens
- 129 Downloadable Samples
- Illumina HiSeq 4000
Description
Whole blood transcriptional signatures distinguishing patients with active tuberculosis from asymptomatic latently infected individuals have been described but, no consensus exists for the composition of optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Overall design: We undertook RNA Sequencing (RNA-Seq) of our earlier Berry et al. 2010 (GSE19444 and GSE19442) cohorts and additionally set up a prospective cohort study at Leicester (UK) in subject groups of incident TB and recent TB contacts, respectively. In the Leicester cohort, we performed systematic longitudinal sampling and clinical characterisation first, to validate our TB signature using RNA-Seq in a new and independent cohort of individuals with active TB and LTBI, and secondly to provide longitudinal data in a low TB incidence setting.
Publication Title
A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection.
Sample Metadata Fields
Sex, Specimen part, Race, Subject
View Samples- Homo sapiens
- 53 Downloadable Samples
- Illumina HiSeq 4000
Description
Whole blood transcriptional signatures distinguishing patients with active tuberculosis from asymptomatic latently infected individuals have been described but, no consensus exists for the composition of optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Overall design: We undertook RNA Sequencing (RNA-Seq) of our earlier Berry et al. 2010 (GSE19444 and GSE19442) cohorts and additionally set up a prospective cohort study at Leicester (UK) in subject groups of incident TB and recent TB contacts, respectively. In the Leicester cohort, we performed systematic longitudinal sampling and clinical characterisation first, to validate our TB signature using RNA-Seq in a new and independent cohort of individuals with active TB and LTBI, and secondly to provide longitudinal data in a low TB incidence setting. All samples in this series were re-analyzed from GSE19444. There are links on each sample page to the original sample.
Publication Title
A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 45 Downloadable Samples
- Illumina HiSeq 4000
Description
Whole blood transcriptional signatures distinguishing patients with active tuberculosis from asymptomatic latently infected individuals have been described but, no consensus exists for the composition of optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Overall design: We undertook RNA Sequencing (RNA-Seq) of our earlier Berry et al. 2010 (GSE19444 and GSE19442) cohorts and additionally set up a prospective cohort study at Leicester (UK) in subject groups of incident TB and recent TB contacts, respectively. In the Leicester cohort, we performed systematic longitudinal sampling and clinical characterisation first, to validate our TB signature using RNA-Seq in a new and independent cohort of individuals with active TB and LTBI, and secondly to provide longitudinal data in a low TB incidence setting. 43 of the 47 samples in this series were re-analyzed from GSE19442. These samples include links to the original sample at the foot of the page.
Publication Title
A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection.
Sample Metadata Fields
Specimen part, Subject
View Samples- Arabidopsis thaliana
- 175 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to temperature and light
Publication Title
High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions.
Sample Metadata Fields
Specimen part, Time
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Of the members of mitochondrial transcription termination factors (mTERFs) found in metazoans and plants known to regulate organellar gene expression at various levels, plant mTERF6 promotes maturation of a tRNA
Publication Title
Definition of a core module for the nuclear retrograde response to altered organellar gene expression identifies GLK overexpressors as gun mutants.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
GUN1 integrates retrograde signals in the chloroplast but the underlying mechanism is elusive. FUG1, a chloroplast translation initiation factor, and GUN1 are co-expressed at the transcript level, and FUG1 co-immunoprecipitates with GUN1. We used mutants of GUN1 (gun1-103) and FUG1 (fug1-3) to analyse their functional relationship at the physiological and systems-wide level, the latter including transcriptome and proteome analyses. Absence of GUN1 aggravates the effects of decreased FUG1 levels on chloroplast protein translation, resulting in transient additive phenotypes with respect to photosynthesis, leaf coloration, growth and cold acclimation. Variegation of the var2 mutant is enhanced by gun1-103 in terms of increasing the fraction of white sectors, in contrast to fug1-3 that acts as suppressor. The transcriptomes of fug1-3 and gun1-103 are very similar, but absence of GUN1 alone has almost no effects on protein levels, whereas chloroplast protein accumulation is markedly decreased in fug1-3. In gun1 fug1 double mutants, effects on transcriptomes and particularly proteomes are enhanced. Our results show that GUN1 function becomes critical when chloroplast proteostasis is perturbed by decreased translation (fug1) or degradation (var2) of chloroplast proteins. The functions of FUG1 and GUN1 appear to be related, corroborating the view that GUN1 operates in chloroplast proteostasis. Overall design: Examination of differential gene expression in the Arabdidopsis thaliana gun1, fug1 and gun1 fug1 mutants compared to wild type in three replicates
Publication Title
Relationship of GUN1 to FUG1 in chloroplast protein homeostasis.
Sample Metadata Fields
Subject
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Changes ins organellar gene expression trigger retrograde signalling. Prolyl-tRNA synthetase (PRORS1) is located in chloroplasts and mitochondria. Thus, prors1-2 mutants are impaired in chloroplast and mitochondrial gene expression.
Publication Title
Identification of target genes and transcription factors implicated in translation-dependent retrograde signaling in Arabidopsis.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 57 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The in vitro test battery of the European research consortium ESNATS (novel stem cell-based test systems) has been used to screen for potential human developmental toxicants. As part of this effort, the migration of neural crest (MINC) assay has been used to evaluate chemical effects on neural crest function. It identified some drug-like compounds in addition to known environmental toxicants. The hits included the HSP90 inhibitor geldanamycin, the chemotherapeutic arsenic trioxide, the flame-retardant PBDE-99, the pesticide triadimefon and the histone deacetylase inhibitors valproic acid and trichostatin A. Transcriptome changes triggered by these substances in human neural crest cells were recorded and analysed here to answer three questions: (1) can toxicants be individually identified based on their transcript profile; (2) how can the toxicity pattern reflected by transcript changes be compacted/ dimensionality-reduced for practical regulatory use; (3) how can a reduced set of biomarkers be selected for large-scale follow up? Transcript profiling allowed clear separation of different toxicants and the identification of toxicant types in a blinded test study. We also developed a diagrammatic system to visualize and compare toxicity patterns of a group of chemicals by giving a quantitative overview of altered superordinate biological processes (e.g. activation of KEGG pathways or overrepresentation of gene ontology terms). The transcript data were mined for potential markers of toxicity, and 39 transcripts were selected to either indicate general developmental toxicity or distinguish compounds with different modes-of-action in read-across. In summary, we found inclusion of transcriptome data to largely increase the information from the MINC phenotypic test.
Publication Title
Identification of transcriptome signatures and biomarkers specific for potential developmental toxicants inhibiting human neural crest cell migration.
Sample Metadata Fields
Sex, Specimen part
View Samples- Arabidopsis thaliana
- 24 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Comparison of expression of Arabidopsis thaliana Col-0 and T-DNA insertion line of RAP2.4a under time dependent light stress by transfer to high light
Publication Title
Meta-analysis of retrograde signaling in Arabidopsis thaliana reveals a core module of genes embedded in complex cellular signaling networks.
Sample Metadata Fields
Specimen part
View Samples