GEO DataSets

(Submitter supplied) Transcriptome analysis is of great interest in clinical research, where significant differences between individuals can be translated into biomarkers of disease. Although next generation sequencing provides robust, comparable and highly informative expression profiling data, with several million of tags per blood sample, reticulocyte globin transcripts can constitute up to 76% of total mRNA compromising the detection of low abundant transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

12 Samples

Download data: TXT

(Submitter supplied) Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is complicated by the need to minimize artifacts associated with highly abundant globin RNA transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL201

24 Samples

Download data: CEL, CHP

(Submitter supplied) In this study we aimed to assess technical variability associated with globin depletion in addition to assessing general technical variability in RNA-Seq from whole blood derived samples. We compared technical and biological replicates having undergone globin depletion or not and found that globin depletion removed approximately 80% of globin transcripts, improved the correlation of technical replicates, allowed for reliable detection of thousands of additional transcripts and generally increased transcript abundance measures.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

47 Samples

Download data: TXT

(Submitter supplied) Microarray-based gene expression analysis of peripheral whole blood is a common strategy in the development of clinically relevant biomarker panels for a variety of human diseases. However, the results of such an analysis are often plagued by decreased sensitivity and reliability due to the effects of relatively high levels of globin mRNA in whole blood. Globin reduction assays have been shown to overcome such effects, but they require large amounts of total RNA and may induce distinct gene expression profiles. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL6883 GPL8432

64 Samples

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(Submitter supplied) Background: There are challenges in generating mRNA-Seq data from whole-blood derived RNA as globin gene and rRNA are frequent contaminants. Given the abundance of erythrocytes in whole blood, globin genes comprise some 80% or more of the total RNA. Therefore, depletion of globin gene RNA and rRNA are critical steps required to have adequate coverage of reads mapping to the reference transcripts and thus reduce the total cost of sequencing. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

18 Samples

Download data: TXT

(Submitter supplied) RNA stabilizing reagents have been developed to ensure that transcription profiles of whole blood samples reflect the physiological state at the time of the blood drawn. Ability to preserve and maintain the in vivo gene expression status ex vivo is essential for gene expression profiling and biomarker discovery from clinical sample material. We compared transcriptional profiles obtained from samples collected using two established peripheral blood RNA collection systems, TEMPUS™ and PAXgene™. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2700

14 Samples

Download data: TXT

(Submitter supplied) Room temperature whole blood mRNA stabilization procedures, such as the PAX gene system, are critical for the application of transcriptional analysis to population-based clinical studies. Global transcriptome analysis of whole blood RNA using microarrays has proven to be challenging due to the high abundance of globin transcripts that constitute 70% of whole blood mRNA in the blood. This is a particular problem in patients with sickle-cell disease, secondary to the high abundance of globin-expressing nucleated red blood cells and reticulocytes in the circulation . more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

30 Samples

Download data: CEL

(Submitter supplied) Peripheral whole blood-based gene expression profiling has become one of the most common strategies exploited in the development of clinically relevant biomarkers. However, the ability to identify biologically meaningful conclusions from gene expression patterns in whole blood is highly problematic. First, it is difficult to know whether or not expression patterns in whole blood capture those in primary tissues. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

36 Samples

Download data: CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

34 Samples

Download data: CEL

(Submitter supplied) To determine differential gene expression in peripheral blood of asthmatic individuals undergoing allergen inhalation challenge, post-challenge compared to pre-challenge

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

18 Samples

Download data: CEL

(Submitter supplied) Detecting differential changes in the peripheral whole-blood transcriptome, post-challenge compared to pre-challenge; using non-globin reduced PAXgene (PAX.NGR) tubes Blood was collected immediately prior to, and two hours after challenge

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL

(Submitter supplied) Detecting differential changes in the peripheral whole-blood transcriptome, post-challenge compared to pre-challenge; using globin reduced PAXgene (PAX.GR) tubes

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

8 Samples

Download data: CEL

(Submitter supplied) Background: Allergen inhalation challenge in mild asthmatics induces airflow obstruction, airway hyperresponsiveness and inflammation, providing a model for hypothesis-generating experiments to understand regulation of these responses. We have sought to evaluate the peripheral whole blood transcriptome, post-challenge compared to pre-challenge, and to determine the effect of globin mRNA reduction methodology. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

30 Samples

Download data: CEL

(Submitter supplied) Reticulocytes were purified from fresh blood samples obtained from 10 healthy adult volunteers (5 women and 5 men) after informed consent. The donors had normal blood cell counts, blood smears, hemoglobin electrophoresis, red cells membrane resistance tests and no biological evidence of hemolysis. Whole blood samples were centrifuged, the supernatant and the buffy coat containing white blood cells (WBC) and platelets were removed. more...

Organism:

Homo sapiens

Type:

Expression profiling by SAGE

Platform:

GPL6

1 Sample

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(Submitter supplied) To compare the impact of haemoglobin depletion by hybridisation-based removal or bioinformatic removal of reads on the outcome of differential gene expression analysis. This comparisons was performed using RNA-seq data from 58 human tuberculosis (TB) patient whole blood samples – 29 globin kit-depleted and 29 matched non-depleted – a subset of which were taken at TB diagnosis and at six months post-TB treatment from the same patient

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

58 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

77 Samples

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(Submitter supplied) The goal of this study was to define relationships between peripheral blood miRNAs and mRNAs of women undergoing idiopathic preterm labor (PTL) and compare network level changes to control women that deliver at term.Using RNA Sequencing we have performed global miRNA and mRNA profiling in both monocytes and whole blood leukocytes of women who underwent PTL (N=15) matched to non-pathological controls (N=30) as a part of the Ontario Birth Study cohort. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

38 Samples

Download data: TXT

(Submitter supplied) The goal of this study was to define relationships between peripheral blood miRNAs and mRNAs of women undergoing idiopathic preterm labor (PTL) and compare network level changes to control women that deliver at term.Using RNA Sequencing we have performed global miRNA and mRNA profiling in both monocytes and whole blood leukocytes of women who underwent PTL (N=15) matched to non-pathological controls (N=30) as a part of the Ontario Birth Study cohort. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

39 Samples

Download data: TXT

(Submitter supplied) The main aim of the study was to compare genome-wide gene expression profiles obtained from the two widely used commercially available whole blood RNA collection systems - PAXgeneTM and TempusTM tubes. Comparisons of present call rates, variances, correlations and influence of globin reduction across the two collection systems was performed using in vivo glucocorticoid stimulation in 24 peripheral blood samples from three individuals. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

24 Samples

Download data: TXT