GEO DataSets

(Submitter supplied) Readily accessible samples such as peripheral blood or cell lines are increasingly being used in large cohorts to characterise gene expression differences between a patient group and healthy controls. However, cell and RNA isolation procedures and the variety of cell types that make up whole blood can affect gene expression measurements. We therefore systematically investigated global gene expression profiles in peripheral blood from six individuals collected during two visits by comparing five of the following cell and RNA isolation methods: whole blood (PAXgene), peripheral blood mononuclear cells (PBMCs), lymphoblastoid cell lines (LCLs), CD19 and CD20 specific B-cell subsets. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7350

56 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

48 Samples

Download data: CEL

(Submitter supplied) 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 Keywords: micorarray quality assurance

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

20 Samples

Download data: CEL

(Submitter supplied) 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 Keywords: micorarray quality assurance, phytohemagglutinin (PHA)

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

28 Samples

Download data: CEL

(Submitter supplied) #G017 Burn/Trauma Study. This is a Glue Grant Study comparison between gene expression analyses performed in eight trauma/burn subjects using either a buffy coat isolation of whole blood or using the PAXgene system Keywords: other

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS917

Platform:

GPL96

16 Samples

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Comparison of RNA isolation from whole blood using the PAXgene system to that from leukocytes using the buffy coat procedure. Blood of healthy subjects and trauma patients examined. Results indicate that RNA isolated from whole blood produced more noise than that from leukocytes.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 protocol, 2 tissue sets

Platform:

GPL96

Series:

GSE1343

16 Samples

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(Submitter supplied) Peripheral Blood gene expression is widely used in the discovery of biomarkers and development of therapeutics. Recently, a spate of commercial blood collection and preservation systems have been introduced with proprietary variations that may differentially impact the transcriptomic profiles. Comparative analysis of these collection platforms will help optimize protocols to detect, identify, and reproducibly validate true biological variance among subjects. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17077

64 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

101 Samples

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(Submitter supplied) Analysis of long-term freezing on the stability of transcriptome profiles in PAXgene stabilized whole blood samples. In the present study it was tested if long-term freezing of PAXgene RNA tubes (up to one year) has an influence on the transcriptome profile of peripheral whole blood samples. Results indicated that gene expression profiles of whole blood samples stabilized with PAXgene RNA tubes remain stable for at least 1 year.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

24 Samples

Download data: TXT

(Submitter supplied) Analysis of effect of long-term cryopreservation on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that long-term cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with decreasing signal intensities over time.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

53 Samples

Download data: TXT

(Submitter supplied) Analysis of cryopreservation effects on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with a strong loss of signal intensities to background levels for several transcripts.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6102

24 Samples

Download data: TXT

(Submitter supplied) New and effective therapeutical options are available for the treatment of Rheumatoid Arthritis. One of such treatments is rituximab, and chimeric anti-CD20 antibody that selectively depletes the CD20+ B cell subpopulation. Similar to established anti-TNF alpha therapies, there is a subgroup of RA patients that do not experience significant clinical response. Therefore, one of the major necessities in actual RA therapeutical management is to identify reliable predictors of the response to this therapies. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL2507

23 Samples

Download data: TXT

(Submitter supplied) The research hypothesis was that the unique expression profile of monocytes in response to Interferon-beta (IFN-β) might be masked by the response profile of the more abundant T cells. The analysis of monocytes response may highlight novel IFN-β functions and pathways that have not been recognized previously. The aim of this study was to characterized the IFN-β transcriptional response in monocytes, a small but influential cell-subset, using gene expression profile and pathway analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

12 Samples

Download data: TXT

(Submitter supplied) This study demonstrates quantitative and qualitative differences between type I IFN signatures in autoimmunity and viral infection using purified CD4pos T cells and CD16pos- and CD16neg-monocyte subsets. We were able to discriminate between cell-specific viral response signatures and the pathogenically amplified IFN signatures observed in autoimmunity. The differences were of both a qualitative and quantitative nature, as the signatures in the patients with SLE were characterized by much more complexly compiled gene patterns with increased absolute gene expression levels.

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS4888 GDS4889 GDS4890

Platform:

GPL570

36 Samples

Download data: CEL, CHP

Analysis of CD16+ monocytes from SLE patients and YFV-immunized healthy donors. The YFV immunization can be regarded as a real viral infection, based on clinical/serological manifestations. Results provide insight into differences in type I interferon responses in autoimmunity and viral infection.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state, 7 individual, 3 protocol sets

Platform:

GPL570

Series:

GSE51997

10 Samples

Download data: CEL, CHP

Analysis of CD16- monocytes from SLE patients and YFV-immunized healthy donors. The YFV immunization can be regarded as a real viral infection, based on clinical/serological manifestations. Results provide insight into differences in type I interferon responses in autoimmunity and viral infection.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state, 8 individual, 3 protocol sets

Platform:

GPL570

Series:

GSE51997

12 Samples

Download data: CEL, CHP

Analysis of CD4+ T cells from SLE patients and YFV-immunized healthy donors. The YFV immunization can be regarded as a real viral infection, based on clinical/serological manifestations. Results provide insight into differences in type I interferon responses in autoimmunity and viral infection.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 disease state, 10 individual, 3 protocol sets

Platform:

GPL570

Series:

GSE51997

14 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL8490 GPL6947

192 Samples

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(Submitter supplied) Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. A lingering concern, however, is that the changes associated with EBV transformation of LCLs reduce the usefulness of LCLs as a surrogate model for primary tissues. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

96 Samples

Download data: TXT