GEO DataSets

(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) 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 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) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL5175 GPL5188

40 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

20 Samples

Download data: CEL

(Submitter supplied) Background:Alternative splicing and isoform level expression profiling is an emerging field of interest within genomics. Splicing sensitive microarrays, with probes targeted to individual exons or exon-junctions, are becoming increasingly popular as a tool capable of both expression profiling and finer scale isoform detection. Despite their intuitive appeal, relatively little is known about the performance of such tools, particularly in comparison with more traditional 3’ targeted microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5175

20 Samples

Download data: CEL

(Submitter supplied) Red light can affect a variety of responses in Arabidopsis. We characterize the early gene expression patterns of seedlings exposed to 1 hour of red light using a small sized sample of 5, 7-day-old seedlings and also performed dark controls. Methods that were developed for tissue extraction and labeling for microarrays were tested using these samples Keywords: 1 time point

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

2 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 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) Impact of pre-analytical handling on Bone Marrow (BM) mRNA Gene Expression: We have investigated the impact of RNA extraction protocols and time delays (24 and 48h) between sample aspiration and RNA extraction on RNA quality and gene expression profiles. Intact RNA can be extracted from BM samples stored at room temperature for up to 48h after aspiration. However, storage of BM has dramatic effects on mRNA expression of individual transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS969

Platform:

GPL8300

9 Samples

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Analysis of impact of pre-analytical handling of bone marrow (BM). Time delays of 0, 24, or 48 hours between sample aspiration and RNA extraction examined. Storage of BM has dramatic effects on mRNA expression of individual transcripts.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 time sets

Platform:

GPL8300

Series:

GSE1347

9 Samples

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(Submitter supplied) d-serine is naturally present throughout the human body. It is also used as add-on therapy for treatment-refractory schizophrenia. d-Serine interacts with the strychnine-insensitive glycine binding site of NMDA receptor, and this interaction could lead to potentially toxic activity (i.e., excitotoxicity) in brain tissue. The transcriptomic changes that occur in the brain after d-serine exposure have not been fully explored. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS3643

Platform:

GPL1355

24 Samples

Download data: CEL

Analysis of forebrains of animals treated with up to 500 mg/kg D-serine for 96 hours. D-serine is involved in many physiological processes through its interaction with the glycine binding site of the NMDA receptor. Results provide insight into the impact of D-serine exposure on neuronal functions.

Organism:

Rattus norvegicus

Type:

Expression profiling by array, count, 2 agent, 6 dose sets

Platform:

GPL1355

Series:

GSE10748

24 Samples

Download data: CEL

(Submitter supplied) Investigation of Gene Expression Profiling in Unstaged Head Hair Follicles Plucked from Men and Women Keywords: Gene Expression Profiling of Normal Hair Follicles

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS2356

Platform:

GPL201

10 Samples

Download data: CEL, EXP

Analysis of unstaged hair follicles from males and females. Results provide insight into the feasibility of extracting intact RNA, from a small number of hair follicles, in sufficient quantities for expression profiling.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 2 gender sets

Platform:

GPL201

Series:

GSE3058

10 Samples

Download data: CEL, EXP

(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) Study goal is to disclose features of gene expressio profile of non-cancerous liver-infiltrating lymphocytes of type C hepatitis patients with hepatocellular carcinomas and tumor-infiltrating lymphocytes of type C hepatitis patients with hepatocellular carcinomas. Keywords: gene expression profile, non-cancerous liver-infiltrating lymphocytes, tumor-infiltrating lymphocytes, type C hepatitis, hepatocellular carcinoma

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1291

24 Samples

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(Submitter supplied) Study goal is to disclose features of gene expression profile of peripheral blood mononuclear cells obtained from type C cirrhotic patients with or without hepatocellular carcinomas. Keywords: gene expression profile, peripheral blood mononuclear cells, type C liver cirrhosis

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1291

62 Samples

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