GEO DataSets

(Submitter supplied) Recombinant human erythropoietin administration studies involving transcriptomic approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage and whole blood leftover from standard haematological testing in short-term storage could be used for transcriptomic analysis despite lacking RNA preservative. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

32 Samples

Download data: CEL, CHP

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

30 Samples

Download data

(Submitter supplied) Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in short-term storage could be used for transcriptomic analysis despite lacking RNA preservation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

16 Samples

Download data: TXT

(Submitter supplied) Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in long-term storage could be used for transcriptomic analysis despite lacking RNA preservation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28038

14 Samples

Download data: TXT

(Submitter supplied) Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is an intracellular pathogen that can persist inside host macrophages during infection via a diverse range of mechanisms that subvert the host immune response. In the current study, we have analysed and compared the transcriptomes of M. bovis-infected monocyte-derived macrophages (MDM) purified from six Holstein-Friesian females with the transcriptomes of non-infected control MDM from the same animals over a 24 h period using strand-specific RNA sequencing (RNA-seq). more...

Organism:

Bos taurus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15750

14 Samples

Download data: TXT, XLSX

(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) 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

(Submitter supplied) BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether RNA-Seq could be used to identify IPF expression profiles from archived Formalin-Fixed Paraffin-Embedded (FFPE) lung fibrotic tissue. RESULTS: We isolated total RNA from 7 IPF and 5 control FFPE lung tissues (median archived time 6 years) and performed 50 bp paired-end sequencing on Illumina 2000 HiSeq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

11 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) For decades, formalin-fixing and paraffin embedding (FFPE) has been routinely used to preserve tissue samples for histological analysis. Global gene expression analysis of these archival tissues has the potential to greatly advance research attempting to link perturbations in molecular pathways to disease outcome. We investigated 16-year-old FFPE mouse liver samples treated with phenobarbital and created a protocol for their analysis using Agilent gene expression arrays. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL13912

28 Samples

Download data: TXT

(Submitter supplied) Fetal life is a crucial period for sexual reproduction when bipotential gonads differentiate into either a testis or an ovary. Gaining insights into the complex molecular events underlying this process is central to a better understanding of disorders of sexual development. The present work therefore intends to improve the knowledge on molecular pathways at play during gonad development in humans using RNA-Sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

48 Samples

Download data: BED, GTF, TXT, XLSX

(Submitter supplied) Time series of eleven breast cancer samples subjected to different cold ischemic stress of up to 3 hr post tumor excision. A different 2x2 factorial within this study evaluated the effect of stabilization method (RNAlater vs snap freezing) and stablization delay (0 and 40 min) at room temperature.

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS4088

Platform:

GPL96

86 Samples

Download data: CEL

Analysis of breast tumor samples preserved using 2 different RNA stabilization methods (RNAlater or snap freezing) up to 3 hours post tumor excision. Results provide insight into the effects of tissue handling on RNA integrity and microarray measurements from resected breast cancers.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 11 individual, 35 other, 2 protocol, 6 time sets

Platform:

GPL96

Series:

GSE25011

86 Samples

Download data: CEL

(Submitter supplied) Sickle cell transcriptome was analyzed using whole blood clinical specimens on the Affymetrix Human Exon 1.0 ST arrays and Illumina’s deep sequencing technologies. Data analysis indicated a strong concordance (R=0.64) between exon array and RNA-seq in both gene level and exon level expression of transcripts. The magnitude of fold changes in the expression levels for the differentially expressed genes (p<0.05) was found to be higher in RNA-seq than microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

10 Samples

Download data: CEL

(Submitter supplied) We conducted an animal experiment and used total RNA sequencing (RNA-Seq) to identify novel RNA markers to detect autologous blood transfusion (ABT) doping within red blood cells (RBCs) as a pilot study before human trials. The total RNA-Seq and bioinformatics were performed using rat RBCs that were stored 10- and 20-day periods with citrate–phosphate–dextrose solution with adenine (CPDA) at 4°C In the results, we identified three significant genes whose expression levels were drastically decreased according to the storage period. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20084

12 Samples

Download data: XLSX

(Submitter supplied) The Ixodidea tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Study of gene targets of the tick species provides insight to find novel tick protective antigen for drug development and vaccine targets. To obtain a broader picture of gene sequences and changes in expression level, we aimed to characterize the whole body transcriptome in D. marginatus adult female after engorgement and long-term starvation using RNA-seq. more...

Organism:

Dermacentor marginatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28620

9 Samples

Download data: FASTA, TXT

(Submitter supplied) The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It expresses enzymes for both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. To gain insights into the C. thermocellum genes, using an updated version of the C. thermocellum ATCC 27405 genome annotation, that are required for specific growth on the cellulosic feedstocks of either pretreated switchgrass or Populus, duplicate fermentations were conducted with a 5 g/L solid substrate loading. more...

Organism:

Acetivibrio thermocellus 27405; Acetivibrio thermocellus ATCC 27405

Type:

Expression profiling by array

Platform:

GPL17171

8 Samples

Download data: CALLS, PAIR

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL570 GPL10123

9 Samples

Download data: CEL, TXT

(Submitter supplied) Primary SCEC is a rare malignancy without established treatment strategy. Although previous studies suggested that there were similarities between SCEC and SCLC in clinical manifestation and pathological morphology, genetic studies on this highly malignant tumour remains sparse. This study was designed to investigate the copy number variations (CNVs) of SCEC.

Organism:

Homo sapiens

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10123

3 Samples

Download data: TXT

(Submitter supplied) Primary SCEC is a rare malignancy without established treatment strategy. Although previous studies suggested that there were similarities between SCEC and SCLC in clinical manifestation and pathological morphology, genetic studies on this highly malignant tumour remained sparse. This study was designed to investigate the gene expression profile of SCEC, and compare it with the known expression data of SCLC and EC.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL