GEO DataSets

Analysis of cell-free plasma from pregnant women during the first, second, third trimesters and immediately post-partum. Results provide insight into a noninvasive means to monitor the expression status of many tissues and measure temporal expression of genes longitudinally during development.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 5 development stage, 15 individual sets

Platform:

GPL6244

Series:

GSE56899

48 Samples

Download data: CEL

(Submitter supplied) Circulating cell-free RNA in the blood provides a potential window into the health, phenotype, and developmental programs of a variety of human organs. We employed high throughput methods of RNA analysis such as microarrays and next-generation sequencing to characterize the global landscape circulating RNA in a cohort of human subjects. By focusing on genes whose expression is highly specific to certain tissues, we were able to identify the relative contributions of these tissues to circulating RNA, and to monitor changes in tissue development and health. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS5088

Platform:

GPL6244

48 Samples

Download data: CEL

(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

Download data

(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) Digestive Gland Samples: A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum. Total RNA was extracted from three (3) independent biological replicates of digestive gland for each sampling site, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified1,127 probes differentially expressed. more...

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL10900

12 Samples

Download data: TXT

(Submitter supplied) A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in digestive gland of R. philippinarum sampled in four seasons in 4 different areas of Venice Lagoon. For each tissue, total RNA was extracted from four (4) independent biological replicates of digestive gland, each consisting of tissue pools of five (5) animals.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL10900

64 Samples

Download data: TXT

(Submitter supplied) A manila clam oligo microarray platform (GPL10900) was used to profile gene expression in gills and digestive gland of R. philippinarum. For each tissue, total RNA was extracted from three (3) independent biological replicates of digestive gland and gills, each consisting of tissue pools of five (5) animals. Statistical analysis with SAM (Significance Analysis of Microarray) identified 8,257 probes differentially expressed between the two different tissues.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL10900

6 Samples

Download data: TXT

(Submitter supplied) Four pools of digestive glands were treated as biological replicates in order to evaluate the repeatability of Ruditapes philippinarum oligo microarray platform.

Organism:

Ruditapes philippinarum

Type:

Expression profiling by array

Platform:

GPL10900

4 Samples

Download data: TXT

(Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

6 Samples

Download data: BAM, TXT, XLS

(Submitter supplied) Background The combination of high-throughput transcript profiling and next-generation sequencing technologies is a prerequisite for genome-wide comprehensive transcriptome analysis. Our recent innovation of deepSuperSAGE is based on an advanced SuperSAGE protocol and its combination with massively parallel pyrosequencing on Roche’s 454 sequencing platform. As a demonstration of the power of this combination, we have chosen the salt stress transcriptomes of roots and nodules of the third most important legume crop chickpea (Cicer arietinum L.). more...

Organism:

Cicer arietinum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11675

4 Samples

Download data

(Submitter supplied) Whole blood was collected as part of monthly veterinary checkups of bottlenose dolphins housed at Dolphing Quest in Waikoloa, Hawaii, USA. Gene expression from 5 samples was analyzed for comparison to the blood transcriptome of the beluga whale.

Organism:

Tursiops truncatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21538

5 Samples

Download data: FASTA, XLSX

(Submitter supplied) Four captive bottlenose dolpins housed in Kona, Hawaii, were serially sampled at approximately monthly intervals over the course of one year, in order to establish baseline information on the content and variation of the dolphin blood transcriptome.

Organism:

Tursiops truncatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21538

31 Samples

Download data: FASTA, PDF, XLS, XLSX

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL9052 GPL13695

16 Samples

Download data: CEL, TXT

(Submitter supplied) Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13695

8 Samples

Download data: CEL, TXT

(Submitter supplied) Whole-genome transcriptome measurements are pivotal for characterizing carcinogenic mechanisms of chemicals and predicting toxic classes, such as genotoxicity, from in vitro and in vivo assays. DNA microarrays have evolved as the gold standard for this purpose. In recent years deep sequencing technologies have been developed that hold the promise of measuring the transcriptome with RNA-seq in a more accurate and unbiased manner than microarrays. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9052

8 Samples

Download data: TXT

(Submitter supplied) Circulating RNAs are a less invasive and easy accessed source of samples for biomedical research and clinical applications. However, circulating mRNA is mostly fragmented and less abundant. High throughput RNA sequencing (RSEQ) and DASL assay have been both applied to profile such fragmented RNA samples. In this study, we compared the ability of transcriptomic profiling of the two platforms. Circulating RNAs from three non-small cell lung cancer patients and three age-matched healthy controls were analyzed by RSEQ and DASL assay. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14951

6 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL570 GPL11154

10 Samples

Download data: CEL, FPKM_TRACKING

(Submitter supplied) The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The objective of this study was to compare the suitability of two technologies for profiling the human fetal transcriptome: RNA-Seq and expression microarray. Comparisons were based on total numbers of gene detected, rank-order gene expression, and functional genomic analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

5 Samples

Download data: CEL