Similar studies for GEO DataSets (Select 200045892) - GEO DataSets

Links from GEO DataSets

Items: 20

Select item 2000458921.

Temporal Concordance between Apical and Transcriptional Points-of-Departure for Chemical Risk Assessment

(Submitter supplied) The number of legacy chemicals without toxicity reference values combined with the rate of new chemical development are overwhelming the capacity of the traditional risk assessment paradigm. More efficient approaches are needed to quantitatively estimate chemical risks. In this study, rats were dosed orally with multiple doses of six chemicals for 5 days, 2, 4, and 13 weeks. Target organs were analyzed for traditional histological and organ weight changes and transcriptional changes using microarrays. more...

Organism:: Rattus norvegicus

Type:: Expression profiling by array

Platform:: GPL16985
720 Samples

Download data: CEL

Series

Accession:: GSE45892

ID:: 200045892

Select item 2000212102.

Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic Acid on rat kidneys

(Submitter supplied) RNA-Seq has been increasingly used for the quantification and characterization of transcriptomes. The ongoing development of the technology promises the more accurate measurement of gene expression. However, its benefits over widely accepted microarray technologies have not been adequately assessed, especially in toxicogenomics studies. The goal of this study is to enhance the scientific community's understanding of the advantages and challenges of RNA-Seq in the quantification of gene expression by comparing analysis results from RNA-Seq and microarray data on a toxicogenomics study. more...

Organism:: Rattus norvegicus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL10287
8 Samples

Download data: TXT

Series

Accession:: GSE21210

ID:: 200021210

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000362443.

Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells

(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

Series

Accession:: GSE36244

ID:: 200036244

Select item 2000362434.

Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (Affymetrix)

(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

Series

Accession:: GSE36243

ID:: 200036243

Select item 2000362425.

Transcriptomic response to benzo[a]pyrene treatment in HepG2 cells (RNA-Seq)

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9052
8 Samples

Download data: TXT

Series

Accession:: GSE36242

ID:: 200036242

Select item 2000629036.

RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice

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

Organism:: Mus musculus

Type:: Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:: GPL7202 GPL17021
93 Samples

Download data: GPR, TXT

Series

Accession:: GSE62903

ID:: 200062903

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000629027.

RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice [RNA-Seq]

(Submitter supplied) Dose-dependent hepatic gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure as well as compare the performance of RNA-Seq and Agilent oligonucleotide microarrays for detection and identificatioin of differentially expressed genes.

Organism:: Mus musculus

Type:: Expression profiling by high throughput sequencing

Platform:: GPL17021
45 Samples

Download data: TXT

Series

Accession:: GSE62902

ID:: 200062902

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000628508.

RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice [Array]

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL7202
48 Samples

Download data: GPR

Series

Accession:: GSE62850

ID:: 200062850

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2000658329.

RNA-Seq atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications

(Submitter supplied) Purpose: provide evidence that RNA-seq can add information to transcriptome profiling already discovered by other technologies for atopic dermatitis Methods: mRNA profiles of 20 atopic dermatitis were analyzed to compare lesional and non-lesional skin, then transcriptomes found by reads were compared to Microarray and RT-PCR Results:RNA-seq provided complementary genes to AD transcriptome IL-36 and TREM-1 Conclusions: Our study represents the first analysis of lesional AD tissue by RNA-seq and comparison to microarray and RT-PCR

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL10999
40 Samples

Download data: TXT

Series

Accession:: GSE65832

ID:: 200065832

Select item 20000230310.

Rat liver response to Clofibrate, DEHP or VPA

(Submitter supplied) The project had 2 goals: 1) To evaluate the transcriptional response of 3 prototypical toxicants (Clofibrate, VPA, and DEHP) on rat lever. 2) To evaluate the impact pooling samples has on data analysis. Keywords = Clofibrate Keywords = Diethylhexyl phthalate Keywords = Phthalic acid bis(2-ethylhexyl ester) Keywords = Sodium Valproate Keywords = Valproic Acid Keywords = VPA Keywords = vehicle Keywords: other

Organism:: Rattus norvegicus

Type:: Expression profiling by array

Dataset:: GDS1451
Platform:: GPL85
94 Samples

Download data: CEL, CHP, EXP

Series

Accession:: GSE2303

ID:: 200002303

Select item 145111.

Toxicants effect on liver: pooled and individual sample comparison

Analysis of livers of Sprague-Dawley males at various time points up to 168 hours after treatment with clofibrate, diethylhexylphthalate, or valproic acid. Expression profiles from pooled and individual samples compared. Results provide insight into the impact of pooling on experimental analysis.

Organism:: Rattus norvegicus

Type:: Expression profiling by array, count, 3 agent, 2 protocol, 4 time sets

Platform:: GPL85
Series:: GSE2303
94 Samples

Download data: CEL, CHP, EXP

DataSet

Accession:: GDS1451

ID:: 1451

Select item 20003314112.

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

(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

Series

Accession:: GSE33141

ID:: 200033141

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20000244113.

Hepatic Gene Expression Changes Throughout the Day in the Fischer Rat

(Submitter supplied) One µg of total RNA from either an individual rat or from a pooled sample was amplified and labeled with a fluorescent dye (either Cy3 or Cy5) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s protocol. The amount and quality of the resulting fluorescently labeled cRNA was assessed using a Nanodrop ND-100 spectrophometer and an Agilent Bioanalyzer. more...

Organism:: Rattus norvegicus

Type:: Expression profiling by array

Platform:: GPL890
20 Samples

Download data

Series

Accession:: GSE2441

ID:: 200002441

Select item 20006536514.

A Nested Parallel Experiment Demonstrates Differences in Intensity-Dependence Between RNA-Seq and Microarrays

(Submitter supplied) We carried out a parallel nested experiment performed simultaneously on RNA-Seq and microarrays that systematically split variation into four stages (treatment, biological variation, library preparation, and chip/lane noise), allowing a separation and comparison of the sources of variation in a well-controlled cellular system, Saccharomyces cerevisiae.

Organism:: Saccharomyces cerevisiae

Type:: Expression profiling by array

Platform:: GPL11382
16 Samples

Download data: TXT

Series

Accession:: GSE65365

ID:: 200065365

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20006546915.

RNA-seq and Microarray in Transcriptome Profiling of Anterior Cruciate Ligament Tears: Implications for Prognostic Biomarkers Discovery

(Submitter supplied) Injury to anterior cruciate ligament (ACL) is common in young individuals and a frequent cause of functional instability and early onset of osteoarthritis. The healing potential of an injured ACL is known to decay over time. The molecular origin of this healing deficiency largely remains elusive but plausibly involves gene transcripts associated with tissue healing. To explore this possibility, we set out to identify transcript expression differences in injured ACL remnants recovered at the time of surgical reconstruction, via microarray (n=24) and RNA-seq (n=8) technologies in transcriptome profiling. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL16791
8 Samples

Download data: TXT

Series

Accession:: GSE65469

ID:: 200065469

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20006138516.

Transcript Expression Changes over Time-from-injury in Anterior Cruciate Ligament Tears: Implications for Reconstruction and Repair

(Submitter supplied) The anterior cruciate ligament (ACL) is an essential stabilizer of the tibiofemoral articulation. ACL tears often lead to functional instability and are associated with an increased risk for osteoarthritis. The healing potential of the injured ACL is poorly understood and is considered to be limited. Transcriptome-wide expression profiles of 24 human ACL remnants recovered at the time of surgical reconstruction were analyzed utilizing the Agilent human 8x60K microarray platform. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL17077
24 Samples

Download data: TXT

Series

Accession:: GSE61385

ID:: 200061385

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20000614017.

Cross platform microarray analysis for robust identification of differentially expressed genes

(Submitter supplied) Microarrays have been widely used for the analysis of gene expression and several commercial platforms are available. The combined use of multiple platforms can overcome the inherent biases of each approach, and may represent an alternative that is complementary to RT-PCR for identification of the more robust changes in gene expression profiles. In this paper, we combined statistical and functional analysis for the cross platform validation of two oligonucleotide-based technologies, Affymetrix (AFFX) and Applied Biosystems (ABI), and for the identification of differentially expressed genes. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platforms:: GPL570 GPL1426
12 Samples

Download data: CEL

Series

Accession:: GSE6140

ID:: 200006140

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20002602418.

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarray

(Submitter supplied) C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs). more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platforms:: GPL6885 GPL1261
44 Samples

Download data: CEL, TXT

Series

Accession:: GSE26024

ID:: 200026024

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20003175719.

A Systematic Comparison and Evaluation of High Density Exon Arrays and RNA-seq technology in Unraveling the Peripheral Blood Transcriptome of Sickle Cell Disease.

(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...