GEO DataSets

(Submitter supplied) Rat mammary glands were obtained from individual rats in RXR treated (a) and control (b) conditions (12 rats in each condition). The 24 samples were hybridized individually. Also, in each condition, samples were combined into different pools of 2, pools of 3, pools of 12. Technical replicates were also run. Keywords: other

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Dataset:

GDS1452

Platform:

GPL341

56 Samples

Download data: CEL

Analysis of mammary glands from Wistar Furth females fed a diet supplemented with the retinoic X receptor ligand LG100268. 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, transformed count, 2 agent, 2 protocol sets

Platform:

GPL341

Series:

GSE2331

56 Samples

Download data: CEL

(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

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

(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) Abstract: BACKGROUND: Obtaining reliable and reproducible two-color microarray gene expression data is critically important for understanding the biological significance of perturbations made on a cellular system. Microarray design, RNA preparation and labeling, hybridization conditions and data acquisition and analysis are variables difficult to simultaneously control. A useful tool for monitoring and controlling intra- and inter-experimental variation is Universal Reference RNA (URR), developed with the goal of providing hybridization signal at each microarray probe location (spot). more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

6 related Platforms

31 Samples

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(Submitter supplied) RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL3304

14 Samples

Download data

(Submitter supplied) Microarray coverage of UHRR was determined by counting the number of spots with intensities exceeding the 1% and 5% false positive rates defined using the yeast negative control spots. Seven microarrays from different print runs were used. In four experiments, the UHRR was labeled with Cy5 and in three experiments with Cy3. Labeled UHRR was co-hybridized with Common Reference RNA (CRF) developed at Stanford University (8) labeled with the alternate dye. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

4 related Platforms

7 Samples

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(Submitter supplied) Total RNA isolated from 10 individual human cell lines were reverse-transcribed to cDNA, labeled with Cy5 and co-hybridized with Cy3-labeled UHRR onto 43,000-spot cDNA microarrays (Stanford University). The data was analyzed using GeneTraffic software. Approximately 6000-8000 spots out of 43,000 (14-18 %) were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics in only one cell line was determined. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1835

Platform:

GPL3305

10 Samples

Download data

Analysis of individual cell lines representing different tissues against a Universal Reference RNA (URR). URR prepared from pooled RNA from the individual cell lines. Results indicate the individual cell lines contribute their own unique set of genes, thereby diversifying gene representation in URR.

Organism:

Homo sapiens

Type:

Expression profiling by array, log2 ratio, 10 cell line sets

Platform:

GPL3305

Series:

GSE3972

10 Samples

Download data

(Submitter supplied) Paired End PolyA-+ RNA-sequencing of NGP cells with and without NGP treatment in 10 replicates.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

20 Samples

Download data: TSV

(Submitter supplied) Both spotted long oligonucleotide arrays and Affymetrix GeneChips were used to measure differential gene expression in two RNA samples (K562 erythroleukemia RNA and the Stratagene Universal Human Reference RNA). For Affymetrix technology, the two RNAs were analyzed separately. There are two replicates for K562 RNA (GSM4843 and GSM4844) and three for the Stratagene Universal reference (GSM4845-GSM4847). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Datasets:

GDS222 GDS223

Platforms:

GPL273 GPL8300 GPL274

23 Samples

Download data: CEL

Part of a comparison of spotted long oligonucleotide arrays with in situ synthesized 25-mer arrays. Examination of amplified and unamplified K562 erythroleukemia RNA and Stratagene Universal Human Reference RNA.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 cell type sets

Platform:

GPL8300

Series:

GSE344

5 Samples

Download data: CEL

Part of a comparison of spotted long oligonucleotide arrays with in situ synthesized 25-mer arrays. Examination of amplified and unamplified K562 erythroleukemia RNA and Stratagene Universal Human Reference RNA.

Organism:

Homo sapiens

Type:

Expression profiling by array, log ratio, 3 protocol sets

Platform:

GPL273

Series:

GSE344

14 Samples

Download data

(Submitter supplied) Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array; Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL20115 GPL22722 GPL16791

55 Samples

Download data: TXT

(Submitter supplied) Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL22722

4 Samples

Download data: TXT, XLSX

(Submitter supplied) Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL22722

21 Samples

Download data: TXT, XLSX

(Submitter supplied) Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20115

10 Samples

Download data: TXT, XLSX

(Submitter supplied) Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their expressions in tumor and plasma are largely unknown. Here, our study firstly suggested that microarray should be more efficient than RNA sequencing for circRNA profiling. Then, we detected ~80,000 circRNAs expressed in cervical tumors and matched normal tissues by microarray, and ~23,000 of them are differently expressed. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL22722

10 Samples

Download data: TXT, XLSX