GEO DataSets

(Submitter supplied) Background: DNA microarrays provide a powerful method for global analysis of gene expression. The application of this technology to specific cell types and tissues, however, is typically limited by small amounts of available mRNA, thereby necessitating amplification. Here we compare microarray results obtained with two different methods of RNA amplification to profile gene expression in the C. elegans larval nervous system. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

8 Samples

Download data: CEL, CHP

(Submitter supplied) Background: With its fully sequenced genome and simple, well-defined nervous system, the nematode C. elegans offers a unique opportunity to correlate gene expression with neuronal differentiation. The lineal origin, cellular morphology and synaptic connectivity of each of the 302 neurons are known. In many instances, specific behaviors can be attributed to particular neurons or circuits. Here we describe microarray-based methods that monitor gene expression in C. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

24 Samples

Download data: CEL, CHP, EXP

(Submitter supplied) Background: Differential gene expression specifies the highly diverse cell types that constitute the nervous system. With its sequenced genome and simple, well-defined neuroanatomy, the nematode C. elegans is a useful model system in which to correlate gene expression with neuron identity. The UNC-4 transcription factor is expressed in thirteen embryonic motor neurons where it specifies axonal morphology and synaptic function. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Dataset:

GDS2786

Platform:

GPL200

7 Samples

Download data: CEL, EXP

Analysis of embryonic motor neurons marked with an unc-4::GFP reporter transgene. UNC-4 is a homoedomain transcription factor expressed in 13 embryonic motor neurons. Results contribute to a comprehensive picture of gene expression in a subset of motor neurons.

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array, count, 2 cell type sets

Platform:

GPL200

Series:

GSE8159

7 Samples

Download data: CEL, EXP

(Submitter supplied) Experiment 1: U133A arrays (2) hybridized to duplicate sscDNA samples prepared from 20 ng Clontech UHR RNA Experiment 2: Mu6500A arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 5 ng mouse liver RNA and 3 x 100 ng mouse liver RNA Experiment 3: U95Av2 arrays (6) hybridized to triplicate sscDNA samples prepared from 3 x 10 ng K562 RNA and 3 x 10 ng Stratagene UHR RNA Experiment 4: U95Av2 array (1) hybridized to sscDNA sample prepared from template minus reaction (negative control) Keywords: parallel sample

Organism:

Mus musculus; unidentified; Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL8300 GPL96 GPL1857

15 Samples

Download data: CEL, EXP

(Submitter supplied) For more than a decade, microarrays have been a powerful and widely used tool to explore the transcriptome of biological systems. However, the amount of biological material from cell sorting or laser capture microdissection is much too small to perform microarray studies. To address this issue, RNA amplification methods have been developed to generate sufficient targets from picogram amounts of total RNA to perform microarray hybridisation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

27 Samples

Download data: CEL, CHP

(Submitter supplied) We have demonstrated in vitro transcription (IVT) of cDNA sequences from purified Jurkat T-cell mRNA immobilization on microfluidic packed beads down to single-cell quantities. The microfluidic amplified aRNA was nearly identical in length and quantity compared with benchtop reactions using the same starting sample quantities. Microarrays were used to characterize the number and population of genes in each sample, allowing comparison of the microfluidic and benchtop processes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6098

36 Samples

Download data

(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) Nociceptive neurons develop a complex dendritic arbor to sense noxious stimuli, which enables animals to react to environmental insults and perform self-protective behaviours. The genetic programs controlling neuronal dendritic morphogenesis are poorly understood. In C. elegans, the PVD sensory neuron generates a complex dendritic arbor that envelops the body of the animal. This nociceptive neuron enables study of dendrite formation in vivo. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by array

Platform:

GPL200

6 Samples

Download data: CEL

(Submitter supplied) Differential gene expression between groups of homogenous cell types is a biological question whose time has come. RNA can be extracted from small numbers of cells, such as those isolated by laser capture microdissection, but the small amounts obtained often require amplification to enable whole genome transcriptome profiling by technologies such as microarray analysis and RNA-seq. Recently, advances in amplification procedures make amplification directly from whole cell lysates possible. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

20 Samples

Download data: CEL

(Submitter supplied) Considerable variation in gene expression data from different DNA microarray platforms has been demonstrated. However, no characterization of the source of variation arising from labeling protocols has been performed. To analyze the variation associated with T7-based RNA amplification/labeling methods, aliquots of the Stratagene Human Universal Reference RNA were labeled using 3 eukaryotic target preparation methods and hybridized to a single array type (Affymetrix U95Av2). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS1954

Platform:

GPL8300

20 Samples

Download data: CEL, EXP

Comparison of expression profiles generated using various T7 RNA polymerase-based in vitro transcription (IVT) RNA labeling methods. The length of the IVT reactions ranged from 4 to 16 hours. Results provide evidence for amplification method-dependent biases in gene expression data.

Organism:

Homo sapiens

Type:

Expression profiling by array, count, 3 protocol, 3 time sets

Platform:

GPL8300

Series:

GSE3254

20 Samples

Download data: CEL, EXP

(Submitter supplied) Gene expression profiling has become a tool of choice to study pathological or developmental questions but in most cases the material is scarce and requires sample amplification. Two main procedures have been used: in vitro transcription (IVT) and polymerase chain reaction (PCR), the former known as linear and the latter as exponential. Previous reports identified enzymatic pitfalls in PCR and IVT protocols; however the possible differences between the sequences affected by these amplification defaults were only rarely explored. more...

Organism:

Bos taurus

Type:

Expression profiling by array

Platform:

GPL6284

96 Samples

Download data

(Submitter supplied) To characterize the properties and evaluate the performance of the TAcKLE procedure, a novel method providing effective transcriptome amplification for expression analyses on oligonucleotide microarrays, we performed 20 two-color hybridizations using self-spotted Operon 27k arrays. A single source of universal human reference RNA (pooled from 10 cell lines) and RNA extracted from healthy breast tissue was used for all experiments to avoid differences in transcript abundance imposed by the RNA preparation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1384

20 Samples

Download data: TIFF

(Submitter supplied) Spotted long oligonucleotide array produced using the Operon Human Genome Oligo Set Version 2.1 (21,329 70mer oligonucleotides, based on build 147 of the Human UniGene database and the Human RefSeq Database, plus 24 controls) and the Operon Human Genome Oligo Set Version 2.1 Upgrade (5,462 70mer oligonucleotides, based on build 13.31 of the Human Ensembl Database). Spotting was performed in duplicates (replicate arrays) with 4x6 SMP3 pins (Telechem) at 18-20 °C and 40-50% RH on epoxysilane coated slides (Quantifoil) using 40 µM oligos in FBNC spotting buffer (G. more...

Organism:

Homo sapiens

2 Series

32 Samples

Download data

(Submitter supplied) Two T7 based methods One round of Amplification (Affymetrix) and Two round of Amplification were compared to two Ribo-SPIA based systems, RiboSPIA and pico Ribo SPIA systems. Data for Pico-RiboSPIA are listed here. All Hybridisation were performed using Affymetrix Mouse 430-2 gene chips. Data were all scaled to 500. For 12 chips performed with pico Ribo SPIA the scaling factor average was 2.0 +/- 0.3, background intensities 74.4 +/- 12.7 , noise 3.9 +/- 0.6, rawQ 2.5 +/- 0.3 Keywords: ordered

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL

(Submitter supplied) Two T7 based methods One round of Amplification (Affymetrix) and Two round of Amplification were compared to two Ribo-SPIA based systems, RiboSPIA and pico Ribo SPIA systems. Data for One Round of amplification , Two round of amplification and RiboSPIA are listed here. All Hybridisation were performed using Affymetrix Mouse 430-2 gene chips. Data were all scaled to 500 and scaling factor average was 3.6 +/- 0.9, background intensities 46 +/- 5 , noise 2.9 +/- 0.6, rawQ 1.5 +/- 0.2 Keywords: other

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

27 Samples

Download data: CEL, RPT, TXT

(Submitter supplied) Background: With lower manufacturing cost, high spot density, and flexible probe design, genomic tiling microarrays are ideal for comprehensive transcriptome studies. Typically, transcriptome profiling using microarrays involves reverse transcription, which converts RNA to cDNA. The cDNA is then labeled and hybridized to the probes on the arrays, thus the RNA signals are detected indirectly. Reverse transcription is known to generate artifactual cDNA, in particular the synthesis of second-strand cDNA, leading to false discovery of antisense RNA. more...

Organism:

Porphyromonas gingivalis; Porphyromonas gingivalis W83

Type:

Expression profiling by genome tiling array

Platform:

GPL11291

18 Samples

Download data: PAIR

(Submitter supplied) Spermatogenesis is a multi-step yet tightly regulated developmental process to produce male gemetes for reproduction. In mouse spermatogenesis, a sub-group of type A spermatogonia (Spga) known as spermatogonial stem cells (SSCs) maintain their population by self-renewal, and differentiate through mitosis and meiosis to form tetraploid (4n) pacchytene spermatocytes (Spcy) and haploid (n) round spermatids (Sptd), which further differentiate into functional sperms. more...

Organism:

Mus musculus

Type:

Expression profiling by genome tiling array

14 related Platforms

126 Samples

Download data: BAR, 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; Expression profiling by RT-PCR

Platforms:

GPL17989 GPL570 GPL16288

64 Samples

Download data: CEL