GEO DataSets

(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) We tested the performance of three methods for amplifying single-cell amounts of RNA under ideal conditions: T7-based in vitro transcription; switching mechanism at 5' end of RNA template (SMART) PCR amplification; and global PCR amplification. All methods introduced amplification-dependent noise when mRNA was amplified 108-fold, compared with data from unamplified cDNA. PCR-amplified cDNA demonstrated the smallest number of differences between two parallel replicate samples and the best correlation between independent amplifications from the same cell type, with SMART outperforming global PCR amplification. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL2584

56 Samples

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(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) 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) The in-house microarray consists of 167 RT-PCR derived DNA fragments representing 167 ORFs from bovine. The DNA fragments are printed 4 times on the surface of the microarray (four-replicate blocks). The 167 immune and endocrine genes grouped into the following categories: cytokine genes, chemoattractants or chemokines and their respective receptor genes, immune regulatory genes, T-cell associated genes, pattern recognition or innate host defense genes, immunglobin (Ig) or Ig-related genes, complement genes, antigen processing or presenting genes, and genes encoding endocrine hormones or their receptors. more...

Organism:

Arabidopsis thaliana; Bos taurus

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(Submitter supplied) Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from (1) human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20µM) for 24h, and (2) neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10µM) for 24h. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL8300 GPL885

20 Samples

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(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

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(Submitter supplied) This is a chicken multi-tissue cDNA microarray with 12752 elements. It comprises clones from chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. Sequence information is available from GenBank for all features on the array. Protocol: The clone-set was amplified in 96 well plates and re-arrayed into a 384-well Montage (Millipore) filtration plate to isolate the amplified DNA products. more...

Organism:

Gallus gallus

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(Submitter supplied) Background The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes. Results We have produced cDNA arrays using chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. From a total of 363,838 chicken ESTs representing 24 different adult or embryonic tissues, a set of 11,447 non-redundant ESTs were selected and added to an existing collection of clones (4,162) from immune tissues and a chicken bursal cell line (DT40). more...

Organism:

Gallus gallus

5 Series

60 Samples

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(Submitter supplied) For microarray experiments starting with nanogram amounts of RNA it is essential to implement reproducible and powerful RNA amplification techniques. Available methods were mainly tested for reproducibility, only a few studies concentrated on potential amplification bias. We evaluated three amplification protocols, which are less time-consuming than the commonly used T7-RNA polymerase based in vitro transcription protocols and therefore may be more suitable for clinical use: Template Switching (TS)-PCR (SMART-PCR Kit, BD), Ribo-SPIA (single primer isothermal amplification, Oviation, Nugen) and a random primer-based PCR. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL4190 GPL4203 GPL4192

41 Samples

Download data: GPR, SPT, 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) The publicly available genome sequence information of two rice strains, japonica cultivar Nipponbare and indica cultivar 93-11, opens a great opportunity for investigation of performances DNA genotyping by high-density oligonucleotide arrays. Here, we compare single feature polymorphism (SFP) detection performances between whole genome hybridization and transcript hybridization using Affymetrix Rice Expression Array and the two rice cultivars.

Organism:

Oryza sativa; Oryza sativa Indica Group; Oryza sativa Japonica Group

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL2025

27 Samples

Download data: CEL, CHP

(Submitter supplied) Since the early stages of tumorigenesis involve adhesion, escape from immune surveillance, vascularization and angiogenesis, we devised a strategy to study the expression profiles of all publicly known and putative secreted and cell surface genes. We designed a custom oligonucleotide microarray containing probes for 3531 secreted and cell surface genes to study 5 diverse human transformed cell lines and their derivative xenograft tumors. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1814

98 Samples

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(Submitter supplied) 25x75 mm in dimension. Protocol: 21K 60-mer oligo probes were designed from the MaizeGDB EST contigs and synthesized in situ by an ink-jet printing method employing standard phosphoramidite chemistry on glass slides.

Organism:

Zea mays

1 Series

24 Samples

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(Submitter supplied) See Talla et al. 2003 (PMID : 14499002)

Organism:

Saccharomyces cerevisiae

1 Series

22 Samples

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(Submitter supplied) See Talla et al. 2003 (PMID : 14499002)

Organism:

Saccharomyces cerevisiae

1 Series

18 Samples

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(Submitter supplied) The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. more...

Organism:

Saccharomyces cerevisiae

3 Series

16 Samples

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(Submitter supplied) The yeast 5803 ORFs MicroArray is composed of 32 subgrids, which follow a pattern of 8 metarows and 4 metacolumns. Each subgrid contains 20 columns and 20 rows with a dot spacing of 200 µm. Probes are spotted as closed duplicates. In order to provide a friendly environment, the first subgrid row on each array metarow contains all the normalization controls, which include the controls with serial dilution of the Renilla LuxA cDNA PCR product. more...

Organism:

Saccharomyces cerevisiae

1 Series

6 Samples

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(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

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