GEO DataSets

(Submitter supplied) Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

20 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; Expression profiling by RT-PCR

Platforms:

GPL16288 GPL570 GPL17989

64 Samples

Download data: CEL

(Submitter supplied) Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16288

10 Samples

Download data: XLSX

(Submitter supplied) Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16288

12 Samples

Download data: XLSX

(Submitter supplied) Accurate profiling of RNA expression of single cells is a valuable approach for broadening our understanding of cancer biology and mechanisms of dissemination, but requires the development of reliable methods for their molecular characterization. Here we evaluate a single cell methodology which generates microgram amounts of cDNA suitable for next generation sequencing (RNA-Seq), high throughput RT-qPCR and Affymetrix array analysis. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL17989

22 Samples

Download data: TXT

(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) Diverse cell types have unique transcriptional signatures that are best interrogated at single-cell resolution. Here we describe a novel RNA amplification approach that allows for high fidelity gene profiling of individual cells. This technique significantly diminishes the problem of 3’bias and therefore enables detection of all regions of transcripts, including the recognition of mRNA with short or completely absent polyA tails, identification of noncoding RNAs, and discovery of the full array of splice isoforms from any given gene product. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

21 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL13447 GPL10999

21 Samples

Download data: BEDGRAPH, CEL, TXT

(Submitter supplied) mRNA expression was profiled from pooled bronchial airway epithelial cell brushings (n=3 patients/pool) obtained during bronchoscopy from healthy never (NS) and current smokers (S) and smokers with (C) and without (NC) lung cancer

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

8 Samples

Download data: BEDGRAPH, GTF, TXT

(Submitter supplied) mRNA expression was assayed from bronchial epithelial cell samples from smokers with and without lung cancer. A subset of the samples (2 of the lung cancer samples and 3 of the no cancer samples) were pooled and underwent whole transcriptome sequencing. The goals were to compare whole transcriptome sequencing gene expression levels to gene expression levels derived from these samples run on the Affymetrix HGU133A 2.0 platform.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL13447

13 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL24082

60 Samples

Download data: CEL

(Submitter supplied) In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

30 Samples

Download data: TXT

(Submitter supplied) In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL24082

30 Samples

Download data: CEL

(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

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