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Items: 20

1.

Microarray Based Comparison of three Amplification Methods For Nanogram Amounts of Total RNA

(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
Series
Accession:
GSE2019
ID:
200002019
2.

Microarray Based Comparison of two Amplification Methods For Nanogram Amounts of Total RNA

(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
Series
Accession:
GSE1435
ID:
200001435
3.

Use of an Isothermal Linear Amplification Method with Small Samples on DNA Microarrays

(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
Series
Accession:
GSE2252
ID:
200002252
4.

Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling

(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
Series
Accession:
GSE15398
ID:
200015398
5.

cRNA amplification methods enhance microarray identification of transcripts expressed in the nervous system

(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
Series
Accession:
GSE9485
ID:
200009485
6.

Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating 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; Expression profiling by RT-PCR
Platforms:
GPL17989 GPL570 GPL16288
64 Samples
Download data: CEL
Series
Accession:
GSE52717
ID:
200052717
7.

Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: RNA-Seq MCF7 and MCF10A single cell data

(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
Series
Accession:
GSE52716
ID:
200052716
8.

Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: RNA-Seq CIC data

(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
Series
Accession:
GSE52715
ID:
200052715
9.

Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: RT-PCR

(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
Series
Accession:
GSE52714
ID:
200052714
10.

Flexible multiplatform RNA profiling at the single cell level applied to enriched cancer initiating cells: Affymetrix array data

(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
Series
Accession:
GSE52712
ID:
200052712
11.

Small Sample Amplification Technologies

(Submitter supplied) This sample is part of a study that compares small sample amplification technologies. The analysis looks at differential gene expression when compared to one round of T7 amplification. A tumor cell line was used in comparison to a human reference RNA in this study. Keywords = amplification Keywords = small sample Keywords = Affymetrix Keywords: other
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL571
30 Samples
Download data: CEL, EXP
Series
Accession:
GSE2723
ID:
200002723
12.

Gene Expression Profiling of Whole Blood: Comparison of target preparation methods

(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
Series
Accession:
GSE13292
ID:
200013292
13.

Comparison of linear and exponential amplification techniques for expression profiling at the single-cell level

(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
Download data
Series
Accession:
GSE5136
ID:
200005136
14.

Comparison of RNA Amplification Techniques meeting the demands for the Expression Profiling of Clinical Cancer Samples

(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
Series
Accession:
GSE5588
ID:
200005588
15.

Evaluation of the performance of the Arabidopsis Pathoarray 464_001: an example of detailed analysis of mutants

(Submitter supplied) The Arabidopsis Pathoarray 464_001 (GPL3638) was used to compare response of wild-type, rps2-101C (Bent et al., 1994; Mindorinos et al., 1994) and ndr1-1 (Century et al., 1995) to Pseudomonas syringae strain expressing avrRpt2. The two mutants are compromised in RPS2-mediated resistance but distinct difference between them has not been described. The results suggested that ndr1-1 affects a defense signaling pathway(s) in addition to the RPS2-dependent pathway, and indicate that the microarray is a powerful tool for systems analysis of the Arabidopsis disease signaling network. more...
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL3638
8 Samples
Download data: GPR
Series
Accession:
GSE5308
ID:
200005308
16.

Evaluation of performance of Arabidopsis Pathoarray 464_001: comparison with ATH1

(Submitter supplied) To evaluate technical reproducibility of Arabidopsis Pathoarray 464_001 (GPL3638), two slides were hybridized with labeled amplified RNA prepared from identical RNA. The RNA was prepared from Pseudomonas syringae ES4326- and 5mM MgSO4- injected samples (Psm 24h set C and mock 24h set C. See also GSE4429, GSM99793 and GSM99794). Keywords: Evaluation of a custom microarray performance
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL3638
4 Samples
Download data: GPR
Series
Accession:
GSE4632
ID:
200004632
17.

Analysis of Arabidopsis thaliana gene expression in response to the bacterial pathogen Pseudomonas syringae ES4326

(Submitter supplied) In order to protect themselves from pathogens, plants activate a battery of defense pathways, many of which involve changes in gene expression. We are interested in identifying plant genes that are differentially expressed in response to pathogen exposure, with the ultimate goal of studying the roles of these genes in plant defense. Keywords: disease response
Organism:
Arabidopsis thaliana
Type:
Expression profiling by array
Platform:
GPL198
2 Samples
Download data
Series
Accession:
GSE4429
ID:
200004429
18.

Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

(Submitter supplied) Abstract: BACKGROUND: T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays. RESULTS: Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
4 related Platforms
73 Samples
Download data
Series
Accession:
GSE4349
ID:
200004349
19.

Correlation between expression levels of different tumors measured by poly(A)+RNA and aRNA

(Submitter supplied) Zhao et al. Amplification Table 7 This experiment was designed to determine the correlation between expression levels of defferent tumors (BC2 and BC91) measured by poly(A)+RNA and aRNA for each tumor. Total RNA was amplified using the Jeffrey lab protocol with G50 cleanup. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
Organism:
Homo sapiens
Type:
Expression profiling by array
Platforms:
GPL3045 GPL1282 GPL3046
13 Samples
Download data
Series
Accession:
GSE3563
ID:
200003563
20.

Effect of column cleanup on T7 based RNA linear amplification

(Submitter supplied) Zhao et al. Amplification Table 4 This experiment was designed to evaluate the effect of column cleanup on the fidelity and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol with or without G50 cleanup. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
Organism:
Homo sapiens
Type:
Expression profiling by array
Platforms:
GPL3047 GPL1282 GPL3046
12 Samples
Download data
Series
Accession:
GSE3562
ID:
200003562
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