GEO DataSets

(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:

GPL1282 GPL3046 GPL3045

13 Samples

Download data

(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

(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

(Submitter supplied) Zhao et al. Amplification Table 3 This experiment was designed to evaluate the effect of ligase used in the second strand cDNA synthesis on the fidelity of T7 based RNA linear amplification. BC2 total RNA was amplified with or without ligase using Affymetrix protocol. 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:

GPL3046 GPL3047

11 Samples

Download data

(Submitter supplied) Zhao et al. Amplification Table 1 This experiment was designed to determine the effects of template switching (TS) primer and the type of columns used in ds cDNA cleanup on the fidelity of the T7 based RNA linear amplification. BC91 total RNA was amplified with or without TS primer and with two different ds cDNA cleanup protocols. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3045

20 Samples

Download data

(Submitter supplied) Zhao et al. Amplification BC2 uM This experiment was designed to assess the reproducibility of microarray hybridization using poly(A)+RNA. BC2 total RNA was isolated from which poly(A)+RNA was subsequently isolated. Three arrays were hybridized on the same day using arrays from the same batch. Two were done three months later using poly(A)+RNA freshly isolated from the same total RNA. A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL3046 GPL1282

5 Samples

Download data

(Submitter supplied) Zhao et al. Amplification Figure 1 This experiment was designed to evaluate the effect of in vitro transcription time on the fidelity, reproducibility, and yield of T7 based linear amplification. Duplicate reactions were performed at 37 degree for 2, 3, 4, 5, and 6 hours. Two additional 5-hour incubation reactions were stored at 4 degree overnight to determine the effect of low temperature incubation on amplification. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3046

12 Samples

Download data

(Submitter supplied) Zhao et al. Amplification Table 9 This experiment was designed to evaluate the effect of the amount of input total RNA on the fidelity, reproducibility, and yield of T7 based RNA linear amplification. BC2 total RNA was amplified using the Jeffrey lab protocol. Different amounts of T7 primer were used according to the quantity of input total RNA. Multiple amplifications were done for each quantity of input total RNA to minimize experimental variations. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL3047 GPL1282

9 Samples

Download data

(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

(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) We have developed a method of mRNA amplification based on T7 polymerase, where T7 promoter is attached to a oligonucleotide containing the mini-exon sequence, which will hybridize with cDNA molecules containing the anti-ME sequence

Organism:

Trypanosoma cruzi; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL23054

46 Samples

Download data: TXT

(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:

GPL96 GPL1857 GPL8300

15 Samples

Download data: CEL, EXP

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

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL4720

12 Samples

Download data: GPR