GEO DataSets

(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:

GPL23054 GPL11154

46 Samples

Download data: TXT

(Submitter supplied) To generate a high quality, annotated gene expression database of T. cruzi trypomastigotes(TRP), amastigotes (AMA), epimastigotes (EPI), and metacyclic trypomastigotes (MET). The global assessment of transcript abundances in each life-cycle stage of T. cruzi will identify stage-regulated genes and provide an essential element of an integrated database of T. cruzi genomic, proteomic, and transcriptomic data. more...

Organism:

Trypanosoma cruzi

Type:

Expression profiling by array

Platform:

GPL8132

4 Samples

Download data: MEV

(Submitter supplied) As Trypanosoma cruzi, the etiological agent of Chagas disease, multiplies in the cytoplasm of nucleated host cells, infection with this parasite is highly likely to affect host cells. We performed an exhaustive transcriptome analysis of T. cruzi-infected HeLa cells using an oligonucleotide microarray containing probes for greater than 47,000 human gene transcripts. In comparison with uninfected cells, those infected with T. more...

Organism:

Homo sapiens; Trypanosoma cruzi

Type:

Expression profiling by array

Platform:

GPL570

7 Samples

Download data: CEL, CHP

(Submitter supplied) Using the Deep Seq transcriptome sequencing we characterized the heme induced transcriptome of epimastigotes and determined that most of the upregulated genes were related to glucose metabolism inside the glycosomes.

Organism:

Trypanosoma cruzi

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27740

5 Samples

Download data: TXT

(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) A growing body of evidence in mammalian cells indicates that secreted vesicles can be used to mediate intercellular communication processes by transferring various bioactive molecules, including mRNAs and microRNAs. Based on these findings, we decided to analyze whether T. cruzi-derived extracellular vesicles contain RNA molecules and performed a deep sequencing and genome-wide analysis of a size-fractioned cDNA library (16–40 nt) from extracellular vesicles secreted by noninfective epimastigote and infective metacyclic trypomastigote forms. more...

Organism:

Trypanosoma cruzi

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18172

3 Samples

Download data: FASTA

(Submitter supplied) Trypanosoma cruzi is an organism highly resistant to ionizing radiation. Following a dose of 500 Gy of gamma radiation, the fragmented genomic DNA is gradually reconstructed and the pattern of chromosomal bands is restored in less than 48 hours. Cell growth arrests after irradiation but, while DNA is completely fragmented, RNA maintains its integrity. In this work we compared the transcriptional profiles of irradiated and non-irradiated epimastigotes at different time points after irradiation using microarray. more...

Organism:

Trypanosoma cruzi

Type:

Expression profiling by array

Platform:

GPL5906

5 Samples

Download data: GPR

(Submitter supplied) We examined the extent to which different Trypanosoma cruzi strains induce transcriptomic changes in cultured L6E9 myoblasts 72 hours or 48 hours after infection with four strains of the parasite [Brazil (TCI); Y, CL and Tulahuen (TC II) strains]. Expression of 6,289 distinct fully annotated unigenes was quantified with 27k rat oligonucleotide arrays in each of the four replicas of all control and infected RNA samples. more...

Organism:

Rattus norvegicus

Type:

Expression profiling by array

Platform:

GPL9207

20 Samples

Download data: GPR

(Submitter supplied) Type of experiment: This study used microarray experiments to evaluate the reproducibility and fidelity of Whole Transcriptome Amplification (WTA). Experimental factors: This study contains multiple categories of microarray experiments. Self-self hybridizations from WTA amplified total RNA were performed to evaluate the reproducibility of WTA. To evaluate the fidelity of WTA, the same total RNA, isolated from tissue samples or cell lines, was either directly used for microarray analysis or subjected to WTA amplification before hybridization. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL2012 GPL2013

41 Samples

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(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

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(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

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(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

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(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

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(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

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(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

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(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

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(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) Transcriptomics data obtained from limiting amounts of mRNA is often noisy, providing primarily qualitative changes in transcript expressions. So far, technical variations arising out of the library preparation protocols have not been adequately characterized at reduced levels of mRNA. Here, we generated sequencing libraries from limiting amounts of mRNA using three amplification-based methods, viz. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

52 Samples

Download data: TXT

(Submitter supplied) We describe a novel quantitative cDNA expression profiling strategy, involving amplification of the majority of mouse transcriptome using a defined set of 44 heptamer primers. The amplification protocol allows for efficient amplification from as low as 50pg of mRNA and did not alter the expression of the transcripts even with 200 fold dilution of the minimum requirement of the starting material (10ng of mRNA) for standard RNA-seq protocols. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL11002

33 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