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SRP032173
Zea mays
18 Downloadable Samples
Illumina HiSeq 2000
Description
Transformation of the Arabidopsis ATHB17 gene into maize results in the expression of a truncated protein (smaller by 113 amino acids) that functions as a dominant-negative regulator that can modify activity of endogenous maize HD-Zip II transcription factors. This RNASeq experiment indicates that the observed effects of ATHB17d113 on the maize ear inflorescence and ear transcriptome are very small. Expression of ATHB17delta113 protein in maize leads to changes in ear growth resulting in increased ear size at early reproductive stages and, potentially increased sink size. Overall design: Two ATHB17delta113 expressing events (Event 1 and Event 2) were compared to control plants (herein referred to as WT) in the context of Monsanto Elite Maize hybrid line NN6306. Three bioreps of both Ear inflorescence and Ear tissues were sampled for the WT and each of the two transgenic events.
Publication Title
Expression of a truncated ATHB17 protein in maize increases ear weight at silking.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 19 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
These samples have been analyzed for global alternative splicing variation on exon-level expression data using the FIRMA algorithm. We have identified and described transcriptome instability as a genome-wide, pre-mRNA splicing related characteristic of solid cancers.
Publication Title
Transcriptome instability as a molecular pan-cancer characteristic of carcinomas.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 331 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 165 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series.
Publication Title
Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 166 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Colorectal cancer is a heterogeneous disease molecularly characterized by inherent genomic instabilities, chromosome instability and microsatellite instability. In the present study we propose transcriptome instability as an analogue to genomic instability on the transcriptome level. Exon microarray data from two independent series of altoghether 160 colorectal cancer tissue samples was used for global alternative splicing detection using the FIRMA algorithm (aroma.affymetrix). The sample-wise amounts of these alternative splicing scores exceeding a defined threshold (deviating exon usage amounts) were summarized to provide the basis for description of transcriptome instability. This characteristic was shown to be associated with splicing factor expression levels and patient survival in both independent sample series.
Publication Title
Transcriptome instability in colorectal cancer identified by exon microarray analyses: Associations with splicing factor expression levels and patient survival.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 95 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
This series is part of a larger series (GSE24549) of colorectal cancer tissue samples analyzed for global gene expression. The expression measures were used to develope a gene signature for prediction of prognosis in stage II and III colorectal cancer.
Publication Title
ColoGuideEx: a robust gene classifier specific for stage II colorectal cancer prognosis.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 50 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
By the use of whole genome transcription analysis, we aimed to develop a gene expression classifier to increase the likelihood of identifying stage II colorectal cancer (CRC) samples with a poor prognostic outcome. Gene expression measurement were measured by the GeneChip Human Exon 1.0 ST Arrays from Affymetrix.
Publication Title
ColoGuideEx: a robust gene classifier specific for stage II colorectal cancer prognosis.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
We have looked for fusion genes in ovarian carcinomas. We combined previously known genomic aberrations, detected by karyotyping, and gene expression analysis. We found recurrent DPP9 gene expression deregulation with matching translocations. In additon, candidate fusion partner genes from the exon-level expression analysis were ranked according to deviating expression compared to the median of the sample set. The results were collated with data obtained from the RNA-seq analysis.
Publication Title
Involvement of DPP9 in gene fusions in serous ovarian carcinoma.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 77 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)
Description
These colorectal cancer (CRC) samples have been analyzed by exon expression profiling to identify genes with overexpression of 3 parts. By characterizing underlying transcript structures of such genes with a combination of rapid amplification of cDNA ends and deep-sequencing (RACE-seq), we identify and describe novel RNA-variants in CRC.
Publication Title
Novel RNA variants in colorectal cancers.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 31 Downloadable Samples
- Affymetrix Human Gene 2.1 ST Array (hugene21st)
Description
Atopic dermatitis (AD) is a common inflammatory skin disease with underlying defects in epidermal function and immune responses. The goal of this study was to investigate differences in gene expression in lesional skin from patients with mild extrinsic or intrinsic AD compared to skin from healthy controls and from lesional psoriasis skin. The aim was to identify differentially expressed genes involved in skin barrier formation and inflammation, and to compare our results with those reported for patients with moderate and severe AD.
Publication Title
Distinct molecular signatures of mild extrinsic and intrinsic atopic dermatitis.
Sample Metadata Fields
Specimen part, Disease
View Samples