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Homo sapiens
80 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Genome-wide association studies (GWAS) have identified 19 risk variants associated with colorectal cancer. As most of these risk variants reside outside the coding regions of genes, we conducted cis-expression quantitative trait loci (cis-eQTL) analyses to investigate possible regulatory functions on the expression of neighboring genes.
Publication Title
cis-Expression QTL analysis of established colorectal cancer risk variants in colon tumors and adjacent normal tissue.
Sample Metadata Fields
Disease, Disease stage
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The CMVpp65 protein contains 2 bipartite nuclear localization signals (NLS) at 415-438aa and 537-561aa near the carboxy terminus of CMVpp65 and a phosphate binding site related to kinase activity at lysine-436. A mutation of pp65 having K436N (CMVpp65mII) and further deletion of aa537-561 resulted in a novel protein (pp65mIINLSKO) that is kinase-less and has markedly reduced nuclear localization. The purpose of this report was to study the biologic characterization of this protein and its immunogenicity compared to native pp65.Using RNA microarray analysis, expression of the CMVpp65mIINLSKO had less effect on cell cycle pathways than did the native CMVpp65 and a greater effect on cell surface signalling pathways involving immune activity. It is concluded that the removal of the primary NLS motif from pp65 does not impair its immunogenicity and may actually be advantageous in the design of a vaccine.
Publication Title
Biologic and immunologic effects of knockout of human cytomegalovirus pp65 nuclear localization signal.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 6 Downloadable Samples
- Affymetrix Rat Gene 2.0 ST Array (ragene20st)
Description
The goal of the study was to determine the effect of lentiviral- mediated overexpression of miR-495 (LV-miR-495) on the levels of gene expression in the nuclues accumbens of rats relative to control rats injected with the empty vector (LV-GFP).
Publication Title
In silico identification and in vivo validation of miR-495 as a novel regulator of motivation for cocaine that targets multiple addiction-related networks in the nucleus accumbens.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 40 Downloadable Samples
IlluminaHiSeq2000
Description
The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be normalized, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples are at times the sole means of addressing specific questions – e.g., samples collected in the course of fieldwork.
Publication Title
RNA-seq: impact of RNA degradation on transcript quantification.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE15203- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by histone H2B K111A mutant.
Publication Title
Novel functional residues in the core domain of histone H2B regulate yeast gene expression and silencing and affect the response to DNA damage.
Sample Metadata Fields
No sample metadata fields
View Samples GSE15202- Saccharomyces cerevisiae
- 6 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Total RNA from three replicate cultures of wild-type and mutant strains was isolated and the expression profiles were determined using Affymetrix arrays. Comparisons between the sample groups allow the identification of genes regulated by histone H2B R102A mutant.
Publication Title
Novel functional residues in the core domain of histone H2B regulate yeast gene expression and silencing and affect the response to DNA damage.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 21 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the contribution of the poly(A)binding protein to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and pab2 pab8 double mutant seedlings. The mutants continue to express the PAB4 paralog of PABP.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 17 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the contribution of the RPL24B protein, a component of the large 60S ribosomal subunit, to the translation of specific mRNAs, we compared the ribosome occupancy of mRNAs in wild type Arabidopsis and the rpl24b/stv1-1 T-DNA insertion mutant.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Age, Specimen part
View Samples GSE28223- Arabidopsis thaliana
- 12 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays.
Publication Title
The global translation profile in a ribosomal protein mutant resembles that of an eIF3 mutant.
Sample Metadata Fields
Age, Specimen part
View Samples