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GenomicsComparison of nucleosome positioning among two yeast species and their hybrid for wild-type and deletion mutant strains
To study the evolution of nucleosome positioning we mapped nucleosome positioning in two species of yeasts. Identified differences in nucleosome positioning were classified into cis-based changes or trans-bseed changes based on the pattern of nucleosomes in the hybrid. This analysis was performed fo...
ORGANISM(S): Saccharomyces paradoxus 
2010-03-01 | E-GEOD-18939 | biostudies-arrayexpress
TranscriptomicsComparative analysis of gene expression in two yeast species and their interspecific hybrid
We compared the genome-wide expression profiles of two yeast species (S. cerevisiae and S. paradoxus) using a two-species microarray that contain species-specific probes and can thus measure the expression levels of the two species simultaneosly. In Addition, we used the array to measure expression ...
ORGANISM(S): Saccharomyces paradoxus 
2010-06-20 | E-GEOD-14708 | biostudies-arrayexpress
TranscriptomicsSingle cell RNA-seq of primary human glioblastomas
We report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, ...
ORGANISM(S): Homo sapiens 
2014-06-12 | E-GEOD-57872 | biostudies-arrayexpress
TranscriptomicsCoupled evolution of transcription and mRNA degradation.
We measured mRNA levels of two yeast species (S.cerevisiae and S.paradoxus) and their hybrid, at four time-points (0, 20min, 40min, 60min) following transcription arrest using 1,10-Phenantroline (150ug/ml). This data was used to infer mRNA degradation rates of orthologous genes, study the divergence...
ORGANISM(S): Saccharomyces cerevisiae 
2011-07-31 | E-GEOD-28849 | biostudies-arrayexpress
TranscriptomicsChromatin regulators as capacitors of inter-species expression variations
We analyzed the genome-wide expression profiles of mutant strains of two yeast species in which eight different chromatin regulators and one transcription factor were deleted (one gene deleted in each strain). Comparison of the inter-species expression differences between the wild-types of these spe...
ORGANISM(S): Saccharomyces paradoxus 
2010-11-01 | E-GEOD-23866 | biostudies-arrayexpress
GenomicsNucleosome positioning for 4 yeast species
We describe the genome-wide nucleosome profiles of four related yeast species. All species display the same global organization features first described in S. cerevisiae: a stereotypical nucleosome organization along genes, and the classification of promoters into these which contain or lack a prono...
ORGANISM(S): Saccharomyces cerevisiae 
2011-12-09 | E-GEOD-23577 | biostudies-arrayexpress
TranscriptomicsMating response of three yeast species (S. cerevisiae, S. paradoxus and S. mikatae)
We examined the mating response of three yeast species, by subjecting a-type cells from each of them to alpha-factor (6uM). The expression of cells before and after (60min) addition of alpha-factor were compared using S. cerevisiae cDNA microarrays. In addition, we verified our results with a true m...
ORGANISM(S): Saccharomyces paradoxus 
2010-06-11 | E-GEOD-7525 | biostudies-arrayexpress
TranscriptomicsSingle cell RNA-seq analysis of melanoma
To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq. Tumors were disaggregated, sorted into single cells, and profiled by Smart-seq2. *Raw data fil...
ORGANISM(S): Homo sapiens 
2016-04-05 | E-GEOD-72056 | biostudies-arrayexpress
TranscriptomicsRNA-seq of pre-treatment and post-relapse matched samples from melanoma patients
RNA-seq of pre-treatment and post-relapse matched samples from melanoma patients RNA-seq was performed for matched samples before treatment and after relapse from six patients that have been treated with RAF or RAF+MEK inhibitors. Submitter declares that raw sequence data will be submitted to dbGaP...
ORGANISM(S): Homo sapiens 
2016-02-25 | E-GEOD-77940 | biostudies-arrayexpress
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