Filters
Technology
Platform
SRP002218
Saccharomyces cerevisiae
6 Downloadable Samples
Illumina Genome Analyzer II
Description
Using RNA-seq, we analyzed the transcriptomes of isogenic haploid (MATa) and tetraploid (MATaaaa) budding yeast strains in the Sigma 1278b background and identified genes whose regulation was altered by ploidy. Overall design: Analysis of poly(A)+ RNA from 2 biological replicates of haploid (MATa) and tetraploid (MATaaaa) strains.
Publication Title
Control of transcription by cell size.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Two human acute lymphoblastic leukemia cell lines (Molt-4 and CCRF-CEM) were treated with direct (A-769662) and indirect (AICAR) AMPK activators. Molt-4 and CCRF-CEM cells were obtained from ATCC (CRL-1582 and CCL-119). Control samples were used for the analysis of metabolic differences between cell lines. Therefore the data was analyzed in combination with, metabolomic data, and the genome-scale reconstruction of human metabolism. For experiments cells were grown in serum-free medium containing DMSO (0.67%) at a cell concentration of 5 x 105 cells/mL.
Publication Title
Prediction of intracellular metabolic states from extracellular metabolomic data.
Sample Metadata Fields
Cell line, Treatment
View Samples- Saccharomyces cerevisiae
- 23 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
We used microarrays to detail the global program of gene expression underlying rRNA processing gene regulation during heat shock. PBF1 is YBL054W (TOD6) and PBF2 is YER088C (DOT6).
Publication Title
High-resolution DNA-binding specificity analysis of yeast transcription factors.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 2 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Two major subsets of rat natural killer (NK) cells can be distinguished based on their expression of either the Ly49s3 or the NKR-P1B lectin-like receptor. Ly49s3+ NK cells, but not NKR-P1B+ NK cells, express a wide range of Ly49 receptors.
Publication Title
Two complementary rat NK cell subsets, Ly49s3+ and NKR-P1B+, differ in phenotypic characteristics and responsiveness to cytokines.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Diabetes and obesity are widespread diseases with signifciant socioeconomic implications. We used three different types of human adipose tissue (epigastric, visceral, and subcutaneous) in order to determine differences in global gene expression between these adipose depots in severely obese patients.
Publication Title
Gene expression profiling in subcutaneous, visceral and epigastric adipose tissues of patients with extreme obesity.
Sample Metadata Fields
Specimen part, Race
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2000
Description
Oxidative DNA damage has been associated with cognitive decline. The Ogg1 and Mutyh DNA glycosylases cooperate to prevent mutations caused by 8-oxoG, a major premutagenic oxidative DNA base lesion. Here, we have examined behavior and cognitive function in mice deficient of these glycosylases. We found that Ogg1-/-Mutyh-/- mice were more active and less anxious and that their learning ability was impaired. In contrast, Mutyh-/- mice showed moderately improved memory compared to WT. There was no change in genomic 8-oxoG levels, suggesting that Ogg1 and Mutyh play minor roles in global repair in adult brain. Notably, transcriptome analysis of hippocampus revealed that differentially expressed genes in the mutant mice belong to pathways known to be involved in anxiety and cognitive function. Thus, beyond their involvement in DNA repair, Ogg1 and Mutyh modulate cognitive function and behavior, and related hippocampal gene expression, suggesting a novel role for 8-oxoG in regulating adaptive behavior. Overall design: The mRNA profiles from hippocampus of WT, Ogg1-/-, Mutyh-/- and Ogg1-/- Mutyh-/- C57BL/6 mice at 6month of age were generated by RNA sequencing using Illumina Hiseq 2000
Publication Title
Synergistic Actions of Ogg1 and Mutyh DNA Glycosylases Modulate Anxiety-like Behavior in Mice.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 66 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Barretts esophagus confers significant risk of esophageal adenocarcinoma. We have established the cloning of patient-matched stem cells of Barretts, gastric, and esophageal epithelium. Barrett's esophagus stem cells (BE), gastric cardia stem cells (GC) and normal esophagus stem cells (Eso) from 12 patients were cloned (For BE: 12 patients, GC: 12 patients and Eso: 2 patients). Keratin 5 positive and Keratin 7 positive cells were cloned from human fetal esophageal epithelium. Using air liquid interface culture system, stem cells were induced to differentiate into mature epithelial structures.
Publication Title
Mutational spectrum of Barrett's stem cells suggests paths to initiation of a precancerous lesion.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples- Homo sapiens
- 19 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Barretts esophagus confers significant risk of esophageal adenocarcinoma. We have established the cloning of patient-matched stem cells of Barretts, gastric, and esophageal epithelium. Transplantation of transformed Barretts stem cells yielded tumors with hallmarks of esophageal adenocarcinoma, whereas transformed esophageal stem cells produced squamous cell carcinomas. These findings define a stem cell target in a precancerous lesion for preemptive therapies.
Publication Title
Mutational spectrum of Barrett's stem cells suggests paths to initiation of a precancerous lesion.
Sample Metadata Fields
Specimen part, Disease
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)
Description
Barretts esophagus is a precancerous lesion that confers a significant risk of esophageal adenocarcinoma. Strategies for selective eradication of Barretts have been stymied by our inability to identify the Barretts stem cell. Here we employ novel technologies to clone patient-matched stem cells of Barretts, gastric, and esophageal epithelium. Genomic analyses of Barretts stem cells reveal a patient-specific mutational spectrum ranging from low somatic variation similar to patient-matched gastric epithelial stem cells to ones marked by extensive heterozygous alteration of genes implicated in tumor suppression, epithelial planarity, and epigenetic regulation. Transplantation of transformed Barretts stem cells yields tumors with hallmarks of esophageal adenocarcinoma, whereas transformed esophageal stem cells yield squamous cell carcinomas. Thus Barretts develops from cells distinct from local eponymous epithelia, emerges without obvious driver mutations, and likely progresses through and from the generation of dominant clones. These findings define a stem cell target for preemptive therapies of a precancerous lesion.
Publication Title
Mutational spectrum of Barrett's stem cells suggests paths to initiation of a precancerous lesion.
Sample Metadata Fields
Specimen part, Disease, Disease stage
View Samples- Drosophila melanogaster
- 24 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
Genes relevant to manifestion of and variation in aggression behavior might be differentially expressed in lines selected for divergent levels of aggression.
Publication Title
Quantitative genomics of aggressive behavior in Drosophila melanogaster.
Sample Metadata Fields
No sample metadata fields
View Samples